From 914c5a3e0959632732e625e9912f6eb84eb2390b Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Thu, 6 Oct 2016 10:39:40 +0100 Subject: [PATCH 01/16] Try to use when appropriate --- README.md | 20 ++++++++------------ ariba/clusters.py | 2 ++ 2 files changed, 10 insertions(+), 12 deletions(-) diff --git a/README.md b/README.md index 024f5823..bc52e03e 100644 --- a/README.md +++ b/README.md @@ -96,16 +96,18 @@ are put in a temporary directory made by ARIBA. The total size of these files is small, but there can be a many of them. This can be a problem when running large numbers (100s or 1000s) of jobs simultaneously on the same file system. -By default, ARIBA creates a temporary directory for these files -inside the output directory of each run. +The parent directory of the temporary directory is determined in the +following order of precedence: + +1. The value of the option `--tmp_dir` (if that option was used) +2. The environment variable `$ARIBA_TMPDIR` (if it is set) +3. The environment variable `$TMPDIR` (if it is set) +4. If none of the above is found, then use the run's output directory. Each temporary directory is unique to one run of ARIBA, and is automatically deleted at the end of the run (even if ARIBA was killed by the user or crashed). -The parent directory of the temporary -directory can be changed using the environment variable -`$ARIBA_TMPDIR`. The temporary directory for each run will be made -inside `$ARIBA_TMPDIR`. For example, +For example, export $ARIBA_TMPDIR=/tmp @@ -117,12 +119,6 @@ will have a name of the form where the suffix `abcdef` is a random string of characters, chosen such that `/tmp/ariba.tmp.abcdef` does not already exist. -The temporary directory can also be changed using the option -`--tmp_dir` when running `ariba run`. Using this option takes precedence -over the environment variable `$ARIBA_TMPDIR`. If neither are -set, then ARIBA creates the temporary directory inside -the output directory given to `ariba run`. - The exception to the above is if the option `--noclean` is used. This forces the temporary directory to be placed in the output directory, and temporary files are kept. It is intended for diff --git a/ariba/clusters.py b/ariba/clusters.py index 605cc060..6936447d 100644 --- a/ariba/clusters.py +++ b/ariba/clusters.py @@ -137,6 +137,8 @@ def __init__(self, if tmp_dir is None: if 'ARIBA_TMPDIR' in os.environ: tmp_dir = os.path.abspath(os.environ['ARIBA_TMPDIR']) + elif 'TMPDIR' in os.environ: + tmp_dir = os.path.abspath(os.environ['TMPDIR']) else: tmp_dir = self.outdir From 470d05451f439e9070c3b6aaceb2b5664ebf6a92 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Thu, 6 Oct 2016 11:11:40 +0100 Subject: [PATCH 02/16] Add debug option --- ariba/ref_genes_getter.py | 20 +++++++++++++++----- ariba/tasks/getref.py | 3 ++- scripts/ariba | 1 + 3 files changed, 18 insertions(+), 6 deletions(-) diff --git a/ariba/ref_genes_getter.py b/ariba/ref_genes_getter.py index 882b4339..34b4d8ce 100644 --- a/ariba/ref_genes_getter.py +++ b/ariba/ref_genes_getter.py @@ -25,10 +25,11 @@ class Error (Exception): pass class RefGenesGetter: - def __init__(self, ref_db, version=None): + def __init__(self, ref_db, version=None, debug=False): if ref_db not in allowed_ref_dbs: raise Error('Error in RefGenesGetter. ref_db must be one of: ' + str(allowed_ref_dbs) + ', but I got "' + ref_db) self.ref_db=ref_db + self.debug = debug self.genetic_code = 11 self.max_download_attempts = 3 self.sleep_time = 2 @@ -185,6 +186,9 @@ def _get_from_card(self, outprefix): pyfastaq.utils.close(f_out_tsv) pyfastaq.utils.close(f_out_log) os.chdir(current_dir) + if not self.debug: + shutil.rmtree(tmpdir) + print('Extracted data and written ARIBA input files\n') print('Finished. Final files are:', final_fasta, final_tsv, sep='\n\t', end='\n\n') print('You can use them with ARIBA like this:') @@ -244,7 +248,8 @@ def _get_from_resfinder(self, outprefix): pyfastaq.utils.close(fout_tsv) print('\nFinished combining files\n') os.chdir(current_dir) - shutil.rmtree(tmpdir) + if not self.debug: + shutil.rmtree(tmpdir) print('Finished. Final files are:', final_fasta, final_tsv, sep='\n\t', end='\n\n') print('You can use them with ARIBA like this:') print('ariba prepareref -f', final_fasta, '-m', final_tsv, 'output_directory\n') @@ -286,7 +291,8 @@ def _get_from_argannot(self, outprefix): pyfastaq.utils.close(f_out_tsv) pyfastaq.utils.close(f_out_fa) - shutil.rmtree(tmpdir) + if not self.debug: + shutil.rmtree(tmpdir) print('Finished. Final files are:', final_fasta, final_tsv, sep='\n\t', end='\n\n') print('You can use them with ARIBA like this:') @@ -339,7 +345,8 @@ def _get_from_plasmidfinder(self, outprefix): pyfastaq.utils.close(fout_tsv) print('\nFinished combining files\n') os.chdir(current_dir) - shutil.rmtree(tmpdir) + if not self.debug: + shutil.rmtree(tmpdir) print('Finished. Final files are:', final_fasta, final_tsv, sep='\n\t', end='\n\n') print('You can use them with ARIBA like this:') print('ariba prepareref -f', final_fasta, '-m', final_tsv, 'output_directory\n') @@ -371,6 +378,8 @@ def _get_from_srst2_argannot(self, outprefix): pyfastaq.utils.close(f_out_fa) pyfastaq.utils.close(f_out_meta) + if not self.debug: + os.unlink(srst2_fa) print('Finished downloading and converting data. Final files are:', final_fasta, final_tsv, sep='\n\t', end='\n\n') print('You can use them with ARIBA like this:') @@ -403,7 +412,8 @@ def _get_from_vfdb_common(self, outprefix, filename, info_text): print('Extracting files ... ', end='', flush=True) vparser = vfdb_parser.VfdbParser(zipfile, outprefix) vparser.run() - shutil.rmtree(tmpdir) + if not self.debug: + shutil.rmtree(tmpdir) print('done') final_fasta = outprefix + '.fa' final_tsv = outprefix + '.tsv' diff --git a/ariba/tasks/getref.py b/ariba/tasks/getref.py index d5cc6187..b744454e 100644 --- a/ariba/tasks/getref.py +++ b/ariba/tasks/getref.py @@ -5,7 +5,8 @@ def run(options): getter = ref_genes_getter.RefGenesGetter( options.db, - version=options.version + version=options.version, + debug=options.debug ) getter.run(options.outprefix) diff --git a/scripts/ariba b/scripts/ariba index 31bd25fc..cf10ac8b 100755 --- a/scripts/ariba +++ b/scripts/ariba @@ -49,6 +49,7 @@ subparser_getref = subparsers.add_parser( usage='ariba getref [options] ', description='Download reference data from one of a few supported public resources', ) +subparser_getref.add_argument('--debug', action='store_true', help='Do not delete temporary downloaded files') subparser_getref.add_argument('--version', help='Version of reference data to download. If not used, gets the latest version. Only applies to card') subparser_getref.add_argument('db', help='Database to download. Must be one of: ' + ' '.join(allowed_dbs), choices=allowed_dbs, metavar="DB name") subparser_getref.add_argument('outprefix', help='Prefix of output filenames') From cb7ef0e2cf83412564d441b920c0394e0ce4aef3 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Thu, 6 Oct 2016 11:36:29 +0100 Subject: [PATCH 03/16] Add --force option --- ariba/ref_preparer.py | 6 ++++++ ariba/tasks/prepareref.py | 1 + ariba/tasks/run.py | 4 ++++ scripts/ariba | 2 ++ 4 files changed, 13 insertions(+) diff --git a/ariba/ref_preparer.py b/ariba/ref_preparer.py index c2cb310b..3e96fa9e 100644 --- a/ariba/ref_preparer.py +++ b/ariba/ref_preparer.py @@ -1,5 +1,6 @@ import sys import os +import shutil import pickle import pyfastaq from ariba import reference_data @@ -23,6 +24,7 @@ def __init__(self, clusters_file=None, threads=1, verbose=False, + force=False, ): self.extern_progs = extern_progs @@ -43,6 +45,7 @@ def __init__(self, self.clusters_file = clusters_file self.threads = threads self.verbose = verbose + self.force = force @classmethod @@ -136,6 +139,9 @@ def _rename_clusters(clusters_in): def run(self, outdir): original_dir = os.getcwd() + if self.force and os.path.exists(outdir): + shutil.rmtree(outdir) + if os.path.exists(outdir): raise Error('Error! Output directory ' + outdir + ' already exists. Cannot continue') diff --git a/ariba/tasks/prepareref.py b/ariba/tasks/prepareref.py index ef52684a..29c699e1 100644 --- a/ariba/tasks/prepareref.py +++ b/ariba/tasks/prepareref.py @@ -25,6 +25,7 @@ def run(options): clusters_file=options.cdhit_clusters, threads=options.threads, verbose=options.verbose, + force=options.force, ) preparer.run(options.outdir) diff --git a/ariba/tasks/run.py b/ariba/tasks/run.py index 668b69d3..db3bd324 100644 --- a/ariba/tasks/run.py +++ b/ariba/tasks/run.py @@ -1,5 +1,6 @@ import argparse import os +import shutil import sys import ariba @@ -27,6 +28,9 @@ def run(options): print('Input directory', options.prepareref_dir, 'not found. Cannot continue', file=sys.stderr) sys.exit(1) + if options.force and os.path.exists(options.outdir): + shutil.rmtree(options.outdir) + if os.path.exists(options.outdir): print('Output directory already exists. ARIBA makes the output directory. Cannot continue.', file=sys.stderr) sys.exit(1) diff --git a/scripts/ariba b/scripts/ariba index cf10ac8b..0f5e162d 100755 --- a/scripts/ariba +++ b/scripts/ariba @@ -80,6 +80,7 @@ other_group = subparser_prepareref.add_argument_group('other options') other_group.add_argument('--min_gene_length', type=int, help='Minimum allowed length in nucleotides of reference genes [%(default)s]', metavar='INT', default=6) other_group.add_argument('--max_gene_length', type=int, help='Maximum allowed length in nucleotides of reference genes [%(default)s]', metavar='INT', default=10000) other_group.add_argument('--genetic_code', type=int, help='Number of genetic code to use. Currently supported 1,4,11 [%(default)s]', choices=[1,4,11], default=11, metavar='INT') +other_group.add_argument('--force', action='store_true', help='Overwrite output directory, if it already exists') other_group.add_argument('--threads', type=int, help='Number of threads (currently only applies to cdhit) [%(default)s]', default=1, metavar='INT') other_group.add_argument('--verbose', action='store_true', help='Be verbose') @@ -146,6 +147,7 @@ other_group.add_argument('--threads', type=int, help=argparse.SUPPRESS, default= other_group.add_argument('--assembled_threshold', type=float, help='If proportion of gene assembled (regardless of into how many contigs) is at least this value then the flag gene_assembled is set [%(default)s]', default=0.95, metavar='FLOAT (between 0 and 1)') other_group.add_argument('--gene_nt_extend', type=int, help='Max number of nucleotides to extend ends of gene matches to look for start/stop codons [%(default)s]', default=30, metavar='INT') other_group.add_argument('--unique_threshold', type=float, help='If proportion of bases in gene assembled more than once is <= this value, then the flag unique_contig is set [%(default)s]', default=0.03, metavar='FLOAT (between 0 and 1)') +other_group.add_argument('--force', action='store_true', help='Overwrite output directory, if it already exists') other_group.add_argument('--noclean', action='store_true', help='Do not clean up intermediate files') other_group.add_argument('--tmp_dir', help='Existing directory in which to create a temporary directory used for local assemblies') other_group.add_argument('--verbose', action='store_true', help='Be verbose') From 1c06dfcc57cf56d63459641cdab5f0bdf2fef3d7 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Thu, 6 Oct 2016 11:46:25 +0100 Subject: [PATCH 04/16] Unique option group names --- scripts/ariba | 34 +++++++++++++++++----------------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/scripts/ariba b/scripts/ariba index 0f5e162d..381c69c1 100755 --- a/scripts/ariba +++ b/scripts/ariba @@ -76,13 +76,13 @@ cdhit_group.add_argument('--cdhit_clusters', help='File specifying how the seque cdhit_group.add_argument('--cdhit_min_id', type=float, help='Sequence identity threshold (cd-hit option -c) [%(default)s]', default=0.9, metavar='FLOAT') cdhit_group.add_argument('--cdhit_min_length', type=float, help='length difference cutoff (cd-hit option -s) [%(default)s]', default=0.9, metavar='FLOAT') -other_group = subparser_prepareref.add_argument_group('other options') -other_group.add_argument('--min_gene_length', type=int, help='Minimum allowed length in nucleotides of reference genes [%(default)s]', metavar='INT', default=6) -other_group.add_argument('--max_gene_length', type=int, help='Maximum allowed length in nucleotides of reference genes [%(default)s]', metavar='INT', default=10000) -other_group.add_argument('--genetic_code', type=int, help='Number of genetic code to use. Currently supported 1,4,11 [%(default)s]', choices=[1,4,11], default=11, metavar='INT') -other_group.add_argument('--force', action='store_true', help='Overwrite output directory, if it already exists') -other_group.add_argument('--threads', type=int, help='Number of threads (currently only applies to cdhit) [%(default)s]', default=1, metavar='INT') -other_group.add_argument('--verbose', action='store_true', help='Be verbose') +other_prep_group = subparser_prepareref.add_argument_group('other options') +other_prep_group.add_argument('--min_gene_length', type=int, help='Minimum allowed length in nucleotides of reference genes [%(default)s]', metavar='INT', default=6) +other_prep_group.add_argument('--max_gene_length', type=int, help='Maximum allowed length in nucleotides of reference genes [%(default)s]', metavar='INT', default=10000) +other_prep_group.add_argument('--genetic_code', type=int, help='Number of genetic code to use. Currently supported 1,4,11 [%(default)s]', choices=[1,4,11], default=11, metavar='INT') +other_prep_group.add_argument('--force', action='store_true', help='Overwrite output directory, if it already exists') +other_prep_group.add_argument('--threads', type=int, help='Number of threads (currently only applies to cdhit) [%(default)s]', default=1, metavar='INT') +other_prep_group.add_argument('--verbose', action='store_true', help='Be verbose') subparser_prepareref.add_argument('outdir', help='Output directory (must not already exist)') subparser_prepareref.set_defaults(func=ariba.tasks.prepareref.run) @@ -141,16 +141,16 @@ assembly_group = subparser_run.add_argument_group('Assembly options') assembly_group.add_argument('--assembly_cov', type=int, help='Target read coverage when sampling reads for assembly [%(default)s]', default=50, metavar='INT') assembly_group.add_argument('--min_scaff_depth', type=int, help='Minimum number of read pairs needed as evidence for scaffold link between two contigs [%(default)s]', default=10, metavar='INT') -other_group = subparser_run.add_argument_group('Other options') -#other_group.add_argument('--threads', type=int, help='Number of threads [%(default)s]', default=1, metavar='INT') -other_group.add_argument('--threads', type=int, help=argparse.SUPPRESS, default=1, metavar='INT') -other_group.add_argument('--assembled_threshold', type=float, help='If proportion of gene assembled (regardless of into how many contigs) is at least this value then the flag gene_assembled is set [%(default)s]', default=0.95, metavar='FLOAT (between 0 and 1)') -other_group.add_argument('--gene_nt_extend', type=int, help='Max number of nucleotides to extend ends of gene matches to look for start/stop codons [%(default)s]', default=30, metavar='INT') -other_group.add_argument('--unique_threshold', type=float, help='If proportion of bases in gene assembled more than once is <= this value, then the flag unique_contig is set [%(default)s]', default=0.03, metavar='FLOAT (between 0 and 1)') -other_group.add_argument('--force', action='store_true', help='Overwrite output directory, if it already exists') -other_group.add_argument('--noclean', action='store_true', help='Do not clean up intermediate files') -other_group.add_argument('--tmp_dir', help='Existing directory in which to create a temporary directory used for local assemblies') -other_group.add_argument('--verbose', action='store_true', help='Be verbose') +other_run_group = subparser_run.add_argument_group('Other options') +#other_run_group.add_argument('--threads', type=int, help='Number of threads [%(default)s]', default=1, metavar='INT') +other_run_group.add_argument('--threads', type=int, help=argparse.SUPPRESS, default=1, metavar='INT') +other_run_group.add_argument('--assembled_threshold', type=float, help='If proportion of gene assembled (regardless of into how many contigs) is at least this value then the flag gene_assembled is set [%(default)s]', default=0.95, metavar='FLOAT (between 0 and 1)') +other_run_group.add_argument('--gene_nt_extend', type=int, help='Max number of nucleotides to extend ends of gene matches to look for start/stop codons [%(default)s]', default=30, metavar='INT') +other_run_group.add_argument('--unique_threshold', type=float, help='If proportion of bases in gene assembled more than once is <= this value, then the flag unique_contig is set [%(default)s]', default=0.03, metavar='FLOAT (between 0 and 1)') +other_run_group.add_argument('--force', action='store_true', help='Overwrite output directory, if it already exists') +other_run_group.add_argument('--noclean', action='store_true', help='Do not clean up intermediate files') +other_run_group.add_argument('--tmp_dir', help='Existing directory in which to create a temporary directory used for local assemblies') +other_run_group.add_argument('--verbose', action='store_true', help='Be verbose') subparser_run.set_defaults(func=ariba.tasks.run.run) From fba4903f1c4848e10755060f850d6e21b237bea9 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Thu, 6 Oct 2016 15:01:42 +0100 Subject: [PATCH 05/16] new method _has_any_part_of_ref_assembled --- ariba/summary_cluster.py | 8 ++++++++ ariba/tests/summary_cluster_test.py | 17 +++++++++++++++++ 2 files changed, 25 insertions(+) diff --git a/ariba/summary_cluster.py b/ariba/summary_cluster.py index 58734ce7..57bb4ec1 100644 --- a/ariba/summary_cluster.py +++ b/ariba/summary_cluster.py @@ -96,6 +96,14 @@ def pc_id_of_longest(self): return identity + def _has_any_part_of_ref_assembled(self): + for d in self.data: + if isinstance(d['ref_base_assembled'], int) and d['ref_base_assembled'] > 0: + return True + + return False + + def _to_cluster_summary_assembled(self): if len(self.data) == 0: return 'no' diff --git a/ariba/tests/summary_cluster_test.py b/ariba/tests/summary_cluster_test.py index 27d363e2..4f7798c3 100644 --- a/ariba/tests/summary_cluster_test.py +++ b/ariba/tests/summary_cluster_test.py @@ -68,6 +68,23 @@ def test_add_data_dict(self): cluster.add_data_dict(data_dict3) + def test_has_any_part_of_ref_assembled(self): + '''Test _has_any_part_of_ref_assembled''' + line1 = 'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t.\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text' + line2 = 'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t0\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text' + line3 = 'ariba_refname\trefname\t1\t0\t19\t78\tcluster\t120\t100\t98.33\tctg_name\t279\t24.4\t1\tSNP\tn\tA14T\t1\tA14T\tSNP\t13\t13\tA\t84\t84\tT\t17\tT\t17\tnoncoding1:1:0:A14T:id1:ref has wild type, foo bar\tsome free text' + data_dict1 = summary_cluster.SummaryCluster.line2dict(line1) + data_dict2 = summary_cluster.SummaryCluster.line2dict(line2) + data_dict3 = summary_cluster.SummaryCluster.line2dict(line3) + cluster = summary_cluster.SummaryCluster() + cluster.add_data_dict(data_dict1) + self.assertFalse(cluster._has_any_part_of_ref_assembled()) + cluster.add_data_dict(data_dict2) + self.assertFalse(cluster._has_any_part_of_ref_assembled()) + cluster.add_data_dict(data_dict3) + self.assertTrue(cluster._has_any_part_of_ref_assembled()) + + def test_pc_id_of_longest(self): '''Test pc_id_of_longest''' cluster = summary_cluster.SummaryCluster() From 7c21590e622b7d1af28f8b30944dbd8d48dcb42f Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Fri, 7 Oct 2016 09:30:33 +0100 Subject: [PATCH 06/16] Fix coverage column to have 3 values --- ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv b/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv index f5652989..642064f5 100644 --- a/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv +++ b/ariba/tests/data/summary_gather_unfiltered_output_data.in.1.tsv @@ -3,4 +3,4 @@ ariba_noncoding_ref1 noncoding_ref1 0 0 19 78 noncoding1 120 120 98.33 noncoding ariba_noncoding_ref2 noncoding_ref2 0 0 19 78 noncoding2 120 120 98.33 noncoding2.scaffold.1 279 10.0 1 SNP n A42T 1 A42T SNP 42 42 A 84 84 T 17 T 17 noncoding_ref2:0:0:A42T:id2:ref has wild type, reads have variant so should report generic description of noncoding1 ariba_noncoding_ref2 noncoding_ref2 0 0 19 78 noncoding2 120 120 98.33 noncoding2.scaffold.1 279 10.0 1 SNP n A52T 1 A52T SNP 42 42 A 84 84 T 17 T,G 20,30 noncoding_ref2:0:0:A42T:id2:ref has wild type, reads have variant so should report generic description of noncoding1 ariba_presence_absence_ref1 presence_absence_ref1 1 0 27 88 presence_absence1 96 96 98.96 presence_absence1.scaffold.1 267 20.1 0 SNP p A10V . A10V NONSYN 27 29 GCA 112 114 GTA 29;28;27 G;T;A 29;28;27 presence_absence_ref1:1:0:A10V:.:Ref has wild, reads have variant so report Generic description of presence_absence1 -ariba_presence_absence_ref2 presence_absence_ref2 1 0 528 232 presence_absence2 1005 554 99.1 presence_absence2.scaffold.1 1032 22.3 0 . p . 0 V175L NONSYN 522 524 GTA 265 267 CTA 36 C;T;A 36;37;34 . Description foo bar +ariba_presence_absence_ref2 presence_absence_ref2 1 0 528 232 presence_absence2 1005 554 99.1 presence_absence2.scaffold.1 1032 22.3 0 . p . 0 V175L NONSYN 522 524 GTA 265 267 CTA 36;37;34 C;T;A 36;37;34 . Description foo bar From 7049412da2db326088fa70c0e056a859b2e5bea7 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Fri, 7 Oct 2016 09:32:28 +0100 Subject: [PATCH 07/16] Add partial as an option for assembled column --- ariba/summary.py | 5 +++++ ariba/summary_cluster.py | 6 +++--- ariba/tests/summary_cluster_test.py | 9 +++++++-- ariba/tests/summary_test.py | 13 ++++++++----- 4 files changed, 23 insertions(+), 10 deletions(-) diff --git a/ariba/summary.py b/ariba/summary.py index a8772e44..fc0a2b0d 100644 --- a/ariba/summary.py +++ b/ariba/summary.py @@ -256,6 +256,7 @@ def _add_phandango_colour_columns(cls, header, matrix): 'het': '#fdbf6f', 'fragmented': '#1f78b4', 'interrupted': '#a6cee3', + 'partial': '#fdbf6f', } cols_to_add_colour_col.reverse() @@ -287,6 +288,10 @@ def _matrix_to_csv(cls, matrix, header, outfile, remove_nas=False): @staticmethod def _distance_score_between_values(value1, value2): + if value1 == 'partial': + value1 = 'no' + if value2 == 'partial': + value2 = 'no' value_set = {value1, value2} if value_set.isdisjoint(required_keys_for_difference) or value1 == value2 or value_set == {'NA', 'no'}: return 0 diff --git a/ariba/summary_cluster.py b/ariba/summary_cluster.py index 57bb4ec1..f3f952c7 100644 --- a/ariba/summary_cluster.py +++ b/ariba/summary_cluster.py @@ -113,10 +113,10 @@ def _to_cluster_summary_assembled(self): else: has_complete_gene = self.flag.has('complete_gene') - if self.flag.has('assembly_fail') or \ - (not self.flag.has('assembled')) or \ - self.flag.has('ref_seq_choose_fail'): + if self.flag.has('assembly_fail') or self.flag.has('ref_seq_choose_fail'): return 'no' + elif not self.flag.has('assembled'): + return 'partial' if self._has_any_part_of_ref_assembled() else 'no' elif self.flag.has('assembled_into_one_contig') and has_complete_gene: if self.flag.has('unique_contig') and \ (not self.flag.has('scaffold_graph_bad')) and \ diff --git a/ariba/tests/summary_cluster_test.py b/ariba/tests/summary_cluster_test.py index 4f7798c3..2cf8f19b 100644 --- a/ariba/tests/summary_cluster_test.py +++ b/ariba/tests/summary_cluster_test.py @@ -107,7 +107,7 @@ def test_to_cluster_summary_number(self): data_dict = summary_cluster.SummaryCluster.line2dict(line) tests = [ - ('0', 0, 'no'), + ('0', 0, 'partial'), ('0', 64, 'no'), ('0', 1024, 'no'), ('0', 1, 'fragmented'), @@ -117,7 +117,7 @@ def test_to_cluster_summary_number(self): ('0', 51, 'yes_nonunique'), ('0', 147, 'yes_nonunique'), ('0', 275, 'yes_nonunique'), - ('1', 0, 'no'), + ('1', 0, 'partial'), ('1', 64, 'no'), ('1', 1024, 'no'), ('1', 1, 'fragmented'), @@ -135,6 +135,11 @@ def test_to_cluster_summary_number(self): data_dict['flag'] = flag.Flag(f) cluster.add_data_dict(data_dict) self.assertEqual(expected, cluster._to_cluster_summary_assembled()) + if expected == 'partial': + original_number = cluster.data[0]['ref_base_assembled'] + cluster.data[0]['ref_base_assembled'] = 0 + self.assertEqual('no', cluster._to_cluster_summary_assembled()) + cluster.data[0]['ref_base_assembled'] = original_number def test_has_known_variant(self): diff --git a/ariba/tests/summary_test.py b/ariba/tests/summary_test.py index 957b2d04..e54a0fd6 100644 --- a/ariba/tests/summary_test.py +++ b/ariba/tests/summary_test.py @@ -111,12 +111,12 @@ def test_gather_unfiltered_output_data(self): }, 'presence_absence2': { 'summary': { - 'assembled': 'no', - 'known_var': 'NA', + 'assembled': 'partial', + 'known_var': 'no', 'match': 'no', - 'novel_var': 'NA', - 'pct_id': 'NA', - 'ref_seq': 'NA' + 'novel_var': 'yes', + 'pct_id': '99.1', + 'ref_seq': 'presence_absence_ref2' }, 'groups': {}, 'vars': {} @@ -212,6 +212,7 @@ def test_gather_unfiltered_output_data(self): } } + self.maxDiff = None s = summary.Summary('out', filenames=infiles) s.samples = summary.Summary._load_input_files(infiles, 90) s._gather_unfiltered_output_data() @@ -244,7 +245,9 @@ def test_gather_unfiltered_output_data(self): self.assertEqual(expected_all, s.all_data) expected_potential_cols['presence_absence1']['vars'] = {'A10V'} + expected_potential_cols['presence_absence2']['vars'] = {'V175L'} expected_all[infiles[0]]['presence_absence1']['vars'] = {'A10V': 'yes'} + expected_all[infiles[0]]['presence_absence2']['vars'] = {'V175L': 'yes'} expected_all[infiles[1]]['presence_absence1']['vars'] = {'A10V': 'yes'} s = summary.Summary('out', filenames=infiles, show_var_groups=True, show_known_vars=True, show_novel_vars=True) s.samples = summary.Summary._load_input_files(infiles, 90) From 6eef738e6975ef95d81efb4702b0c96519fe65cb Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Fri, 7 Oct 2016 14:33:56 +0100 Subject: [PATCH 08/16] Run mash sketch on fasta of all ref seqs --- ariba/mash.py | 14 +++++++++----- ariba/ref_preparer.py | 7 ++++++- ariba/tests/ref_preparer_test.py | 1 + 3 files changed, 16 insertions(+), 6 deletions(-) diff --git a/ariba/mash.py b/ariba/mash.py index 97a94961..c69d29e8 100644 --- a/ariba/mash.py +++ b/ariba/mash.py @@ -19,9 +19,13 @@ def __init__(self, self.extern_progs = extern_progs - def _sketch(self, infile, individual): + @classmethod + def sketch(cls, infile, individual, extern_progs, verbose=True, verbose_filehandle=None): + if verbose: + assert verbose_filehandle is not None + cmd_list = [ - self.extern_progs.exe('mash'), + extern_progs.exe('mash'), 'sketch', '-s 100000' ] @@ -30,7 +34,7 @@ def _sketch(self, infile, individual): cmd_list.append('-i') cmd_list.append(infile) - common.syscall(' '.join(cmd_list), verbose=True, verbose_filehandle=self.log_fh) + common.syscall(' '.join(cmd_list), verbose=verbose, verbose_filehandle=verbose_filehandle) def _dist(self, outfile): @@ -45,8 +49,8 @@ def _dist(self, outfile): def run(self, outfile): - self._sketch(self.reference_fa, True) - self._sketch(self.query_fa, False) + Masher.sketch(self.reference_fa, True, self.extern_progs, verbose=True, verbose_filehandle=self.log_fh) + Masher.sketch(self.query_fa, False, self.extern_progs, verbose=True, verbose_filehandle=self.log_fh) self._dist(outfile) if os.path.getsize(outfile) == 0: return None diff --git a/ariba/ref_preparer.py b/ariba/ref_preparer.py index 3e96fa9e..ecacd65f 100644 --- a/ariba/ref_preparer.py +++ b/ariba/ref_preparer.py @@ -3,7 +3,7 @@ import shutil import pickle import pyfastaq -from ariba import reference_data +from ariba import reference_data, mash class Error (Exception): pass @@ -210,3 +210,8 @@ def run(self, outdir): with open(clusters_pickle_file, 'wb') as f: pickle.dump(clusters, f) + if self.verbose: + print('\nMash-sketching all reference sequences', flush=True) + + mash.Masher.sketch(os.path.join(outdir, '02.cdhit.all.fa'), True, self.extern_progs, self.verbose, sys.stdout) + diff --git a/ariba/tests/ref_preparer_test.py b/ariba/tests/ref_preparer_test.py index 00b979dd..0e25a4e0 100644 --- a/ariba/tests/ref_preparer_test.py +++ b/ariba/tests/ref_preparer_test.py @@ -132,6 +132,7 @@ def test_run(self): got = os.path.join(tmp_out, filename) self.assertTrue(filecmp.cmp(expected, got, shallow=False)) + self.assertTrue(os.path.exists(os.path.join(tmp_out, '02.cdhit.all.fa.msh'))) shutil.rmtree(tmp_out) From 48c3c79e52ca649ee7ca89222728cd2f1ed75edc Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Fri, 7 Oct 2016 16:26:27 +0100 Subject: [PATCH 09/16] Run mash against all ref seqs, not just the cluster refs --- ariba/assembly.py | 18 ++- ariba/cluster.py | 11 +- ariba/clusters.py | 1 + ariba/mash.py | 3 +- ariba/tests/assembly_test.py | 14 +- ariba/tests/cluster_test.py | 19 +++ ...ter_test_full_run_ref_not_in_cluster.in.fa | 6 + ...er_test_full_run_ref_not_in_cluster.in.tsv | 6 + ...r_test_full_run_ref_not_in_cluster.mash.fa | 9 ++ ...st_full_run_ref_not_in_cluster.mash.fa.msh | Bin 0 -> 2760 bytes .../reads_1.fq | 144 ++++++++++++++++++ .../reads_2.fq | 144 ++++++++++++++++++ .../references.fa | 6 + 13 files changed, 370 insertions(+), 11 deletions(-) create mode 100644 ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa create mode 100644 ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv create mode 100644 ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.mash.fa create mode 100644 ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.mash.fa.msh create mode 100644 ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq create mode 100644 ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq create mode 100644 ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa diff --git a/ariba/assembly.py b/ariba/assembly.py index 88fd1c3d..87c22738 100644 --- a/ariba/assembly.py +++ b/ariba/assembly.py @@ -18,6 +18,7 @@ def __init__(self, final_assembly_fa, final_assembly_bam, log_fh, + mash_reference_fasta, scaff_name_prefix='scaffold', kmer=0, assembler='fermilite', @@ -42,6 +43,7 @@ def __init__(self, self.final_assembly_fa = os.path.abspath(final_assembly_fa) self.final_assembly_bam = os.path.abspath(final_assembly_bam) self.log_fh = log_fh + self.mash_reference_fasta = os.path.abspath(mash_reference_fasta) self.scaff_name_prefix = scaff_name_prefix self.ref_seq_name = None @@ -377,14 +379,26 @@ def run(self): self.log_fh = None return - masher = mash.Masher(self.ref_fastas, self.gapfilled_length_filtered, self.log_fh, self.extern_progs) + masher = mash.Masher(self.mash_reference_fasta, self.gapfilled_length_filtered, self.log_fh, self.extern_progs) self.ref_seq_name = masher.run(self.mash_dist_file) if self.ref_seq_name is None: print('Could not determine closest reference sequence', file=self.log_fh) self.log_fh = None return - faidx.write_fa_subset({self.ref_seq_name}, self.ref_fastas, self.ref_fasta) + file_reader = pyfastaq.sequences.file_reader(self.ref_fastas) + for ref_seq in file_reader: + if self.ref_seq_name == ref_seq.id: + f_out = pyfastaq.utils.open_file_write(self.ref_fasta) + print(ref_seq, file=f_out) + pyfastaq.utils.close(f_out) + break + else: + print('Closest reference sequence ', self.ref_seq_name, ' does not belong to this cluster', file=self.log_fh) + self.ref_seq_name = None + self.log_fh = None + return + print('Closest reference sequence according to mash: ', self.ref_seq_name, file=self.log_fh) contigs_both_strands = self._fix_contig_orientation(self.gapfilled_length_filtered, self.ref_fasta, self.final_assembly_fa, min_id=self.nucmer_min_id, min_length=self.nucmer_min_len, breaklen=self.nucmer_breaklen) diff --git a/ariba/cluster.py b/ariba/cluster.py index 33d44f04..bdda65af 100644 --- a/ariba/cluster.py +++ b/ariba/cluster.py @@ -6,7 +6,7 @@ import shutil import sys import pyfastaq -from ariba import assembly, assembly_compare, assembly_variants, external_progs, flag, mapping, report, samtools_variants +from ariba import assembly, assembly_compare, assembly_variants, external_progs, flag, mapping, mash, report, samtools_variants class Error (Exception): pass @@ -17,6 +17,7 @@ def __init__(self, root_dir, name, refdata, + refdata_seqs_fasta_for_mash=None, total_reads=None, total_reads_bases=None, fail_file=None, @@ -126,6 +127,13 @@ def __init__(self, else: self.extern_progs = extern_progs + if refdata_seqs_fasta_for_mash is None: + mash.Masher.sketch(self.references_fa, True, self.extern_progs, verbose=False) + self.refdata_seqs_fasta_for_mash = self.references_fa + else: + self.refdata_seqs_fasta_for_mash = os.path.abspath(refdata_seqs_fasta_for_mash) + assert os.path.exists(self.refdata_seqs_fasta_for_mash + '.msh') + self.random_seed = random_seed wanted_signals = [signal.SIGABRT, signal.SIGINT, signal.SIGSEGV, signal.SIGTERM] for s in wanted_signals: @@ -312,6 +320,7 @@ def _run(self): self.final_assembly_fa, self.final_assembly_bam, self.log_fh, + self.refdata_seqs_fasta_for_mash, scaff_name_prefix=self.name, kmer=self.assembly_kmer, assembler=self.assembler, diff --git a/ariba/clusters.py b/ariba/clusters.py index 6936447d..993a78b6 100644 --- a/ariba/clusters.py +++ b/ariba/clusters.py @@ -388,6 +388,7 @@ def _init_and_run_clusters(self): new_dir, cluster_name, self.refdata, + refdata_seqs_fasta_for_mash=self.all_ref_seqs_fasta, fail_file=os.path.join(self.fails_dir, cluster_name), read_store=self.read_store, reference_names=self.cluster_ids[cluster_name], diff --git a/ariba/mash.py b/ariba/mash.py index c69d29e8..b4c3ffb3 100644 --- a/ariba/mash.py +++ b/ariba/mash.py @@ -49,7 +49,8 @@ def _dist(self, outfile): def run(self, outfile): - Masher.sketch(self.reference_fa, True, self.extern_progs, verbose=True, verbose_filehandle=self.log_fh) + if not os.path.exists(self.reference_fa + '.msh'): + Masher.sketch(self.reference_fa, True, self.extern_progs, verbose=True, verbose_filehandle=self.log_fh) Masher.sketch(self.query_fa, False, self.extern_progs, verbose=True, verbose_filehandle=self.log_fh) self._dist(outfile) if os.path.getsize(outfile) == 0: diff --git a/ariba/tests/assembly_test.py b/ariba/tests/assembly_test.py index 7ac81b8e..740234cf 100644 --- a/ariba/tests/assembly_test.py +++ b/ariba/tests/assembly_test.py @@ -68,7 +68,7 @@ def test_assemble_with_fermilite(self): tmp_log = 'tmp.test_assemble_with_fermilite.log' tmp_log_fh = open(tmp_log, 'w') print('First line', file=tmp_log_fh) - a = assembly.Assembly(reads1, reads2, 'not needed', 'not needed', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', tmp_log_fh) + a = assembly.Assembly(reads1, reads2, 'not needed', 'not needed', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', tmp_log_fh, 'not needed') a._assemble_with_fermilite() self.assertTrue(a.assembled_ok) tmp_log_fh.close() @@ -87,7 +87,7 @@ def test_assemble_with_fermilite_fails(self): tmp_log = 'tmp.test_assemble_with_fermilite_fails.log' tmp_log_fh = open(tmp_log, 'w') print('First line', file=tmp_log_fh) - a = assembly.Assembly(reads1, reads2, 'not needed', 'not needed', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', tmp_log_fh) + a = assembly.Assembly(reads1, reads2, 'not needed', 'not needed', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', tmp_log_fh, 'not needed') a._assemble_with_fermilite() self.assertFalse(a.assembled_ok) tmp_log_fh.close() @@ -104,7 +104,7 @@ def test_assemble_with_spades(self): reads2 = os.path.join(data_dir, 'assembly_test_assemble_with_spades_reads_2.fq') ref_fasta = os.path.join(data_dir, 'assembly_test_assemble_with_spades_ref.fa') tmp_dir = 'tmp.test_assemble_with_spades' - a = assembly.Assembly(reads1, reads2, 'not needed', ref_fasta, tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout) + a = assembly.Assembly(reads1, reads2, 'not needed', ref_fasta, tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout, 'not needed') a._assemble_with_spades(unittest=True) self.assertTrue(a.assembled_ok) shutil.rmtree(tmp_dir) @@ -117,7 +117,7 @@ def test_assemble_with_spades_fail(self): reads2 = os.path.join(data_dir, 'assembly_test_assemble_with_spades_reads_2.fq') ref_fasta = os.path.join(data_dir, 'assembly_test_assemble_with_spades_ref.fa') tmp_dir = 'tmp.test_assemble_with_spades' - a = assembly.Assembly(reads1, reads2, 'not needed', ref_fasta, tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout) + a = assembly.Assembly(reads1, reads2, 'not needed', ref_fasta, tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout, 'not needed') a._assemble_with_spades(unittest=False) self.assertFalse(a.assembled_ok) shutil.rmtree(tmp_dir) @@ -130,7 +130,7 @@ def test_scaffold_with_sspace(self): reads2 = os.path.join(data_dir, 'assembly_test_assemble_with_spades_reads_2.fq') ref_fasta = os.path.join(data_dir, 'assembly_test_assemble_with_spades_ref.fa') tmp_dir = 'tmp.test_scaffold_with_sspace' - a = assembly.Assembly(reads1, reads2, 'not needed', ref_fasta, tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout) + a = assembly.Assembly(reads1, reads2, 'not needed', ref_fasta, tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout, 'not needed') a.assembly_contigs = os.path.join(data_dir, 'assembly_test_scaffold_with_sspace_contigs.fa') a._scaffold_with_sspace() self.assertTrue(os.path.exists(a.scaffolder_scaffolds)) @@ -162,7 +162,7 @@ def test_gap_fill_with_gapfiller_no_gaps(self): reads1 = os.path.join(data_dir, 'assembly_test_gapfill_with_gapfiller_reads_1.fq') reads2 = os.path.join(data_dir, 'assembly_test_gapfill_with_gapfiller_reads_2.fq') tmp_dir = 'tmp.gap_fill_with_gapfiller_no_gaps' - a = assembly.Assembly(reads1, reads2, 'not needed', 'ref.fa', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout) + a = assembly.Assembly(reads1, reads2, 'not needed', 'ref.fa', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout, 'not needed') a.scaffolder_scaffolds = os.path.join(data_dir, 'assembly_test_gapfill_with_gapfiller.scaffolds_no_gaps.fa') a._gap_fill_with_gapfiller() self.assertTrue(os.path.exists(a.gapfilled_scaffolds)) @@ -175,7 +175,7 @@ def test_gap_fill_with_gapfiller_with_gaps(self): reads1 = os.path.join(data_dir, 'assembly_test_gapfill_with_gapfiller_reads_1.fq') reads2 = os.path.join(data_dir, 'assembly_test_gapfill_with_gapfiller_reads_2.fq') tmp_dir = 'tmp.gap_fill_with_gapfiller_with_gaps' - a = assembly.Assembly(reads1, reads2, 'not needed', 'ref.fa', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout) + a = assembly.Assembly(reads1, reads2, 'not needed', 'ref.fa', tmp_dir, 'not_needed_for_this_test.fa', 'not_needed_for_this_test.bam', sys.stdout, 'not needed') a.scaffolder_scaffolds = os.path.join(data_dir, 'assembly_test_gapfill_with_gapfiller.scaffolds_with_gaps.fa') a._gap_fill_with_gapfiller() self.assertTrue(os.path.exists(a.gapfilled_scaffolds)) diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py index 579ea961..8b2a5ba9 100644 --- a/ariba/tests/cluster_test.py +++ b/ariba/tests/cluster_test.py @@ -130,6 +130,25 @@ def test_full_run_choose_ref_fail(self): shutil.rmtree(tmpdir) + def test_full_run_ref_not_in_cluster(self): + '''test complete run of cluster when nearest ref is outside cluster''' + fasta_in = os.path.join(data_dir, 'cluster_test_full_run_ref_not_in_cluster.in.fa') + tsv_in = os.path.join(data_dir, 'cluster_test_full_run_ref_not_in_cluster.in.tsv') + refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) + tmpdir = 'tmp.test_full_run_ref_not_in_cluster' + ref_for_mash = os.path.join(data_dir, 'cluster_test_full_run_ref_not_in_cluster.mash.fa') + shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_ref_not_in_cluster'), tmpdir) + + c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=72, total_reads_bases=3600, refdata_seqs_fasta_for_mash=ref_for_mash) + c.run() + + expected = '\t'.join(['.', '.', '.', '.', '1024', '72', 'cluster_name'] + ['.'] * 24) + self.assertEqual([expected], c.report_lines) + self.assertTrue(c.status_flag.has('ref_seq_choose_fail')) + self.assertFalse(c.status_flag.has('assembly_fail')) + shutil.rmtree(tmpdir) + + def test_full_run_assembly_fail(self): '''test complete run of cluster when assembly fails''' fasta_in = os.path.join(data_dir, 'cluster_test_full_run_assembly_fail.in.fa') diff --git a/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa new file mode 100644 index 00000000..2a9253db --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.fa @@ -0,0 +1,6 @@ +>noncoding1 +CGTACGCGGGTGGAGACATGTACTCCACTCCCATACATCCCTAAGTTTGTCCCTAAGGCA +GTGCCCGCCGCCCACGAACGAATGCGGTGAGATGCTTAGGGAACGCCTATCCGAGATCAC +>noncoding2 +TCTTTAACTGTTCACGACTGTATCGCGGCTTGCAAATCTTAAGTTCTTCCCAAGCGCGCT +GCGATACAAATCCCAAGTTTAGCGGACAGTTCACGCCGGGTTCTAAGAATGTATGCGTCC diff --git a/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv new file mode 100644 index 00000000..ab4e2bdd --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.in.tsv @@ -0,0 +1,6 @@ +noncoding1 0 0 . . generic description of noncoding1 +noncoding1 0 0 A6G . variant in ref and reads so should report +noncoding1 0 0 G9T . wild type in ref and reads +noncoding1 0 0 A14T . ref has wild type, reads has variant so should report +noncoding1 0 0 A40C . ref has variant, reads has wild type +noncoding2 0 0 . . generic description of noncoding2 diff --git a/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.mash.fa b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.mash.fa new file mode 100644 index 00000000..efcabae4 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.mash.fa @@ -0,0 +1,9 @@ +>noncoding1_closest +CGTACGCGGGTGGAGACATGTACTCCACTCCCATACATCCCTAAGTTTGTCCCTAAGGCA +GTGCCCGCCGCCCACGAACGAATGCGGTGAGATGCTTAGGGAACGCCTATCCGAGATCAC +>noncoding1 +CGTACGCGGGTAGAGACATGTACTCCACTCACATACATCCCTAAGTTTGTCCCTAAGGCA +GTGCCCGCCGCCCACGAACGAATGCGCTGAGATGCTTAGTGAACGCCTATCCGAGATCAC +>noncoding2 +TCTTTAACTGTTCACGACTGTATCGCGGCTTGCAAATCTTAAGTTCTTCCCAAGCGCGCT +GCGATACAAATCCCAAGTTTAGCGGACAGTTCACGCCGGGTTCTAAGAATGTATGCGTCC diff --git a/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.mash.fa.msh b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster.mash.fa.msh new file mode 100644 index 0000000000000000000000000000000000000000..37f5b75b6664d6db7706f471ae7f24cce6bf33e2 GIT binary patch literal 2760 zcma*pc{G&k9{})SvX1P#Y}Z9GO&ATbWQ3co(#?J`NLq%;HOknvF+&n%9U4*8WUR@S zF_h96k!cXQV~8weUnbOV{BBd-e&?R^d*AbYzTfwG-|udhPyAayjkBO9=d&J8{;_{+{{QK>x8U&h2wS6r3VVYy 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VZXRL8clgWJ`BUI48P4$y@E^q!(9!?^ literal 0 HcmV?d00001 diff --git a/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq new file mode 100644 index 00000000..4356e47f --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_1.fq @@ -0,0 +1,144 @@ +@noncoding1:1:77:136/1 +CATGTACTCCACTCCCATACATCACTAAGTTTGTCCCTAAGGCATTGCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:2:48:107/1 +CTGAGTGAAGCGACGTACGCGGGTGGTGACATGTACTCCACTCCCATACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:3:98:159/1 +TCACTAAGTTTGTCCCTAAGGCATTGCCCGCCGCCCACGAACGAACTGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:4:126:185/1 +CGCCGCCCACGAACGAACTGCGGTGAGATGCTTAGGGAACGCCATCCGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:5:26:85/1 +CGTAGCGTACTGAGTCTACTGACTGAGTGAAGCGACGTACGCGGGTGGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:6:85:145/1 +CCACTCCCATACATCACTAAGTTTGTCCCTAAGGCATTGCCCGCCGCCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:7:53:112/1 +TGAAGCGACGTACGCGGGTGGTGACATGTACTCCACTCCCATACATCACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:8:110:170/1 +TCCCTAAGGCATTGCCCGCCGCCCACGAACGAACTGCGGTGAGATGCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:9:73:132/1 +GTGACATGTACTCCACTCCCATACATCACTAAGTTTGTCCCTAAGGCATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:10:51:110/1 +AGTGAAGCGACGTACGCGGGTGGTGACATGTACTCCACTCCCATACATCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:11:123:183/1 +GCCCGCCGCCCACGAACGAACTGCGGTGAGATGCTTAGGGAACGCCATCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:12:63:122/1 +TACGCGGGTGGTGACATGTACTCCACTCCCATACATCACTAAGTTTGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:13:91:150/1 +CCATACATCACTAAGTTTGTCCCTAAGGCATTGCCCGCCGCCCACGAACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:14:7:68/1 +GACTTGACGATCGTACGTACGTAGCGTACTGAGTCTACTGACTGAGTGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:15:104:163/1 +AGTTTGTCCCTAAGGCATTGCCCGCCGCCCACGAACGAACTGCGGTGAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:16:1:60/1 +CGTATCGACTTGACGATCGTACGTACGTAGCGTACTGAGTCTACTGACTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:17:64:123/1 +ACGCGGGTGGTGACATGTACTCCACTCCCATACATCACTAAGTTTGTCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:18:128:185/1 +CCGCCCACGAACGAACTGCGGTGAGATGCTTAGGGAACGCCATCCGAGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:19:28:88/1 +TAGCGTACTGAGTCTACTGACTGAGTGAAGCGACGTACGCGGGTGGTGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:20:97:157/1 +ATCACTAAGTTTGTCCCTAAGGCATTGCCCGCCGCCCACGAACGAACTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:21:22:81/1 +CGTACGTAGCGTACTGAGTCTACTGACTGAGTGAAGCGACGTACGCGGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:22:95:155/1 +ACATCACTAAGTTTGTCCCTAAGGCATTGCCCGCCGCCCACGAACGAACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:23:119:176/1 +CATTGCCCGCCGCCCACGAACGAACTGCGGTGAGATGCTTAGGGAACGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:24:110:169/1 +TCCCTAAGGCATTGCCCGCCGCCCACGAACGAACTGCGGTGAGATGCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:25:110:170.dup.2/1 +TCCCTAAGGCATTGCCCGCCGCCCACGAACGAACTGCGGTGAGATGCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:26:57:117/1 +GCGACGTACGCGGGTGGTGACATGTACTCCACTCCCATACATCACTAAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:27:41:100/1 +CTACTGACTGAGTGAAGCGACGTACGCGGGTGGTGACATGTACTCCACTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:28:18:78/1 +CGTACGTACGTAGCGTACTGAGTCTACTGACTGAGTGAAGCGACGTACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:29:6:65/1 +CGACTTGACGATCGTACGTACGTAGCGTACTGAGTCTACTGACTGAGTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:30:3:63/1 +TATCGACTTGACGATCGTACGTACGTAGCGTACTGAGTCTACTGACTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:31:66:124/1 +GCGGGTGGTGACATGTACTCCACTCCCATACATCACTAAGTTTGTCCCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:32:62:122/1 +GTACGCGGGTGGTGACATGTACTCCACTCCCATACATCACTAAGTTTGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:33:32:91/1 +GTACTGAGTCTACTGACTGAGTGAAGCGACGTACGCGGGTGGTGACATGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:34:28:86/1 +TAGCGTACTGAGTCTACTGACTGAGTGAAGCGACGTACGCGGGTGGTGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:35:3:64/1 +TATCGACTTGACGATCGTACGTACGTAGCGTACTGAGTCTACTGACTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:36:120:181/1 +ATTGCCCGCCGCCCACGAACGAACTGCGGTGAGATGCTTAGGGAACGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq new file mode 100644 index 00000000..b3ba7388 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/reads_2.fq @@ -0,0 +1,144 @@ +@noncoding1:1:77:136/2 +TGAATGTGATCTCGGATGGCGTTCCCTAAGCATCTCACCGCAGTTCGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:2:48:107/2 +GCATCTCACCGCAGTTCGTTCGTGGGCGGCGGGCAATGCCTTAGGGACAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:3:98:159/2 +CGTCGCTGATAGCTGCTCGCTCGTGAATGTGATCTCGGATGGCGTTCCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:4:126:185/2 +AGATCCGCGCGAGAGTATATATCGCTCGTCGCTGATAGCTGCTCGCTCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:5:26:85/2 +TGGGCGGCGGGCAATGCCTTAGGGACAAACTTAGTGATGTATGGGAGTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:6:85:145/2 +GCTCGCTCGTGAATGTGATCTCGGATGGCGTTCCCTAAGCATCTCACCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:7:53:112/2 +CCTAAGCATCTCACCGCAGTTCGTTCGTGGGCGGCGGGCAATGCCTTAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:8:110:170/2 +TATATATCGCTCGTCGCTGATAGCTGCTCGCTCGTGAATGTGATCTCGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:9:73:132/2 +TGTGATCTCGGATGGCGTTCCCTAAGCATCTCACCGCAGTTCGTTCGTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:10:51:110/2 +TAAGCATCTCACCGCAGTTCGTTCGTGGGCGGCGGGCAATGCCTTAGGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:11:123:183/2 +ATCCGCGCGAGAGTATATATCGCTCGTCGCTGATAGCTGCTCGCTCGTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:12:63:122/2 +GATGGCGTTCCCTAAGCATCTCACCGCAGTTCGTTCGTGGGCGGCGGGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:13:91:150/2 +TAGCTGCTCGCTCGTGAATGTGATCTCGGATGGCGTTCCCTAAGCATCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:14:7:68/2 +CTTAGGGACAAACTTAGTGATGTATGGGAGTGGAGTACATGTCACCACCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:15:104:163/2 +CGCTCGTCGCTGATAGCTGCTCGCTCGTGAATGTGATCTCGGATGGCGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:16:1:60/2 +CAAACTTAGTGATGTATGGGAGTGGAGTACATGTCACCACCCGCGTACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:17:64:123/2 +GGATGGCGTTCCCTAAGCATCTCACCGCAGTTCGTTCGTGGGCGGCGGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:18:128:185/2 +AGATCCGCGCGAGAGTATATATCGCTCGTCGCTGATAGCTGCTCGCTCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:19:28:88/2 +TCGTGGGCGGCGGGCAATGCCTTAGGGACAAACTTAGTGATGTATGGGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:20:97:157/2 +TCGCTGATAGCTGCTCGCTCGTGAATGTGATCTCGGATGGCGTTCCCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:21:22:81/2 +CGGCGGGCAATGCCTTAGGGACAAACTTAGTGATGTATGGGAGTGGAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:22:95:155/2 +GCTGATAGCTGCTCGCTCGTGAATGTGATCTCGGATGGCGTTCCCTAAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:23:119:176/2 +CGAGAGTATATATCGCTCGTCGCTGATAGCTGCTCGCTCGTGAATGTGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:24:110:169/2 +ATATATCGCTCGTCGCTGATAGCTGCTCGCTCGTGAATGTGATCTCGGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:25:110:170.dup.2/2 +TATATATCGCTCGTCGCTGATAGCTGCTCGCTCGTGAATGTGATCTCGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:26:57:117/2 +CGTTCCCTAAGCATCTCACCGCAGTTCGTTCGTGGGCGGCGGGCAATGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:27:41:100/2 +ACCGCAGTTCGTTCGTGGGCGGCGGGCAATGCCTTAGGGACAAACTTAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:28:18:78/2 +CGGGCAATGCCTTAGGGACAAACTTAGTGATGTATGGGAGTGGAGTACAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:29:6:65/2 +AGGGACAAACTTAGTGATGTATGGGAGTGGAGTACATGTCACCACCCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:30:3:63/2 +GGACAAACTTAGTGATGTATGGGAGTGGAGTACATGTCACCACCCGCGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:31:66:124/2 +CGGATGGCGTTCCCTAAGCATCTCACCGCAGTTCGTTCGTGGGCGGCGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:32:62:122/2 +GATGGCGTTCCCTAAGCATCTCACCGCAGTTCGTTCGTGGGCGGCGGGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:33:32:91/2 +CGTTCGTGGGCGGCGGGCAATGCCTTAGGGACAAACTTAGTGATGTATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:34:28:86/2 +GTGGGCGGCGGGCAATGCCTTAGGGACAAACTTAGTGATGTATGGGAGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:35:3:64/2 +GGGACAAACTTAGTGATGTATGGGAGTGGAGTACATGTCACCACCCGCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@noncoding1:36:120:181/2 +CCGCGCGAGAGTATATATCGCTCGTCGCTGATAGCTGCTCGCTCGTGAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa new file mode 100644 index 00000000..2a9253db --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_ref_not_in_cluster/references.fa @@ -0,0 +1,6 @@ +>noncoding1 +CGTACGCGGGTGGAGACATGTACTCCACTCCCATACATCCCTAAGTTTGTCCCTAAGGCA +GTGCCCGCCGCCCACGAACGAATGCGGTGAGATGCTTAGGGAACGCCTATCCGAGATCAC +>noncoding2 +TCTTTAACTGTTCACGACTGTATCGCGGCTTGCAAATCTTAAGTTCTTCCCAAGCGCGCT +GCGATACAAATCCCAAGTTTAGCGGACAGTTCACGCCGGGTTCTAAGAATGTATGCGTCC From 340f89fa1a51cf933f5ec8aa04b8b28e51adb3b0 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Mon, 10 Oct 2016 13:00:19 +0100 Subject: [PATCH 10/16] Print stack trace if reporting fails --- ariba/cluster.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/ariba/cluster.py b/ariba/cluster.py index bdda65af..efdc2cce 100644 --- a/ariba/cluster.py +++ b/ariba/cluster.py @@ -1,4 +1,5 @@ import signal +import traceback import os import atexit import random @@ -427,8 +428,12 @@ def _run(self): print('\nCould not get closest reference sequence\n', file=self.log_fh, flush=True) self.status_flag.add('ref_seq_choose_fail') + try: + self.report_lines = report.report_lines(self) + except: + print('Error making report for cluster ', self.name, '... traceback:', file=sys.stderr) + traceback.print_exc(file=sys.stderr) + raise Error('Error making report for cluster ' + self.name) - print('\nMaking report lines', file=self.log_fh, flush=True) - self.report_lines = report.report_lines(self) self._clean() atexit.unregister(self._atexit) From f30f850b6424482d4d6b693bdb959189fdc6f343 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Mon, 10 Oct 2016 13:00:38 +0100 Subject: [PATCH 11/16] Bug fix for synonymous variants --- ariba/report.py | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/ariba/report.py b/ariba/report.py index bc717029..ec55b8a2 100644 --- a/ariba/report.py +++ b/ariba/report.py @@ -212,7 +212,7 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum ctg_start_pos, ctg_start_in_indel = ref_start_hit.qry_coords_from_ref_coord(ref_start_pos, pymummer_variants) if known_var_change not in ['.', 'unknown']: - regex = re.match('^([^0-9])([0-9]+)([^0-9])$', known_var_change) + regex = re.match('^([^0-9]+)([0-9]+)([^0-9]+)$', known_var_change) try: ref_var_string, ref_var_position, ctg_var_string = regex.group(1, 2, 3) except: @@ -221,13 +221,18 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum if '_' in ref_ctg_change: continue else: - regex = re.match('^([^0-9])([0-9]+)([^0-9])$', ref_ctg_change) + regex = re.match('^([^0-9]+)([0-9]+)([^0-9]+)$', ref_ctg_change) try: ref_var_string, ref_var_position, ctg_var_string = regex.group(1, 2, 3) except: raise Error('Error parsing variant ' + ref_ctg_change) + else: + assert var_effect == 'SYN' - if ref_var_string == '.' or var_effect in ['FSHIFT', 'TRUNC', 'INDELS', 'UNKNOWN']: + if var_effect == 'SYN': + ref_end_pos = ref_start_pos + 2 + ctg_end_pos = ctg_start_pos + 2 + elif ref_var_string == '.' or var_effect in ['FSHIFT', 'TRUNC', 'INDELS', 'UNKNOWN']: ref_end_pos = ref_start_pos ctg_end_pos = ctg_start_pos elif cluster.is_gene == '1': From 67306506fcf93e5b52c39a780cee047edfcafaa3 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Tue, 11 Oct 2016 11:28:02 +0100 Subject: [PATCH 12/16] Bug fix handling multiple vars in one codon --- ariba/report.py | 82 +-- ariba/tests/cluster_test.py | 17 + .../cluster_test_full_run_multiple_vars.fa | 5 + .../cluster_test_full_run_multiple_vars.tsv | 2 + .../for_reads.fa | 20 + .../reads_1.fq | 584 ++++++++++++++++++ .../reads_2.fq | 584 ++++++++++++++++++ .../references.fa | 5 + 8 files changed, 1261 insertions(+), 38 deletions(-) create mode 100644 ariba/tests/data/cluster_test_full_run_multiple_vars.fa create mode 100644 ariba/tests/data/cluster_test_full_run_multiple_vars.tsv create mode 100644 ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa create mode 100644 ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq create mode 100644 ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq create mode 100644 ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa diff --git a/ariba/report.py b/ariba/report.py index ec55b8a2..3f4439f3 100644 --- a/ariba/report.py +++ b/ariba/report.py @@ -200,47 +200,53 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum if contributing_vars is None: samtools_columns = [['.'] * 9] else: - ref_start_pos = 3 * position if cluster.is_gene == '1' else position - assert contig_name in cluster.assembly_compare.nucmer_hits - ref_start_hit = None - for hit in cluster.assembly_compare.nucmer_hits[contig_name]: - if hit.ref_name == cluster.ref_sequence.id and hit.ref_coords().distance_to_point(ref_start_pos) == 0: - ref_start_hit = copy.copy(hit) - break - - assert ref_start_hit is not None - ctg_start_pos, ctg_start_in_indel = ref_start_hit.qry_coords_from_ref_coord(ref_start_pos, pymummer_variants) - - if known_var_change not in ['.', 'unknown']: - regex = re.match('^([^0-9]+)([0-9]+)([^0-9]+)$', known_var_change) - try: - ref_var_string, ref_var_position, ctg_var_string = regex.group(1, 2, 3) - except: - raise Error('Error parsing variant ' + known_var_change) - elif ref_ctg_change != '.': - if '_' in ref_ctg_change: - continue - else: - regex = re.match('^([^0-9]+)([0-9]+)([^0-9]+)$', ref_ctg_change) + if var_effect == 'MULTIPLE': + ref_start_pos = min([x.ref_start for x in contributing_vars]) + ref_end_pos = max([x.ref_start for x in contributing_vars]) + ctg_start_pos = min([x.qry_start for x in contributing_vars]) + ctg_end_pos = max([x.qry_start for x in contributing_vars]) + else: + ref_start_pos = 3 * position if cluster.is_gene == '1' else position + assert contig_name in cluster.assembly_compare.nucmer_hits + ref_start_hit = None + for hit in cluster.assembly_compare.nucmer_hits[contig_name]: + if hit.ref_name == cluster.ref_sequence.id and hit.ref_coords().distance_to_point(ref_start_pos) == 0: + ref_start_hit = copy.copy(hit) + break + + assert ref_start_hit is not None + ctg_start_pos, ctg_start_in_indel = ref_start_hit.qry_coords_from_ref_coord(ref_start_pos, pymummer_variants) + + if known_var_change not in ['.', 'unknown']: + regex = re.match('^([^0-9]+)([0-9]+)([^0-9]+)$', known_var_change) try: ref_var_string, ref_var_position, ctg_var_string = regex.group(1, 2, 3) except: - raise Error('Error parsing variant ' + ref_ctg_change) - else: - assert var_effect == 'SYN' - - if var_effect == 'SYN': - ref_end_pos = ref_start_pos + 2 - ctg_end_pos = ctg_start_pos + 2 - elif ref_var_string == '.' or var_effect in ['FSHIFT', 'TRUNC', 'INDELS', 'UNKNOWN']: - ref_end_pos = ref_start_pos - ctg_end_pos = ctg_start_pos - elif cluster.is_gene == '1': - ref_end_pos = ref_start_pos + 3 * len(ref_var_string) - 1 - ctg_end_pos = ctg_start_pos + 3 * len(ctg_var_string) - 1 - else: - ref_end_pos = ref_start_pos + len(ref_var_string) - 1 - ctg_end_pos = ctg_start_pos + len(ctg_var_string) - 1 + raise Error('Error parsing variant ' + known_var_change) + elif ref_ctg_change != '.': + if '_' in ref_ctg_change: + continue + else: + regex = re.match('^([^0-9]+)([0-9]+)([^0-9]+)$', ref_ctg_change) + try: + ref_var_string, ref_var_position, ctg_var_string = regex.group(1, 2, 3) + except: + raise Error('Error parsing variant ' + ref_ctg_change) + else: + assert var_effect == 'SYN' + + if var_effect == 'SYN': + ref_end_pos = ref_start_pos + 2 + ctg_end_pos = ctg_start_pos + 2 + elif ref_var_string == '.' or var_effect in ['FSHIFT', 'TRUNC', 'INDELS', 'UNKNOWN']: + ref_end_pos = ref_start_pos + ctg_end_pos = ctg_start_pos + elif cluster.is_gene == '1': + ref_end_pos = ref_start_pos + 3 * len(ref_var_string) - 1 + ctg_end_pos = ctg_start_pos + 3 * len(ctg_var_string) - 1 + else: + ref_end_pos = ref_start_pos + len(ref_var_string) - 1 + ctg_end_pos = ctg_start_pos + len(ctg_var_string) - 1 smtls_total_depth = [] smtls_alt_nt = [] diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py index 8b2a5ba9..b6a3c0c9 100644 --- a/ariba/tests/cluster_test.py +++ b/ariba/tests/cluster_test.py @@ -495,3 +495,20 @@ def test_full_run_partial_assembly(self): self.assertEqual(expected, c.report_lines) shutil.rmtree(tmpdir) + + def test_full_run_multiple_vars_in_codon(self): + '''Test complete run where there is a codon with a SNP and an indel''' + fasta_in = os.path.join(data_dir, 'cluster_test_full_run_multiple_vars.fa') + tsv_in = os.path.join(data_dir, 'cluster_test_full_run_multiple_vars.tsv') + refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) + tmpdir = 'tmp.cluster_test_full_run_multiple_vars' + shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_multiple_vars'), tmpdir) + c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=292, total_reads_bases=20900) + c.run() + + expected = [ + 'presence_absence1\tpresence_absence1\t1\t0\t539\t292\tcluster_name\t96\t96\t96.91\tcluster_name.scaffold.1\t1074\t20.4\t0\t.\tp\t.\t0\t.\tMULTIPLE\t25\t26\tGA\t487\t489\tCAT\t27;26;25\tC;A;T\t27;26;25\t.\tGeneric description of presence_absence1', + 'presence_absence1\tpresence_absence1\t1\t0\t539\t292\tcluster_name\t96\t96\t96.91\tcluster_name.scaffold.1\t1074\t20.4\t0\t.\tp\t.\t0\tA10fs\tFSHIFT\t28\t28\tG\t491\t491\tG\t26\tG\t26\t.\tGeneric description of presence_absence1', + ] + self.assertEqual(expected, c.report_lines) + shutil.rmtree(tmpdir) diff --git a/ariba/tests/data/cluster_test_full_run_multiple_vars.fa b/ariba/tests/data/cluster_test_full_run_multiple_vars.fa new file mode 100644 index 00000000..c7a01d84 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_multiple_vars.fa @@ -0,0 +1,5 @@ +>presence_absence1 +ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT +ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA +>presence_absence2 +ATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTAA diff --git a/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv b/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv new file mode 100644 index 00000000..0e711a64 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_multiple_vars.tsv @@ -0,0 +1,2 @@ +presence_absence1 1 0 . . Generic description of presence_absence1 +presence_absence2 1 0 . . Generic description of presence_absence2 diff --git a/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa b/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa new file mode 100644 index 00000000..3d5115f0 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_multiple_vars/for_reads.fa @@ -0,0 +1,20 @@ +>presence_absence1 +GTCTAGGCCATTATCGATCGACAAGTTGCCGTAATTTGCGTAAAATAGCACGAACCCGAA +ACTTCCTGATATGTCTTGAGTGAATCCATAACCGACCAATTCCCTGCACACGGGAAATCT +TCACATATAGGACTTCCTTGGGATAAGATAATTGCTCCTATTGGGGTTACACGCCATTAC +TTTGGGCGCCCCGTATACAGGGAATCACAGATCACCGTGCCTCCAGAGCCGCCCTGGGTT +GCAGCTGGAACCAGCAAAGTAGGCCTATCACCGACCTCGATAGTCGTTTCCTACGTGTAG +TTTTAACAGAGGCTTGTTCAATACAGTGGGGCCGGTCCAGGGGCATGTGTAATCCGGTGT +CGTCACGAGGACAATGTTTGATGACTCTATGATACTCACCGTCAGTACTTCCTCCTCAAT +GGTGACTGGTTGAAGTCCCTCGTGCCACCATGTTGAAAAGCGGTCGCTTAAAATAGTGAA +ATGGATCGCGAAGCGATGACCCATCATAGCACCGAACGCGCGAGCACCAACATTAGCCAT +ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA +CGTAGGCTCGAACATCCCGACCACGTGGTAATTTTGGGCTCGGCTACTCCTGGCTGTGGA +GCACGTAATGGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGA +ATGACCAGGCGATTCATGGGGGGTCCGTATACTCTCCCGTCTGTTAGGAATTATCTTGCC +TGAAGCTAAGGCCACGGGATGCCCAACCCCTTTACTAGATGTTAGATTAAGCGGGTACCA +GTATCATTTCAAGCAGGAACCCTAGGAGACGCTTAGGCGCCCTTAGACTTCATGATACTA +CCATAAATGAGGTCTCGTTCCATGATATAGGGAGATGACGAATGCTTGCCAAGACAAATG +AATTTTCTGGGATGAGGCAGCGGGTCCGGGAGTCACGCCAAACATTGAAAAACTCTCCGA +CAACAGTTGAAAACTCACTTGTTCATCCCTGACCTTAGCCGACCACCGCTGGGTAATGAG +CTCGGTACTGTCTGGCCTGGCACGCAAACAAATGGCTTAG diff --git a/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq b/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq new file mode 100644 index 00000000..52d79adb --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_1.fq @@ -0,0 +1,584 @@ +@presence_absence1:1:768:842/1 +CCACGGGATGCCCAACCCCTTTACTAGATGTTAGATTAAGCGGGTACCAGTATCATTTCAAGCAGGAACCCTAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:2:395:471/1 +CTCACCGTCAGTACTTCCTCCTCAATGGTGACTGGTTGAAGTCCCTCGTGCCACCATGTTGAAAAGCGGTCGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:3:732:807/1 +CCCGTCTGTTAGGAATTATCTTGCCTGAAGCTAAGGCCACGGGATGCCCAACCCCTTTACTAGATGTTAGATTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:4:745:820/1 +AATTATCTTGCCTGAAGCTAAGGCCACGGGATGCCCAACCCCTTTACTAGATGTTAGATTAAGCGGGTACCAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:5:245:320/1 +CTGGAACCAGCAAAGTAGGCCTATCACCGACCTCGATAGTCGTTTCCTACGTGTAGTTTTAACAGAGGCTTGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:6:280:354/1 +ATAGTCGTTTCCTACGTGTAGTTTTAACAGAGGCTTGTTCAATACAGTGGGGCCGGTCCAGGGGCATGTGTAATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:7:617:690/1 +CGGCTACTCCTGGCTGTGGAGCACGTAATGGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:8:646:721/1 +GGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGAATGACCAGGCGATTCATGGGGGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:9:239:312/1 +TTGCAGCTGGAACCAGCAAAGTAGGCCTATCACCGACCTCGATAGTCGTTTCCTACGTGTAGTTTTAACAGAGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:10:770:844/1 +ACGGGATGCCCAACCCCTTTACTAGATGTTAGATTAAGCGGGTACCAGTATCATTTCAAGCAGGAACCCTAGGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:11:198:273/1 +CAGGGAATCACAGATCACCGTGCCTCCAGAGCCGCCCTGGGTTGCAGCTGGAACCAGCAAAGTAGGCCTATCACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:12:441:516/1 +CGTGCCACCATGTTGAAAAGCGGTCGCTTAAAATAGTGAAATGGATCGCGAAGCGATGACCCATCATAGCACCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:13:650:724/1 +CCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGAATGACCAGGCGATTCATGGGGGGTCCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:14:528:601/1 +CAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACGTAGGCTCGAACATCCCGACCACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:15:840:915/1 +AGGAGACGCTTAGGCGCCCTTAGACTTCATGATACTACCATAAATGAGGTCTCGTTCCATGATATAGGGAGATGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:16:588:663/1 +ACATCCCGACCACGTGGTAATTTTGGGCTCGGCTACTCCTGGCTGTGGAGCACGTAATGGTACCACGGGTGTTAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:17:536:610/1 +GCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACGTAGGCTCGAACATCCCGACCACGTGGTAATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:18:153:229/1 +TGCTCCTATTGGGGTTACACGCCATTACTTTGGGCGCCCCGTATACAGGGAATCACAGATCACCGTGCCTCCAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:19:427:501/1 +TGGTTGAAGTCCCTCGTGCCACCATGTTGAAAAGCGGTCGCTTAAAATAGTGAAATGGATCGCGAAGCGATGACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:20:472:547/1 +AATAGTGAAATGGATCGCGAAGCGATGACCCATCATAGCACCGAACGCGCGAGCACCAACATTAGCCATATTAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:21:498:573/1 +GACCCATCATAGCACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:22:760:836/1 +AGCTAAGGCCACGGGATGCCCAACCCCTTTACTAGATGTTAGATTAAGCGGGTACCAGTATCATTTCAAGCAGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:23:808:884/1 +CGGGTACCAGTATCATTTCAAGCAGGAACCCTAGGAGACGCTTAGGCGCCCTTAGACTTCATGATACTACCATAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:24:912:986/1 +TGACGAATGCTTGCCAAGACAAATGAATTTTCTGGGATGAGGCAGCGGGTCCGGGAGTCACGCCAAACATTGAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:25:151:225/1 +ATTGCTCCTATTGGGGTTACACGCCATTACTTTGGGCGCCCCGTATACAGGGAATCACAGATCACCGTGCCTCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:26:322:398/1 +TACAGTGGGGCCGGTCCAGGGGCATGTGTAATCCGGTGTCGTCACGAGGACAATGTTTGATGACTCTATGATACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:27:790:866/1 +ACTAGATGTTAGATTAAGCGGGTACCAGTATCATTTCAAGCAGGAACCCTAGGAGACGCTTAGGCGCCCTTAGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:28:642:715/1 +TAATGGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGAATGACCAGGCGATTCATGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:29:944:1018/1 +TGGGATGAGGCAGCGGGTCCGGGAGTCACGCCAAACATTGAAAAACTCTCCGACAACAGTTGAAAACTCACTTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:30:358:432/1 +TGTCGTCACGAGGACAATGTTTGATGACTCTATGATACTCACCGTCAGTACTTCCTCCTCAATGGTGACTGGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:31:626:700/1 +CTGGCTGTGGAGCACGTAATGGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGAATGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:32:741:814/1 +TAGGAATTATCTTGCCTGAAGCTAAGGCCACGGGATGCCCAACCCCTTTACTAGATGTTAGATTAAGCGGGTACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:33:419:493/1 +ATGGTGACTGGTTGAAGTCCCTCGTGCCACCATGTTGAAAAGCGGTCGCTTAAAATAGTGAAATGGATCGCGAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:34:140:213/1 +GGGATAAGATAATTGCTCCTATTGGGGTTACACGCCATTACTTTGGGCGCCCCGTATACAGGGAATCACAGATCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:35:443:517/1 +TGCCACCATGTTGAAAAGCGGTCGCTTAAAATAGTGAAATGGATCGCGAAGCGATGACCCATCATAGCACCGAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:36:83:158/1 +AATCCATAACCGACCAATTCCCTGCACACGGGAAATCTTCACATATAGGACTTCCTTGGGATAAGATAATTGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:37:472:548/1 +AATAGTGAAATGGATCGCGAAGCGATGACCCATCATAGCACCGAACGCGCGAGCACCAACATTAGCCATATTAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:38:512:586/1 +CCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACGTAGGCTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:39:637:709/1 +GCACGTAATGGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGAATGACCAGGCGATTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:40:624:697/1 +TCCTGGCTGTGGAGCACGTAATGGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:41:454:528/1 +TGAAAAGCGGTCGCTTAAAATAGTGAAATGGATCGCGAAGCGATGACCCATCATAGCACCGAACGCGCGAGCACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:42:417:492/1 +CAATGGTGACTGGTTGAAGTCCCTCGTGCCACCATGTTGAAAAGCGGTCGCTTAAAATAGTGAAATGGATCGCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:43:928:1003/1 +AGACAAATGAATTTTCTGGGATGAGGCAGCGGGTCCGGGAGTCACGCCAAACATTGAAAAACTCTCCGACAACAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:44:214:287/1 +ACCGTGCCTCCAGAGCCGCCCTGGGTTGCAGCTGGAACCAGCAAAGTAGGCCTATCACCGACCTCGATAGTCGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:45:811:887/1 +GTACCAGTATCATTTCAAGCAGGAACCCTAGGAGACGCTTAGGCGCCCTTAGACTTCATGATACTACCATAAATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:46:492:567/1 +AGCGATGACCCATCATAGCACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:47:875:950/1 +TACCATAAATGAGGTCTCGTTCCATGATATAGGGAGATGACGAATGCTTGCCAAGACAAATGAATTTTCTGGGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:48:913:987/1 +GACGAATGCTTGCCAAGACAAATGAATTTTCTGGGATGAGGCAGCGGGTCCGGGAGTCACGCCAAACATTGAAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:49:721:796/1 +CCGTATACTCTCCCGTCTGTTAGGAATTATCTTGCCTGAAGCTAAGGCCACGGGATGCCCAACCCCTTTACTAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:50:90:163/1 +AACCGACCAATTCCCTGCACACGGGAAATCTTCACATATAGGACTTCCTTGGGATAAGATAATTGCTCCTATTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:51:113:187/1 +GGAAATCTTCACATATAGGACTTCCTTGGGATAAGATAATTGCTCCTATTGGGGTTACACGCCATTACTTTGGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:52:500:574/1 +CCCATCATAGCACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:53:512:584/1 +CCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACGTAGGCTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:54:781:855/1 +AACCCCTTTACTAGATGTTAGATTAAGCGGGTACCAGTATCATTTCAAGCAGGAACCCTAGGAGACGCTTAGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:55:792:867/1 +TAGATGTTAGATTAAGCGGGTACCAGTATCATTTCAAGCAGGAACCCTAGGAGACGCTTAGGCGCCCTTAGACTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:56:713:786/1 +TGGGGGGTCCGTATACTCTCCCGTCTGTTAGGAATTATCTTGCCTGAAGCTAAGGCCACGGGATGCCCAACCCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:57:600:676/1 +CGTGGTAATTTTGGGCTCGGCTACTCCTGGCTGTGGAGCACGTAATGGTACCACGGGTGTTACAAGTGAAGGGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:58:564:640/1 +AAGCATGGAATAACGTAGGCTCGAACATCCCGACCACGTGGTAATTTTGGGCTCGGCTACTCCTGGCTGTGGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:59:355:429/1 +CGGTGTCGTCACGAGGACAATGTTTGATGACTCTATGATACTCACCGTCAGTACTTCCTCCTCAATGGTGACTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:60:382:458/1 +TGACTCTATGATACTCACCGTCAGTACTTCCTCCTCAATGGTGACTGGTTGAAGTCCCTCGTGCCACCATGTTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:61:658:731/1 +GTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGAATGACCAGGCGATTCATGGGGGGTCCGTATACTCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:62:849:923/1 +TTAGGCGCCCTTAGACTTCATGATACTACCATAAATGAGGTCTCGTTCCATGATATAGGGAGATGACGAATGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:63:623:697/1 +CTCCTGGCTGTGGAGCACGTAATGGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:64:659:735/1 +TTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGAATGACCAGGCGATTCATGGGGGGTCCGTATACTCTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:65:909:984/1 +AGATGACGAATGCTTGCCAAGACAAATGAATTTTCTGGGATGAGGCAGCGGGTCCGGGAGTCACGCCAAACATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:66:498:571/1 +GACCCATCATAGCACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:67:223:298/1 +CCAGAGCCGCCCTGGGTTGCAGCTGGAACCAGCAAAGTAGGCCTATCACCGACCTCGATAGTCGTTTCCTACGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:68:151:226/1 +ATTGCTCCTATTGGGGTTACACGCCATTACTTTGGGCGCCCCGTATACAGGGAATCACAGATCACCGTGCCTCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:69:164:238/1 +GGGTTACACGCCATTACTTTGGGCGCCCCGTATACAGGGAATCACAGATCACCGTGCCTCCAGAGCCGCCCTGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:70:665:740/1 +GTGAAGGGATGGTCCTCGCCTATCTAAGCTGAATGACCAGGCGATTCATGGGGGGTCCGTATACTCTCCCGTCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:71:769:842/1 +CACGGGATGCCCAACCCCTTTACTAGATGTTAGATTAAGCGGGTACCAGTATCATTTCAAGCAGGAACCCTAGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:72:855:931/1 +GCCCTTAGACTTCATGATACTACCATAAATGAGGTCTCGTTCCATGATATAGGGAGATGACGAATGCTTGCCAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:73:621:694/1 +TACTCCTGGCTGTGGAGCACGTAATGGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:74:754:828/1 +GCCTGAAGCTAAGGCCACGGGATGCCCAACCCCTTTACTAGATGTTAGATTAAGCGGGTACCAGTATCATTTCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:75:542:616/1 +TTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACGTAGGCTCGAACATCCCGACCACGTGGTAATTTTGGGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:76:586:662/1 +GAACATCCCGACCACGTGGTAATTTTGGGCTCGGCTACTCCTGGCTGTGGAGCACGTAATGGTACCACGGGTGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:77:463:536/1 +GTCGCTTAAAATAGTGAAATGGATCGCGAAGCGATGACCCATCATAGCACCGAACGCGCGAGCACCAACATTAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:78:449:523/1 +CATGTTGAAAAGCGGTCGCTTAAAATAGTGAAATGGATCGCGAAGCGATGACCCATCATAGCACCGAACGCGCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:79:537:612/1 +CCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACGTAGGCTCGAACATCCCGACCACGTGGTAATTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:80:728:802/1 +CTCTCCCGTCTGTTAGGAATTATCTTGCCTGAAGCTAAGGCCACGGGATGCCCAACCCCTTTACTAGATGTTAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:81:550:624/1 +ATTAGCGCGTGGGAAAGCATGGAATAACGTAGGCTCGAACATCCCGACCACGTGGTAATTTTGGGCTCGGCTACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:82:749:824/1 +ATCTTGCCTGAAGCTAAGGCCACGGGATGCCCAACCCCTTTACTAGATGTTAGATTAAGCGGGTACCAGTATCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:83:560:635/1 +GGGAAAGCATGGAATAACGTAGGCTCGAACATCCCGACCACGTGGTAATTTTGGGCTCGGCTACTCCTGGCTGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:84:145:219/1 +AAGATAATTGCTCCTATTGGGGTTACACGCCATTACTTTGGGCGCCCCGTATACAGGGAATCACAGATCACCGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:85:512:588/1 +CCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACGTAGGCTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:86:541:615/1 +ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACGTAGGCTCGAACATCCCGACCACGTGGTAATTTTGGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:87:422:498/1 +GTGACTGGTTGAAGTCCCTCGTGCCACCATGTTGAAAAGCGGTCGCTTAAAATAGTGAAATGGATCGCGAAGCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:88:22:97/1 +CAAGTTGCCGTAATTTGCGTAAAATAGCACGAACCCGAAACTTCCTGATATGTCTTGAGTGAATCCATAACCGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:89:819:895/1 +ATCATTTCAAGCAGGAACCCTAGGAGACGCTTAGGCGCCCTTAGACTTCATGATACTACCATAAATGAGGTCTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:90:615:690/1 +CTCGGCTACTCCTGGCTGTGGAGCACGTAATGGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:91:559:633/1 +TGGGAAAGCATGGAATAACGTAGGCTCGAACATCCCGACCACGTGGTAATTTTGGGCTCGGCTACTCCTGGCTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:92:177:251/1 +TTACTTTGGGCGCCCCGTATACAGGGAATCACAGATCACCGTGCCTCCAGAGCCGCCCTGGGTTGCAGCTGGAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:93:285:359/1 +CGTTTCCTACGTGTAGTTTTAACAGAGGCTTGTTCAATACAGTGGGGCCGGTCCAGGGGCATGTGTAATCCGGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:94:393:470/1 +TACTCACCGTCAGTACTTCCTCCTCAATGGTGACTGGTTGAAGTCCCTCGTGCCACCATGTTGAAAAGCGGTCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:95:566:640/1 +GCATGGAATAACGTAGGCTCGAACATCCCGACCACGTGGTAATTTTGGGCTCGGCTACTCCTGGCTGTGGAGCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:96:709:782/1 +TTCATGGGGGGTCCGTATACTCTCCCGTCTGTTAGGAATTATCTTGCCTGAAGCTAAGGCCACGGGATGCCCAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:97:297:372/1 +GTAGTTTTAACAGAGGCTTGTTCAATACAGTGGGGCCGGTCCAGGGGCATGTGTAATCCGGTGTCGTCACGAGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:98:364:439/1 +CACGAGGACAATGTTTGATGACTCTATGATACTCACCGTCAGTACTTCCTCCTCAATGGTGACTGGTTGAAGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:99:541:614/1 +ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACGTAGGCTCGAACATCCCGACCACGTGGTAATTTTGGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:100:196:270/1 +TACAGGGAATCACAGATCACCGTGCCTCCAGAGCCGCCCTGGGTTGCAGCTGGAACCAGCAAAGTAGGCCTATCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:101:750:823/1 +TCTTGCCTGAAGCTAAGGCCACGGGATGCCCAACCCCTTTACTAGATGTTAGATTAAGCGGGTACCAGTATCATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:102:192:268/1 +CGTATACAGGGAATCACAGATCACCGTGCCTCCAGAGCCGCCCTGGGTTGCAGCTGGAACCAGCAAAGTAGGCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:103:743:817/1 +GGAATTATCTTGCCTGAAGCTAAGGCCACGGGATGCCCAACCCCTTTACTAGATGTTAGATTAAGCGGGTACCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:104:302:376/1 +TTTAACAGAGGCTTGTTCAATACAGTGGGGCCGGTCCAGGGGCATGTGTAATCCGGTGTCGTCACGAGGACAATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:105:456:530/1 +AAAAGCGGTCGCTTAAAATAGTGAAATGGATCGCGAAGCGATGACCCATCATAGCACCGAACGCGCGAGCACCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:106:931:1004/1 +CAAATGAATTTTCTGGGATGAGGCAGCGGGTCCGGGAGTCACGCCAAACATTGAAAAACTCTCCGACAACAGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:107:654:727/1 +GGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGAATGACCAGGCGATTCATGGGGGGTCCGTATAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:108:260:334/1 +TAGGCCTATCACCGACCTCGATAGTCGTTTCCTACGTGTAGTTTTAACAGAGGCTTGTTCAATACAGTGGGGCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:109:468:542/1 +TTAAAATAGTGAAATGGATCGCGAAGCGATGACCCATCATAGCACCGAACGCGCGAGCACCAACATTAGCCATAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:110:558:633/1 +GTGGGAAAGCATGGAATAACGTAGGCTCGAACATCCCGACCACGTGGTAATTTTGGGCTCGGCTACTCCTGGCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:111:865:938/1 +TTCATGATACTACCATAAATGAGGTCTCGTTCCATGATATAGGGAGATGACGAATGCTTGCCAAGACAAATGAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:112:75:149/1 +CTTGAGTGAATCCATAACCGACCAATTCCCTGCACACGGGAAATCTTCACATATAGGACTTCCTTGGGATAAGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:113:39:113/1 +CGTAAAATAGCACGAACCCGAAACTTCCTGATATGTCTTGAGTGAATCCATAACCGACCAATTCCCTGCACACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:114:175:251/1 +CATTACTTTGGGCGCCCCGTATACAGGGAATCACAGATCACCGTGCCTCCAGAGCCGCCCTGGGTTGCAGCTGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:115:787:860/1 +TTTACTAGATGTTAGATTAAGCGGGTACCAGTATCATTTCAAGCAGGAACCCTAGGAGACGCTTAGGCGCCCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:116:206:281/1 +CACAGATCACCGTGCCTCCAGAGCCGCCCTGGGTTGCAGCTGGAACCAGCAAAGTAGGCCTATCACCGACCTCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:117:509:584/1 +GCACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACGTAGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:118:487:564/1 +CGCGAAGCGATGACCCATCATAGCACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:119:515:590/1 +AACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAACGTAGGCTCGAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:120:593:669/1 +CCGACCACGTGGTAATTTTGGGCTCGGCTACTCCTGGCTGTGGAGCACGTAATGGTACCACGGGTGTTACAAGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:121:25:100/1 +GTTGCCGTAATTTGCGTAAAATAGCACGAACCCGAAACTTCCTGATATGTCTTGAGTGAATCCATAACCGACCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:122:111:186/1 +CGGGAAATCTTCACATATAGGACTTCCTTGGGATAAGATAATTGCTCCTATTGGGGTTACACGCCATTACTTTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:123:105:180/1 +TGCACACGGGAAATCTTCACATATAGGACTTCCTTGGGATAAGATAATTGCTCCTATTGGGGTTACACGCCATTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:124:870:945/1 +GATACTACCATAAATGAGGTCTCGTTCCATGATATAGGGAGATGACGAATGCTTGCCAAGACAAATGAATTTTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:125:633:708/1 +TGGAGCACGTAATGGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGAATGACCAGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:126:378:452/1 +TTGATGACTCTATGATACTCACCGTCAGTACTTCCTCCTCAATGGTGACTGGTTGAAGTCCCTCGTGCCACCATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:127:585:659/1 +CGAACATCCCGACCACGTGGTAATTTTGGGCTCGGCTACTCCTGGCTGTGGAGCACGTAATGGTACCACGGGTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:128:25:99/1 +GTTGCCGTAATTTGCGTAAAATAGCACGAACCCGAAACTTCCTGATATGTCTTGAGTGAATCCATAACCGACCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:129:714:791/1 +GGGGGGTCCGTATACTCTCCCGTCTGTTAGGAATTATCTTGCCTGAAGCTAAGGCCACGGGATGCCCAACCCCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:130:554:628/1 +GCGCGTGGGAAAGCATGGAATAACGTAGGCTCGAACATCCCGACCACGTGGTAATTTTGGGCTCGGCTACTCCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:131:65:140/1 +CCTGATATGTCTTGAGTGAATCCATAACCGACCAATTCCCTGCACACGGGAAATCTTCACATATAGGACTTCCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:132:849:925/1 +TTAGGCGCCCTTAGACTTCATGATACTACCATAAATGAGGTCTCGTTCCATGATATAGGGAGATGACGAATGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:133:894:970/1 +TTCCATGATATAGGGAGATGACGAATGCTTGCCAAGACAAATGAATTTTCTGGGATGAGGCAGCGGGTCCGGGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:134:357:431/1 +GTGTCGTCACGAGGACAATGTTTGATGACTCTATGATACTCACCGTCAGTACTTCCTCCTCAATGGTGACTGGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:135:19:93/1 +CGACAAGTTGCCGTAATTTGCGTAAAATAGCACGAACCCGAAACTTCCTGATATGTCTTGAGTGAATCCATAACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:136:616:691/1 +TCGGCTACTCCTGGCTGTGGAGCACGTAATGGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:137:622:694/1 +ACTCCTGGCTGTGGAGCACGTAATGGTACCACGGGTGTTACAAGTGAAGGGATGGTCCTCGCCTATCTAAGCTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:138:484:557/1 +GATCGCGAAGCGATGACCCATCATAGCACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCATTAGCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:139:874:949/1 +CTACCATAAATGAGGTCTCGTTCCATGATATAGGGAGATGACGAATGCTTGCCAAGACAAATGAATTTTCTGGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:140:346:421/1 +TGTGTAATCCGGTGTCGTCACGAGGACAATGTTTGATGACTCTATGATACTCACCGTCAGTACTTCCTCCTCAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:141:931:1005/1 +CAAATGAATTTTCTGGGATGAGGCAGCGGGTCCGGGAGTCACGCCAAACATTGAAAAACTCTCCGACAACAGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:142:795:870/1 +ATGTTAGATTAAGCGGGTACCAGTATCATTTCAAGCAGGAACCCTAGGAGACGCTTAGGCGCCCTTAGACTTCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:143:476:552/1 +GTGAAATGGATCGCGAAGCGATGACCCATCATAGCACCGAACGCGCGAGCACCAACATTAGCCATATTAACGGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:144:776:850/1 +TGCCCAACCCCTTTACTAGATGTTAGATTAAGCGGGTACCAGTATCATTTCAAGCAGGAACCCTAGGAGACGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:145:805:879/1 +AAGCGGGTACCAGTATCATTTCAAGCAGGAACCCTAGGAGACGCTTAGGCGCCCTTAGACTTCATGATACTACCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:146:332:407/1 +CCGGTCCAGGGGCATGTGTAATCCGGTGTCGTCACGAGGACAATGTTTGATGACTCTATGATACTCACCGTCAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq b/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq new file mode 100644 index 00000000..0b3734f5 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_multiple_vars/reads_2.fq @@ -0,0 +1,584 @@ +@presence_absence1:1:768:842/2 +CGTCATCTCCCTATATCATGGAACGAGACCTCATTTATGGTAGTATCATGAAGTCTAAGGGCGCCTAAGCGTCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:2:395:471/2 +TTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTGCTATGATGGGTCATCGCTTCGCGATCCATTTCACTATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:3:732:807/2 +TATGGTAGTATCATGAAGTCTAAGGGCGCCTAAGCGTCTCCTAGGGTTCCTGCTTGAAATGATACTGGTACCCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:4:745:820/2 +ACGAGACCTCATTTATGGTAGTATCATGAAGTCTAAGGGCGCCTAAGCGTCTCCTAGGGTTCCTGCTTGAAATGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:5:245:320/2 +TATCATAGAGTCATCAAACATTGTCCTCGTGACGACACCGGATTACACATGCCCCTGGACCGGCCCCACTGTATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:6:280:354/2 +CAGTCACCATTGAGGAGGAAGTACTGACGGTGAGTATCATAGAGTCATCAAACATTGTCCTCGTGACGACACCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:7:617:690/2 +TAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATACGGACCCCCCATGAATCGCCTGGTCATTCAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:8:646:721/2 +TCTAGTAAAGGGGTTGGGCATCCCGTGGCCTTAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:9:239:312/2 +AGTCATCAAACATTGTCCTCGTGACGACACCGGATTACACATGCCCCTGGACCGGCCCCACTGTATTGAACAAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:10:770:844/2 +TTCGTCATCTCCCTATATCATGGAACGAGACCTCATTTATGGTAGTATCATGAAGTCTAAGGGCGCCTAAGCGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:11:198:273/2 +CATGCCCCTGGACCGGCCCCACTGTATTGAACAAGCCTCTGTTAAAACTACACGTAGGAAACGACTATCGAGGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:12:441:516/2 +TGTTCGAGCCTACGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:13:650:724/2 +ACATCTAGTAAAGGGGTTGGGCATCCCGTGGCCTTAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:14:528:601/2 +CATCCCTTCACTTGTAACACCCGTGGTACCATTACGTGCTCCACAGCCAGGAGTAGCCGAGCCCAAAATTACCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:15:840:915/2 +GTTTTTCAATGTTTGGCGTGACTCCCGGACCCGCTGCCTCATCCCAGAAAATTCATTTGTCTTGGCAAGCATTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:16:588:663/2 +GACGGGAGAGTATACGGACCCCCCATGAATCGCCTGGTCATTCAGCTTAGATAGGCGAGGACCATCCCTTCACTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:17:536:610/2 +GGCGAGGACCATCCCTTCACTTGTAACACCCGTGGTACCATTACGTGCTCCACAGCCAGGAGTAGCCGAGCCCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:18:153:229/2 +AAACTACACGTAGGAAACGACTATCGAGGTCGGTGATAGGCCTACTTTGCTGGTTCCAGCTGCAACCCAGGGCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:19:427:501/2 +TATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTGCTATGATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:20:472:547/2 +AGCCGAGCCCAAAATTACCACGTGGTCGGGATGTTCGAGCCTACGTTATTCCATGCTTTCCCACGCGCTAATGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:21:498:573/2 +CCATTACGTGCTCCACAGCCAGGAGTAGCCGAGCCCAAAATTACCACGTGGTCGGGATGTTCGAGCCTACGTTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:22:760:836/2 +CTCCCTATATCATGGAACGAGACCTCATTTATGGTAGTATCATGAAGTCTAAGGGCGCCTAAGCGTCTCCTAGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:23:808:884/2 +CGCTGCCTCATCCCAGAAAATTCATTTGTCTTGGCAAGCATTCGTCATCTCCCTATATCATGGAACGAGACCTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:24:912:986/2 +CGAGCTCATTACCCAGCGGTGGTCGGCTAAGGTCAGGGATGAACAAGTGAGTTTTCAACTGTTGTCGGAGAGTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:25:151:225/2 +TACACGTAGGAAACGACTATCGAGGTCGGTGATAGGCCTACTTTGCTGGTTCCAGCTGCAACCCAGGGCGGCTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:26:322:398/2 +TTTAAGCGACCGCTTTTCAACATGGTGGCACGAGGGACTTCAACCAGTCACCATTGAGGAGGAAGTACTGACGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:27:790:866/2 +AATTCATTTGTCTTGGCAAGCATTCGTCATCTCCCTATATCATGGAACGAGACCTCATTTATGGTAGTATCATGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:28:642:715/2 +AAAGGGGTTGGGCATCCCGTGGCCTTAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATACGGACCCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:29:944:1018/2 +GCCATTTGTTTGCGTGCCAGGCCAGACAGTACCGAGCTCATTACCCAGCGGTGGTCGGCTAAGGTCAGGGATGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:30:358:432/2 +TGATGGGTCATCGCTTCGCGATCCATTTCACTATTTTAAGCGACCGCTTTTCAACATGGTGGCACGAGGGACTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:31:626:700/2 +CCCGTGGCCTTAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATACGGACCCCCCATGAATCGCCTGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:32:741:814/2 +CCTCATTTATGGTAGTATCATGAAGTCTAAGGGCGCCTAAGCGTCTCCTAGGGTTCCTGCTTGAAATGATACTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:33:419:493/2 +GCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTGCTATGATGGGTCATCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:34:140:213/2 +ACGACTATCGAGGTCGGTGATAGGCCTACTTTGCTGGTTCCAGCTGCAACCCAGGGCGGCTCTGGAGGCACGGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:35:443:517/2 +ATGTTCGAGCCTACGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:36:83:158/2 +GCGGCTCTGGAGGCACGGTGATCTGTGATTCCCTGTATACGGGGCGCCCAAAGTAATGGCGTGTAACCCCAATAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:37:472:548/2 +TAGCCGAGCCCAAAATTACCACGTGGTCGGGATGTTCGAGCCTACGTTATTCCATGCTTTCCCACGCGCTAATGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:38:512:586/2 +AACACCCGTGGTACCATTACGTGCTCCACAGCCAGGAGTAGCCGAGCCCAAAATTACCACGTGGTCGGGATGTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:39:637:709/2 +GTTGGGCATCCCGTGGCCTTAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATACGGACCCCCCATGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:40:624:697/2 +GTGGCCTTAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATACGGACCCCCCATGAATCGCCTGGTCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:41:454:528/2 +ACGTGGTCGGGATGTTCGAGCCTACGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:42:417:492/2 +CTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTGCTATGATGGGTCATCGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:43:928:1003/2 +GCCAGGCCAGACAGTACCGAGCTCATTACCCAGCGGTGGTCGGCTAAGGTCAGGGATGAACAAGTGAGTTTTCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:44:214:287/2 +GACACCGGATTACACATGCCCCTGGACCGGCCCCACTGTATTGAACAAGCCTCTGTTAAAACTACACGTAGGAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:45:811:887/2 +ACCCGCTGCCTCATCCCAGAAAATTCATTTGTCTTGGCAAGCATTCGTCATCTCCCTATATCATGGAACGAGACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:46:492:567/2 +CGTGCTCCACAGCCAGGAGTAGCCGAGCCCAAAATTACCACGTGGTCGGGATGTTCGAGCCTACGTTATTCCATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:47:875:950/2 +GGATGAACAAGTGAGTTTTCAACTGTTGTCGGAGAGTTTTTCAATGTTTGGCGTGACTCCCGGACCCGCTGCCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:48:913:987/2 +CCGAGCTCATTACCCAGCGGTGGTCGGCTAAGGTCAGGGATGAACAAGTGAGTTTTCAACTGTTGTCGGAGAGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:49:721:796/2 +CATGAAGTCTAAGGGCGCCTAAGCGTCTCCTAGGGTTCCTGCTTGAAATGATACTGGTACCCGCTTAATCTAACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:50:90:163/2 +CCAGGGCGGCTCTGGAGGCACGGTGATCTGTGATTCCCTGTATACGGGGCGCCCAAAGTAATGGCGTGTAACCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:51:113:187/2 +TACTTTGCTGGTTCCAGCTGCAACCCAGGGCGGCTCTGGAGGCACGGTGATCTGTGATTCCCTGTATACGGGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:52:500:574/2 +ACCATTACGTGCTCCACAGCCAGGAGTAGCCGAGCCCAAAATTACCACGTGGTCGGGATGTTCGAGCCTACGTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:53:512:584/2 +CACCCGTGGTACCATTACGTGCTCCACAGCCAGGAGTAGCCGAGCCCAAAATTACCACGTGGTCGGGATGTTCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:54:781:855/2 +CTTGGCAAGCATTCGTCATCTCCCTATATCATGGAACGAGACCTCATTTATGGTAGTATCATGAAGTCTAAGGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:55:792:867/2 +AAATTCATTTGTCTTGGCAAGCATTCGTCATCTCCCTATATCATGGAACGAGACCTCATTTATGGTAGTATCATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:56:713:786/2 +AAGGGCGCCTAAGCGTCTCCTAGGGTTCCTGCTTGAAATGATACTGGTACCCGCTTAATCTAACATCTAGTAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:57:600:676/2 +ATAATTCCTAACAGACGGGAGAGTATACGGACCCCCCATGAATCGCCTGGTCATTCAGCTTAGATAGGCGAGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:58:564:640/2 +CATGAATCGCCTGGTCATTCAGCTTAGATAGGCGAGGACCATCCCTTCACTTGTAACACCCGTGGTACCATTACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:59:355:429/2 +TGGGTCATCGCTTCGCGATCCATTTCACTATTTTAAGCGACCGCTTTTCAACATGGTGGCACGAGGGACTTCAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:60:382:458/2 +TGTTGGTGCTCGCGCGTTCGGTGCTATGATGGGTCATCGCTTCGCGATCCATTTCACTATTTTAAGCGACCGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:61:658:731/2 +TAATCTAACATCTAGTAAAGGGGTTGGGCATCCCGTGGCCTTAGCTTCAGGCAAGATAATTCCTAACAGACGGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:62:849:923/2 +GTCGGAGAGTTTTTCAATGTTTGGCGTGACTCCCGGACCCGCTGCCTCATCCCAGAAAATTCATTTGTCTTGGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:63:623:697/2 +GTGGCCTTAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATACGGACCCCCCATGAATCGCCTGGTCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:64:659:735/2 +CGCTTAATCTAACATCTAGTAAAGGGGTTGGGCATCCCGTGGCCTTAGCTTCAGGCAAGATAATTCCTAACAGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:65:909:984/2 +AGCTCATTACCCAGCGGTGGTCGGCTAAGGTCAGGGATGAACAAGTGAGTTTTCAACTGTTGTCGGAGAGTTTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:66:498:571/2 +ATTACGTGCTCCACAGCCAGGAGTAGCCGAGCCCAAAATTACCACGTGGTCGGGATGTTCGAGCCTACGTTATTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:67:223:298/2 +GTCCTCGTGACGACACCGGATTACACATGCCCCTGGACCGGCCCCACTGTATTGAACAAGCCTCTGTTAAAACTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:68:151:226/2 +CTACACGTAGGAAACGACTATCGAGGTCGGTGATAGGCCTACTTTGCTGGTTCCAGCTGCAACCCAGGGCGGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:69:164:238/2 +CCTCTGTTAAAACTACACGTAGGAAACGACTATCGAGGTCGGTGATAGGCCTACTTTGCTGGTTCCAGCTGCAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:70:665:740/2 +GTACCCGCTTAATCTAACATCTAGTAAAGGGGTTGGGCATCCCGTGGCCTTAGCTTCAGGCAAGATAATTCCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:71:769:842/2 +CGTCATCTCCCTATATCATGGAACGAGACCTCATTTATGGTAGTATCATGAAGTCTAAGGGCGCCTAAGCGTCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:72:855:931/2 +CAACTGTTGTCGGAGAGTTTTTCAATGTTTGGCGTGACTCCCGGACCCGCTGCCTCATCCCAGAAAATTCATTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:73:621:694/2 +GCCTTAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATACGGACCCCCCATGAATCGCCTGGTCATTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:74:754:828/2 +ATCATGGAACGAGACCTCATTTATGGTAGTATCATGAAGTCTAAGGGCGCCTAAGCGTCTCCTAGGGTTCCTGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:75:542:616/2 +TAGATAGGCGAGGACCATCCCTTCACTTGTAACACCCGTGGTACCATTACGTGCTCCACAGCCAGGAGTAGCCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:76:586:662/2 +ACGGGAGAGTATACGGACCCCCCATGAATCGCCTGGTCATTCAGCTTAGATAGGCGAGGACCATCCCTTCACTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:77:463:536/2 +AAATTACCACGTGGTCGGGATGTTCGAGCCTACGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:78:449:523/2 +GTCGGGATGTTCGAGCCTACGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:79:537:612/2 +TAGGCGAGGACCATCCCTTCACTTGTAACACCCGTGGTACCATTACGTGCTCCACAGCCAGGAGTAGCCGAGCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:80:728:802/2 +TAGTATCATGAAGTCTAAGGGCGCCTAAGCGTCTCCTAGGGTTCCTGCTTGAAATGATACTGGTACCCGCTTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:81:550:624/2 +ATTCAGCTTAGATAGGCGAGGACCATCCCTTCACTTGTAACACCCGTGGTACCATTACGTGCTCCACAGCCAGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:82:749:824/2 +TGGAACGAGACCTCATTTATGGTAGTATCATGAAGTCTAAGGGCGCCTAAGCGTCTCCTAGGGTTCCTGCTTGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:83:560:635/2 +ATCGCCTGGTCATTCAGCTTAGATAGGCGAGGACCATCCCTTCACTTGTAACACCCGTGGTACCATTACGTGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:84:145:219/2 +TAGGAAACGACTATCGAGGTCGGTGATAGGCCTACTTTGCTGGTTCCAGCTGCAACCCAGGGCGGCTCTGGAGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:85:512:588/2 +GTAACACCCGTGGTACCATTACGTGCTCCACAGCCAGGAGTAGCCGAGCCCAAAATTACCACGTGGTCGGGATGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:86:541:615/2 +AGATAGGCGAGGACCATCCCTTCACTTGTAACACCCGTGGTACCATTACGTGCTCCACAGCCAGGAGTAGCCGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:87:422:498/2 +TCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTGCTATGATGGGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:88:22:97/2 +TGTAACCCCAATAGGAGCAATTATCTTATCCCAAGGAAGTCCTATATGTGAAGATTTCCCGTGTGCAGGGAATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:89:819:895/2 +ACTCCCGGACCCGCTGCCTCATCCCAGAAAATTCATTTGTCTTGGCAAGCATTCGTCATCTCCCTATATCATGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:90:615:690/2 +TAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATACGGACCCCCCATGAATCGCCTGGTCATTCAGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:91:559:633/2 +CGCCTGGTCATTCAGCTTAGATAGGCGAGGACCATCCCTTCACTTGTAACACCCGTGGTACCATTACGTGCTCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:92:177:251/2 +TGTATTGAACAAGCCTCTGTTAAAACTACACGTAGGAAACGACTATCGAGGTCGGTGATAGGCCTACTTTGCTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:93:285:359/2 +TCAACCAGTCACCATTGAGGAGGAAGTACTGACGGTGAGTATCATAGAGTCATCAAACATTGTCCTCGTGACGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:94:393:470/2 +TAATATGGCTAATGTTGGTGCTCGCGCGTTCGGTGCTATGATGGGTCATCGCTTCGCGATCCATTTCACTATTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:95:566:640/2 +CATGAATCGCCTGGTCATTCAGCTTAGATAGGCGAGGACCATCCCTTCACTTGTAACACCCGTGGTACCATTACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:96:709:782/2 +GCGCCTAAGCGTCTCCTAGGGTTCCTGCTTGAAATGATACTGGTACCCGCTTAATCTAACATCTAGTAAAGGGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:97:297:372/2 +GGCACGAGGGACTTCAACCAGTCACCATTGAGGAGGAAGTACTGACGGTGAGTATCATAGAGTCATCAAACATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:98:364:439/2 +GGTGCTATGATGGGTCATCGCTTCGCGATCCATTTCACTATTTTAAGCGACCGCTTTTCAACATGGTGGCACGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:99:541:614/2 +GATAGGCGAGGACCATCCCTTCACTTGTAACACCCGTGGTACCATTACGTGCTCCACAGCCAGGAGTAGCCGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:100:196:270/2 +GCCCCTGGACCGGCCCCACTGTATTGAACAAGCCTCTGTTAAAACTACACGTAGGAAACGACTATCGAGGTCGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:101:750:823/2 +GGAACGAGACCTCATTTATGGTAGTATCATGAAGTCTAAGGGCGCCTAAGCGTCTCCTAGGGTTCCTGCTTGAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:102:192:268/2 +CCCTGGACCGGCCCCACTGTATTGAACAAGCCTCTGTTAAAACTACACGTAGGAAACGACTATCGAGGTCGGTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:103:743:817/2 +AGACCTCATTTATGGTAGTATCATGAAGTCTAAGGGCGCCTAAGCGTCTCCTAGGGTTCCTGCTTGAAATGATAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:104:302:376/2 +TGGTGGCACGAGGGACTTCAACCAGTCACCATTGAGGAGGAAGTACTGACGGTGAGTATCATAGAGTCATCAAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:105:456:530/2 +CCACGTGGTCGGGATGTTCGAGCCTACGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAATATGGCTAATGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:106:931:1004/2 +TGCCAGGCCAGACAGTACCGAGCTCATTACCCAGCGGTGGTCGGCTAAGGTCAGGGATGAACAAGTGAGTTTTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:107:654:727/2 +CTAACATCTAGTAAAGGGGTTGGGCATCCCGTGGCCTTAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:108:260:334/2 +GTACTGACGGTGAGTATCATAGAGTCATCAAACATTGTCCTCGTGACGACACCGGATTACACATGCCCCTGGACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:109:468:542/2 +AGCCCAAAATTACCACGTGGTCGGGATGTTCGAGCCTACGTTATTCCATGCTTTCCCACGCGCTAATGCCGTTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:110:558:633/2 +CGCCTGGTCATTCAGCTTAGATAGGCGAGGACCATCCCTTCACTTGTAACACCCGTGGTACCATTACGTGCTCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:111:865:938/2 +GAGTTTTCAACTGTTGTCGGAGAGTTTTTCAATGTTTGGCGTGACTCCCGGACCCGCTGCCTCATCCCAGAAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:112:75:149/2 +GAGGCACGGTGATCTGTGATTCCCTGTATACGGGGCGCCCAAAGTAATGGCGTGTAACCCCAATAGGAGCAATTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:113:39:113/2 +GCCCAAAGTAATGGCGTGTAACCCCAATAGGAGCAATTATCTTATCCCAAGGAAGTCCTATATGTGAAGATTTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:114:175:251/2 +TGTATTGAACAAGCCTCTGTTAAAACTACACGTAGGAAACGACTATCGAGGTCGGTGATAGGCCTACTTTGCTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:115:787:860/2 +TTTGTCTTGGCAAGCATTCGTCATCTCCCTATATCATGGAACGAGACCTCATTTATGGTAGTATCATGAAGTCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:116:206:281/2 +GGATTACACATGCCCCTGGACCGGCCCCACTGTATTGAACAAGCCTCTGTTAAAACTACACGTAGGAAACGACTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:117:509:584/2 +CACCCGTGGTACCATTACGTGCTCCACAGCCAGGAGTAGCCGAGCCCAAAATTACCACGTGGTCGGGATGTTCGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:118:487:564/2 +GCTCCACAGCCAGGAGTAGCCGAGCCCAAAATTACCACGTGGTCGGGATGTTCGAGCCTACGTTATTCCATGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:119:515:590/2 +TTGTAACACCCGTGGTACCATTACGTGCTCCACAGCCAGGAGTAGCCGAGCCCAAAATTACCACGTGGTCGGGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:120:593:669/2 +CTAACAGACGGGAGAGTATACGGACCCCCCATGAATCGCCTGGTCATTCAGCTTAGATAGGCGAGGACCATCCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:121:25:100/2 +GCGTGTAACCCCAATAGGAGCAATTATCTTATCCCAAGGAAGTCCTATATGTGAAGATTTCCCGTGTGCAGGGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:122:111:186/2 +ACTTTGCTGGTTCCAGCTGCAACCCAGGGCGGCTCTGGAGGCACGGTGATCTGTGATTCCCTGTATACGGGGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:123:105:180/2 +CTGGTTCCAGCTGCAACCCAGGGCGGCTCTGGAGGCACGGTGATCTGTGATTCCCTGTATACGGGGCGCCCAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:124:870:945/2 +AACAAGTGAGTTTTCAACTGTTGTCGGAGAGTTTTTCAATGTTTGGCGTGACTCCCGGACCCGCTGCCTCATCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:125:633:708/2 +TTGGGCATCCCGTGGCCTTAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATACGGACCCCCCATGAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:126:378:452/2 +TGCTCGCGCGTTCGGTGCTATGATGGGTCATCGCTTCGCGATCCATTTCACTATTTTAAGCGACCGCTTTTCAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:127:585:659/2 +GGAGAGTATACGGACCCCCCATGAATCGCCTGGTCATTCAGCTTAGATAGGCGAGGACCATCCCTTCACTTGTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:128:25:99/2 +CGTGTAACCCCAATAGGAGCAATTATCTTATCCCAAGGAAGTCCTATATGTGAAGATTTCCCGTGTGCAGGGAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:129:714:791/2 +AGTCTAAGGGCGCCTAAGCGTCTCCTAGGGTTCCTGCTTGAAATGATACTGGTACCCGCTTAATCTAACATCTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:130:554:628/2 +GGTCATTCAGCTTAGATAGGCGAGGACCATCCCTTCACTTGTAACACCCGTGGTACCATTACGTGCTCCACAGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:131:65:140/2 +TGATCTGTGATTCCCTGTATACGGGGCGCCCAAAGTAATGGCGTGTAACCCCAATAGGAGCAATTATCTTATCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:132:849:925/2 +TTGTCGGAGAGTTTTTCAATGTTTGGCGTGACTCCCGGACCCGCTGCCTCATCCCAGAAAATTCATTTGTCTTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:133:894:970/2 +CGGTGGTCGGCTAAGGTCAGGGATGAACAAGTGAGTTTTCAACTGTTGTCGGAGAGTTTTTCAATGTTTGGCGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:134:357:431/2 +GATGGGTCATCGCTTCGCGATCCATTTCACTATTTTAAGCGACCGCTTTTCAACATGGTGGCACGAGGGACTTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:135:19:93/2 +ACCCCAATAGGAGCAATTATCTTATCCCAAGGAAGTCCTATATGTGAAGATTTCCCGTGTGCAGGGAATTGGTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:136:616:691/2 +TTAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATACGGACCCCCCATGAATCGCCTGGTCATTCAGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:137:622:694/2 +GCCTTAGCTTCAGGCAAGATAATTCCTAACAGACGGGAGAGTATACGGACCCCCCATGAATCGCCTGGTCATTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:138:484:557/2 +AGCCAGGAGTAGCCGAGCCCAAAATTACCACGTGGTCGGGATGTTCGAGCCTACGTTATTCCATGCTTTCCCACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:139:874:949/2 +GATGAACAAGTGAGTTTTCAACTGTTGTCGGAGAGTTTTTCAATGTTTGGCGTGACTCCCGGACCCGCTGCCTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:140:346:421/2 +CGCTTCGCGATCCATTTCACTATTTTAAGCGACCGCTTTTCAACATGGTGGCACGAGGGACTTCAACCAGTCACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:141:931:1005/2 +GTGCCAGGCCAGACAGTACCGAGCTCATTACCCAGCGGTGGTCGGCTAAGGTCAGGGATGAACAAGTGAGTTTTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:142:795:870/2 +AGAAAATTCATTTGTCTTGGCAAGCATTCGTCATCTCCCTATATCATGGAACGAGACCTCATTTATGGTAGTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:143:476:552/2 +GGAGTAGCCGAGCCCAAAATTACCACGTGGTCGGGATGTTCGAGCCTACGTTATTCCATGCTTTCCCACGCGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:144:776:850/2 +CAAGCATTCGTCATCTCCCTATATCATGGAACGAGACCTCATTTATGGTAGTATCATGAAGTCTAAGGGCGCCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:145:805:879/2 +CCTCATCCCAGAAAATTCATTTGTCTTGGCAAGCATTCGTCATCTCCCTATATCATGGAACGAGACCTCATTTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:146:332:407/2 +TTTCACTATTTTAAGCGACCGCTTTTCAACATGGTGGCACGAGGGACTTCAACCAGTCACCATTGAGGAGGAAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa b/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa new file mode 100644 index 00000000..c7a01d84 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_multiple_vars/references.fa @@ -0,0 +1,5 @@ +>presence_absence1 +ATGGATCGCGAAGCGATGACCCATGAAGCGACCGAACGCGCGAGCACCAACATTAGCCAT +ATTAACGGCATTAGCGCGTGGGAAAGCATGGAATAA +>presence_absence2 +ATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTAA From 86f5995d0c2f061dc688e9deac36b9d540160736 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Tue, 11 Oct 2016 13:29:35 +0100 Subject: [PATCH 13/16] Handle inserted or deleted codon --- ariba/report.py | 10 +- ariba/tests/cluster_test.py | 34 + .../cluster_test_full_run_delete_codon.fa | 3 + .../cluster_test_full_run_delete_codon.tsv | 1 + .../for_reads.fa | 20 + .../reads_1.fq | 588 +++++++++++++++++ .../reads_2.fq | 588 +++++++++++++++++ .../references.fa | 3 + .../cluster_test_full_run_insert_codon.fa | 3 + .../cluster_test_full_run_insert_codon.tsv | 1 + .../for_reads.fa | 20 + .../reads_1.fq | 592 ++++++++++++++++++ .../reads_2.fq | 592 ++++++++++++++++++ .../references.fa | 3 + 14 files changed, 2455 insertions(+), 3 deletions(-) create mode 100644 ariba/tests/data/cluster_test_full_run_delete_codon.fa create mode 100644 ariba/tests/data/cluster_test_full_run_delete_codon.tsv create mode 100644 ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa create mode 100644 ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq create mode 100644 ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq create mode 100644 ariba/tests/data/cluster_test_full_run_delete_codon/references.fa create mode 100644 ariba/tests/data/cluster_test_full_run_insert_codon.fa create mode 100644 ariba/tests/data/cluster_test_full_run_insert_codon.tsv create mode 100644 ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa create mode 100644 ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq create mode 100644 ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq create mode 100644 ariba/tests/data/cluster_test_full_run_insert_codon/references.fa diff --git a/ariba/report.py b/ariba/report.py index 3f4439f3..bbe215ce 100644 --- a/ariba/report.py +++ b/ariba/report.py @@ -200,7 +200,7 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum if contributing_vars is None: samtools_columns = [['.'] * 9] else: - if var_effect == 'MULTIPLE': + if var_effect in ['INDELS', 'MULTIPLE']: ref_start_pos = min([x.ref_start for x in contributing_vars]) ref_end_pos = max([x.ref_start for x in contributing_vars]) ctg_start_pos = min([x.qry_start for x in contributing_vars]) @@ -225,7 +225,11 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum raise Error('Error parsing variant ' + known_var_change) elif ref_ctg_change != '.': if '_' in ref_ctg_change: - continue + regex = re.match('^([^0-9]+)([0-9]+)_[^0-9]+[0-9]+([^0-9]+)$', ref_ctg_change) + try: + ref_var_string, ref_var_position, ctg_var_string = regex.group(1, 2, 3) + except: + raise Error('Error parsing variant ' + ref_ctg_change) else: regex = re.match('^([^0-9]+)([0-9]+)([^0-9]+)$', ref_ctg_change) try: @@ -238,7 +242,7 @@ def _report_lines_for_one_contig(cluster, contig_name, ref_cov_per_contig, pymum if var_effect == 'SYN': ref_end_pos = ref_start_pos + 2 ctg_end_pos = ctg_start_pos + 2 - elif ref_var_string == '.' or var_effect in ['FSHIFT', 'TRUNC', 'INDELS', 'UNKNOWN']: + elif ref_var_string == '.' or var_effect in {'INS', 'DEL', 'FSHIFT', 'TRUNC', 'INDELS', 'UNKNOWN'}: ref_end_pos = ref_start_pos ctg_end_pos = ctg_start_pos elif cluster.is_gene == '1': diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py index b6a3c0c9..05a7109a 100644 --- a/ariba/tests/cluster_test.py +++ b/ariba/tests/cluster_test.py @@ -512,3 +512,37 @@ def test_full_run_multiple_vars_in_codon(self): ] self.assertEqual(expected, c.report_lines) shutil.rmtree(tmpdir) + + + def test_full_run_delete_codon(self): + '''Test complete run where there is a deleted codon''' + fasta_in = os.path.join(data_dir, 'cluster_test_full_run_delete_codon.fa') + tsv_in = os.path.join(data_dir, 'cluster_test_full_run_delete_codon.tsv') + refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) + tmpdir = 'tmp.cluster_test_full_delete_codon' + shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_delete_codon'), tmpdir) + c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=292, total_reads_bases=20900) + c.run() + + expected = [ + 'presence_absence1\tpresence_absence1\t1\t0\t539\t292\tcluster_name\t117\t117\t92.31\tcluster_name.scaffold.1\t1104\t20.0\t0\t.\tp\t.\t0\tR25_A26del\tDEL\t73\t73\tA\t553\t553\tA\t27\tA\t27\t.\tGeneric description of presence_absence1', + ] + self.assertEqual(expected, c.report_lines) + shutil.rmtree(tmpdir) + + + def test_full_run_insert_codon(self): + '''Test complete run where there is a inserted codon''' + fasta_in = os.path.join(data_dir, 'cluster_test_full_run_insert_codon.fa') + tsv_in = os.path.join(data_dir, 'cluster_test_full_run_insert_codon.tsv') + refdata = reference_data.ReferenceData([fasta_in], [tsv_in]) + tmpdir = 'tmp.cluster_test_full_insert_codon' + shutil.copytree(os.path.join(data_dir, 'cluster_test_full_run_insert_codon'), tmpdir) + c = cluster.Cluster(tmpdir, 'cluster_name', refdata, spades_other_options='--only-assembler', total_reads=292, total_reads_bases=20900) + c.run() + + expected = [ + 'presence_absence1\tpresence_absence1\t1\t0\t539\t292\tcluster_name\t108\t108\t92.31\tcluster_name.scaffold.1\t1115\t19.9\t0\t.\tp\t.\t0\tS25_M26insELI\tINS\t73\t73\tA\t554\t554\tG\t24\tG\t24\t.\tGeneric description of presence_absence1' + ] + self.assertEqual(expected, c.report_lines) + shutil.rmtree(tmpdir) diff --git a/ariba/tests/data/cluster_test_full_run_delete_codon.fa b/ariba/tests/data/cluster_test_full_run_delete_codon.fa new file mode 100644 index 00000000..021f2f22 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_delete_codon.fa @@ -0,0 +1,3 @@ +>presence_absence1 +ATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACC +TACGGTGATCAAGTTTATAGAGCTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAA diff --git a/ariba/tests/data/cluster_test_full_run_delete_codon.tsv b/ariba/tests/data/cluster_test_full_run_delete_codon.tsv new file mode 100644 index 00000000..da35140b --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_delete_codon.tsv @@ -0,0 +1 @@ +presence_absence1 1 0 . . Generic description of presence_absence1 diff --git a/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa b/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa new file mode 100644 index 00000000..20af6ce5 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_delete_codon/for_reads.fa @@ -0,0 +1,20 @@ +>presence_absence1 +CTTAATTATATATCCAGTACATCAACGGGGGGACGCTACGTGGTATAGCCGGATTACAGC +ACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGT +GTCCACGCGTAAGGCTTCTTATGTCTCACGATCATCCATGTCCTCCTAAACACTAAACCT +GGTTCCGCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCA +AACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAA +TTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAAAGAGACCA +TGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCGGCGCAGTACACGACTTCAATAG +GGTGTAGGGTCAGCCCGTCCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGA +ATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACC +TACGGTGATCAAGTTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAA +TTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGT +TCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCAT +CAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTA +GAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGA +TTGGACCTAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAGAGAAACGCACACGGGA +GTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTT +TCGCCAATGGTCAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCACTATCGGTCT +AGTCTCTGGCACGTCTGACGACTCAATCTCGAGATCGTACACGGCGCTGTAGAGCCATGT +AATCCCTCTGTTAAAGATCTGGCGACCTTAACAATAGAAA diff --git a/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq b/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq new file mode 100644 index 00000000..2269d0be --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_delete_codon/reads_1.fq @@ -0,0 +1,588 @@ +@presence_absence1:1:493:567/1 +GAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTATAGTATGCCCAGTCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:2:556:631/1 +ATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAACGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:3:707:783/1 +ATCAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:4:32:108/1 +GACGCTACGTGGTATAGCCGGATTACAGCACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:5:925:999/1 +ACACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:6:700:774/1 +ATTTATCATCAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:7:770:844/1 +AAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:8:185:261/1 +CCGCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:9:871:946/1 +AGAGAAACGCACACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:10:484:560/1 +GCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTATAGTATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:11:629:704/1 +CACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:12:810:884/1 +GGTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAGAGAAACGCACAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:13:277:351/1 +TTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:14:221:295/1 +ACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:15:778:852/1 +TCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:16:611:685/1 +GGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:17:706:780/1 +CATCAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:18:25:99/1 +ACGGGGGGACGCTACGTGGTATAGCCGGATTACAGCACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:19:70:144/1 +GACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:20:409:482/1 +CGACTTCAATAGGGTGTAGGGTCAGCCCGTCCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:21:767:841/1 +TAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:22:560:635/1 +CCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAACGCACGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:23:83:157/1 +GATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATGTCTCACGATCATCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:24:530:606/1 +GCACCTACGGTGATCAAGTTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATTATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:25:485:561/1 +CGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTATAGTATGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:26:409:483/1 +CGACTTCAATAGGGTGTAGGGTCAGCCCGTCCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:27:553:627/1 +AGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:28:529:599/1 +AGCACCTACGGTGATCAAGTTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATTATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:29:79:155/1 +CAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATGTCTCACGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:30:749:822/1 +CTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:31:882:956/1 +CACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCCAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:32:82:157/1 +TGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATGTCTCACGATCATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:33:578:652/1 +AACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:34:299:373/1 +AATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTTGTAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:35:267:342/1 +AGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:36:80:153/1 +AGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATGTCTCACGATCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:37:320:394/1 +GCGCCACAACGCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTTGTACCAAAAGTTACACCCTATGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:38:616:689/1 +ACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:39:707:781/1 +ATCAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:40:30:104/1 +GGGACGCTACGTGGTATAGCCGGATTACAGCACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:41:249:324/1 +GTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:42:264:337/1 +GTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:43:441:515/1 +CAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:44:553:628/1 +AGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:45:641:716/1 +GCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAATATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:46:385:460/1 +CCCTATGCCACTCGGCGCAGTACACGACTTCAATAGGGTGTAGGGTCAGCCCGTCCCAGGTTGACGAGCAACAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:47:46:121/1 +TAGCCGGATTACAGCACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:48:609:683/1 +CAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:49:169:243/1 +AACACTAAACCTGGTTCCGCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:50:601:677/1 +ATTGGGTGCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:51:295:372/1 +TGTGAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:52:347:422/1 +GAGTAAAGAGACCATGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCGGCGCAGTACACGACTTCAATAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:53:382:456/1 +ACACCCTATGCCACTCGGCGCAGTACACGACTTCAATAGGGTGTAGGGTCAGCCCGTCCCAGGTTGACGAGCAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:54:92:167/1 +ATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATGTCTCACGATCATCCATGTCCTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:55:654:729/1 +CTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAATATTCTCTTATTTGATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:56:524:598/1 +AGCGCAGCACCTACGGTGATCAAGTTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:57:742:816/1 +ATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:58:178:253/1 +CCTGGTTCCGCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:59:755:828/1 +TCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:60:200:274/1 +GACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:61:425:499/1 +TAGGGTCAGCCCGTCCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:62:470:546/1 +GGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:63:198:273/1 +CCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:64:692:766/1 +ATATACAAATTTATCATCAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:65:543:616/1 +TCAAGTTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:66:161:235/1 +TCCTCCTAAACACTAAACCTGGTTCCGCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:67:908:984/1 +TTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCGTACCTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:68:729:805/1 +CGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:69:798:873/1 +CGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:70:760:835/1 +CTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:71:135:210/1 +CTTCTTATGTCTCACGATCATCCATGTCCTCCTAAACACTAAACCTGGTTCCGCTAAAATGAACCGACTATAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:72:443:519/1 +GGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:73:1:75/1 +CTTAATTATATATCCAGTACATCAACGGGGGGACGCTACGTGGTATAGCCGGATTACAGCACAGGACCTGACCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:74:400:474/1 +CGCAGTACACGACTTCAATAGGGTGTAGGGTCAGCCCGTCCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:75:44:118/1 +TATAGCCGGATTACAGCACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:76:865:937/1 +TCTACCAGAGAAACGCACACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:77:702:776/1 +TTATCATCAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:78:199:272/1 +CGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:79:58:132/1 +AGCACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:80:772:848/1 +GTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTACCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:81:748:823/1 +ACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:82:510:583/1 +ACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:83:862:935/1 +TAGTCTACCAGAGAAACGCACACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:84:324:399/1 +CACAACGCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:85:489:563/1 +CGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTATAGTATGCCCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:86:637:711/1 +ATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:87:451:526/1 +AGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:88:713:787/1 +ATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:89:597:671/1 +GATTATTGGGTGCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:90:246:318/1 +CTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:91:658:733/1 +TTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAATATTCTCTTATTTGATGCGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:92:624:700/1 +CAACGCACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:93:275:349/1 +GCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:94:497:572/1 +TTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTATAGTATGCCCAGTCTGTTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:95:204:277/1 +ATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:96:427:502/1 +GGGTCAGCCCGTCCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:97:550:624/1 +TATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:98:188:262/1 +CTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:99:953:1030/1 +CAATGGTCAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCACTATCGGTCTAGTCTCTGGCACGTCTGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:100:924:1000/1 +GACACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:101:236:310/1 +GGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:102:67:141/1 +CCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:103:750:825/1 +TAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:104:746:822/1 +GTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:105:345:419/1 +TCGAGTAAAGAGACCATGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCGGCGCAGTACACGACTTCAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:106:225:300/1 +TAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:107:254:329/1 +ATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:108:783:856/1 +ATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:109:214:290/1 +TAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:110:499:575/1 +GGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTATAGTATGCCCAGTCTGTTTGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:111:439:513/1 +CCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:112:452:525/1 +GCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:113:196:271/1 +AACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:114:68:142/1 +CTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:115:879:956/1 +GCACACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:116:211:286/1 +TGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:117:570:645/1 +TGTTGAAAAACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:118:465:539/1 +AAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:119:701:776/1 +TTTATCATCAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:120:715:789/1 +TCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:121:124:198/1 +CACGCGTAAGGCTTCTTATGTCTCACGATCATCCATGTCCTCCTAAACACTAAACCTGGTTCCGCTAAAATGAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:122:641:715/1 +GCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAATATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:123:368:441/1 +TTGTACCAAAAGTTACACCCTATGCCACTCGGCGCAGTACACGACTTCAATAGGGTGTAGGGTCAGCCCGTCCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:124:654:728/1 +CTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAATATTCTCTTATTTGATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:125:901:976/1 +TAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:126:178:252/1 +CCTGGTTCCGCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:127:825:900/1 +TAGATTGGACCTAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAGAGAAACGCACACGGGAGTGGCTGTGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:128:10:85/1 +ATATCCAGTACATCAACGGGGGGACGCTACGTGGTATAGCCGGATTACAGCACAGGACCTGACCATAATCAGTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:129:116:189/1 +GACGTGTCCACGCGTAAGGCTTCTTATGTCTCACGATCATCCATGTCCTCCTAAACACTAAACCTGGTTCCGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:130:145:221/1 +CTCACGATCATCCATGTCCTCCTAAACACTAAACCTGGTTCCGCTAAAATGAACCGACTATAATAGTGTTAATTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:131:526:602/1 +CGCAGCACCTACGGTGATCAAGTTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:132:934:1009/1 +GTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCACTATCGGTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:133:893:969/1 +CTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:134:774:849/1 +TGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:135:763:836/1 +AGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:136:469:544/1 +AGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:137:905:977/1 +CCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCGTACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:138:108:183/1 +CTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATGTCTCACGATCATCCATGTCCTCCTAAACACTAAACCTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:139:782:855/1 +CATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:140:811:886/1 +GTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAGAGAAACGCACACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:141:383:457/1 +CACCCTATGCCACTCGGCGCAGTACACGACTTCAATAGGGTGTAGGGTCAGCCCGTCCCAGGTTGACGAGCAACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:142:331:405/1 +CAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCGGCGCAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:143:719:794/1 +TTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:144:847:921/1 +GTATTTTGCTCACGCTAGTCTACCAGAGAAACGCACACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:145:330:404/1 +GCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCGGCGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:146:757:831/1 +AGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:147:899:974/1 +CGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq b/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq new file mode 100644 index 00000000..487bff5c --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_delete_codon/reads_2.fq @@ -0,0 +1,588 @@ +@presence_absence1:1:493:567/2 +CCAATGGTCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:2:556:631/2 +ATAAATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:3:707:783/2 +GAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGCGTACCTTCATTGTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:4:32:108/2 +CCAGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGACACGTCCCTCTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:5:925:999/2 +GGATTACATGGCTCTACAGCGCCGTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:6:700:774/2 +ACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGCGTACCTTCATTGTAATGTAGATACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:7:770:844/2 +CATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:8:185:261/2 +TATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:9:871:946/2 +GTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACCATTGGCGAAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:10:484:560/2 +TCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:11:629:704/2 +ATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:12:810:884/2 +CCATTGGCGAAAACTTGTGAGGGACTTTGTGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:13:277:351/2 +ACACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:14:221:295/2 +AAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:15:778:852/2 +GTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:16:611:685/2 +TCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGATAAATTTGTATATCCGTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:17:706:780/2 +CAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGCGTACCTTCATTGTAATGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:18:25:99/2 +GTGTTTAGGAGGACATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGACACGTCCCTCTGAGCTAGAGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:19:70:144/2 +AATTAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:20:409:482/2 +TACTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCATCAGTTTAATATGGCCAAATTCATCGCACGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:21:767:841/2 +CAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:22:560:635/2 +GATGATAAATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:23:83:157/2 +AGGGTTATTGTTTAATTAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:24:530:606/2 +CCGCGGGAGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTGCGTTGCAGAGGGTTTCCCTGCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:25:485:561/2 +GTCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:26:409:483/2 +ATACTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCATCAGTTTAATATGGCCAAATTCATCGCACGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:27:553:627/2 +ATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:28:529:599/2 +AGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:29:79:155/2 +GGTTATTGTTTAATTAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:30:749:822/2 +ACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:31:882:956/2 +GTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:32:82:157/2 +AGGGTTATTGTTTAATTAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:33:578:652/2 +TCAAATAAGAGAATATTGATGATAAATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:34:299:373/2 +CAACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:35:267:342/2 +TGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:36:80:153/2 +TTATTGTTTAATTAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:37:320:394/2 +GTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTACTGCGCCGAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:38:616:689/2 +TCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGATAAATTTGTATATCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:39:707:781/2 +GCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGCGTACCTTCATTGTAATGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:40:30:104/2 +GTTTAGTGTTTAGGAGGACATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGACACGTCCCTCTGAGCTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:41:249:324/2 +CGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:42:264:337/2 +TCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:43:441:515/2 +ATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:44:553:628/2 +AATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:45:641:716/2 +ATTGTAATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:46:385:460/2 +GGTGCTGCGCTGCGGGTTCATCAGTTTAATATGGCCAAATTCATCGCACGCCATTCTGCTAGGCCTGTTTTGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:47:46:121/2 +CATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:48:609:683/2 +TGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGATAAATTTGTATATCCGTATCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:49:169:243/2 +TATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAAATGGGAATACCACCAGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:50:601:677/2 +TAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGATAAATTTGTATATCCGTATCTAGGCCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:51:295:372/2 +AACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:52:347:422/2 +ATTCATCGCACGCCATTCTGCTAGGCCTGTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGGCTGACCCTACAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:53:382:456/2 +CTGCGCTGCGGGTTCATCAGTTTAATATGGCCAAATTCATCGCACGCCATTCTGCTAGGCCTGTTTTGGACGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:54:92:167/2 +TTGGCCATCTAGGGTTATTGTTTAATTAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:55:654:729/2 +ATTGCGTACCTTCATTGTAATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:56:524:598/2 +GTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:57:742:816/2 +ACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:58:178:253/2 +TGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAAATGGGAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:59:755:828/2 +TACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:60:200:274/2 +TCGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:61:425:499/2 +AACAAACAGACTGGGCATACTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCATCAGTTTAATATGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:62:470:546/2 +AGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:63:198:273/2 +CGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:64:692:766/2 +GTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGCGTACCTTCATTGTAATGTAGATACAACTTCTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:65:543:616/2 +CGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTGCGTTGCAGAGGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:66:161:235/2 +TCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAAATGGGAATACCACCAGTTGTTTGGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:67:908:984/2 +ACAGCGCCGTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:68:729:805/2 +CGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:69:798:873/2 +AACTTGTGAGGGACTTTGTGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:70:760:835/2 +AATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:71:135:210/2 +CTGCCAAAGCCGGCTGCTCACAAATGGGAATACCACCAGTTGTTTGGCCATCTAGGGTTATTGTTTAATTAACAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:72:443:519/2 +ATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:73:1:75/2 +GTGAGACATAAGAAGCCTTACGCGTGGACACGTCCCTCTGAGCTAGAGCCAAGAGGATTAGTGAATCACTGATTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:74:400:474/2 +ACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCATCAGTTTAATATGGCCAAATTCATCGCACGCCATTCTGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:75:44:118/2 +TTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGACACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:76:865:937/2 +ACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACCATTGGCGAAAACTTGTGAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:77:702:776/2 +ATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGCGTACCTTCATTGTAATGTAGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:78:199:272/2 +GAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:79:58:132/2 +TATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGACATAAGAAGCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:80:772:848/2 +GTTCCATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:81:748:823/2 +CACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:82:510:583/2 +ATAGTCCGAACTCCTGCCAATGGTCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:83:862:935/2 +TAGACCGATAGTGAGGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACCATTGGCGAAAACTTGTGAGGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:84:324:399/2 +GGCCTGTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTACTGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:85:489:563/2 +TGGTCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:86:637:711/2 +AATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:87:451:526/2 +AATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAACTTGATCACCGTAGGTGCTGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:88:713:787/2 +GCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGCGTACCTTCATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:89:597:671/2 +CGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGATAAATTTGTATATCCGTATCTAGGCCGCGGGAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:90:246:318/2 +GCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:91:658:733/2 +ACAGATTGCGTACCTTCATTGTAATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:92:624:700/2 +AACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGATAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:93:275:349/2 +ACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:94:497:572/2 +TCCTGCCAATGGTCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:95:204:277/2 +TACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:96:427:502/2 +TTCAACAAACAGACTGGGCATACTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCATCAGTTTAATATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:97:550:624/2 +TGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTGCGTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:98:188:262/2 +TTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:99:953:1030/2 +TATTGTTAAGGTCGCCAGATCTTTAACAGAGGGATTACATGGCTCTACAGCGCCGTGTACGATCTCGAGATTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:100:924:1000/2 +GGGATTACATGGCTCTACAGCGCCGTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:101:236:310/2 +TGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:102:67:141/2 +TAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGACAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:103:750:825/2 +GACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:104:746:822/2 +ACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:105:345:419/2 +CATCGCACGCCATTCTGCTAGGCCTGTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGGCTGACCCTACACCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:106:225:300/2 +GGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:107:254:329/2 +TGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:108:783:856/2 +GTGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:109:214:290/2 +GGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:110:499:575/2 +AACTCCTGCCAATGGTCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:111:439:513/2 +TATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:112:452:525/2 +ATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAACTTGATCACCGTAGGTGCTGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:113:196:271/2 +AATGATCTTTTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:114:68:142/2 +TTAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:115:879:956/2 +GTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:116:211:286/2 +TGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:117:570:645/2 +AGAGAATATTGATGATAAATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTCCGAACTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:118:465:539/2 +CCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAACTTGATCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:119:701:776/2 +ATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGCGTACCTTCATTGTAATGTAGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:120:715:789/2 +TAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGCGTACCTTCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:121:124:198/2 +GCTGCTCACAAATGGGAATACCACCAGTTGTTTGGCCATCTAGGGTTATTGTTTAATTAACACTATTATAGTCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:122:641:715/2 +TTGTAATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:123:368:441/2 +ATCAGTTTAATATGGCCAAATTCATCGCACGCCATTCTGCTAGGCCTGTTTTGGACGTTGTTGCTCGTCAACCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:124:654:728/2 +TTGCGTACCTTCATTGTAATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:125:901:976/2 +GTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:126:178:252/2 +GTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAAATGGGAATAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:127:825:900/2 +GAGTAAGCAATATTGACCATTGGCGAAAACTTGTGAGGGACTTTGTGTGTCCGTTCCATCAACGCAATGGATTAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:128:10:85/2 +ATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGACACGTCCCTCTGAGCTAGAGCCAAGAGGATTAGTGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:129:116:189/2 +AAATGGGAATACCACCAGTTGTTTGGCCATCTAGGGTTATTGTTTAATTAACACTATTATAGTCGGTTCATTTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:130:145:221/2 +ATCGACACTGCCTGCCAAAGCCGGCTGCTCACAAATGGGAATACCACCAGTTGTTTGGCCATCTAGGGTTATTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:131:526:602/2 +GGGAGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:132:934:1009/2 +TTTAACAGAGGGATTACATGGCTCTACAGCGCCGTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:133:893:969/2 +ATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTACGAGTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:134:774:849/2 +CGTTCCATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:135:763:836/2 +CAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:136:469:544/2 +GGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAACTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:137:905:977/2 +CGTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:138:108:183/2 +GAATACCACCAGTTGTTTGGCCATCTAGGGTTATTGTTTAATTAACACTATTATAGTCGGTTCATTTTAGCGGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:139:782:855/2 +TGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:140:811:886/2 +GACCATTGGCGAAAACTTGTGAGGGACTTTGTGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:141:383:457/2 +GCTGCGCTGCGGGTTCATCAGTTTAATATGGCCAAATTCATCGCACGCCATTCTGCTAGGCCTGTTTTGGACGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:142:331:405/2 +CTGCTAGGCCTGTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:143:719:794/2 +TAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGCGTACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:144:847:921/2 +GGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACCATTGGCGAAAACTTGTGAGGGACTTTGTGTGTCCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:145:330:404/2 +TGCTAGGCCTGTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:146:757:831/2 +GATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:147:899:974/2 +GTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa b/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa new file mode 100644 index 00000000..021f2f22 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_delete_codon/references.fa @@ -0,0 +1,3 @@ +>presence_absence1 +ATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACC +TACGGTGATCAAGTTTATAGAGCTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAA diff --git a/ariba/tests/data/cluster_test_full_run_insert_codon.fa b/ariba/tests/data/cluster_test_full_run_insert_codon.fa new file mode 100644 index 00000000..be619452 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_insert_codon.fa @@ -0,0 +1,3 @@ +>presence_absence1 +ATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACC +TACGGTGATCAAGTTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAA diff --git a/ariba/tests/data/cluster_test_full_run_insert_codon.tsv b/ariba/tests/data/cluster_test_full_run_insert_codon.tsv new file mode 100644 index 00000000..da35140b --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_insert_codon.tsv @@ -0,0 +1 @@ +presence_absence1 1 0 . . Generic description of presence_absence1 diff --git a/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa b/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa new file mode 100644 index 00000000..3a4a1240 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_insert_codon/for_reads.fa @@ -0,0 +1,20 @@ +>presence_absence1 +CTTAATTATATATCCAGTACATCAACGGGGGGACGCTACGTGGTATAGCCGGATTACAGC +ACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGT +GTCCACGCGTAAGGCTTCTTATGTCTCACGATCATCCATGTCCTCCTAAACACTAAACCT +GGTTCCGCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCA +AACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAA +TTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAAAGAGACCA +TGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCGGCGCAGTACACGACTTCAATAG +GGTGTAGGGTCAGCCCGTCCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGA +ATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACC +TACGGTGATCAAGTTTATAGAGCTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAA +TTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGT +TCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCAT +CAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTA +GAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGA +TTGGACCTAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAGAGAAACGCACACGGGA +GTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTT +TCGCCAATGGTCAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCACTATCGGTCT +AGTCTCTGGCACGTCTGACGACTCAATCTCGAGATCGTACACGGCGCTGTAGAGCCATGT +AATCCCTCTGTTAAAGATCTGGCGACCTTAACAATAGAAA diff --git a/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq b/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq new file mode 100644 index 00000000..160a42ec --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_insert_codon/reads_1.fq @@ -0,0 +1,592 @@ +@presence_absence1:1:79:154/1 +CAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATGTCTCACGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:2:904:979/1 +GTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:3:869:942/1 +GCTAGTCTACCAGAGAAACGCACACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:4:238:314/1 +CCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:5:202:276/1 +CTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:6:560:635/1 +ATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:7:321:394/1 +CGCCACAACGCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTTGTACCAAAAGTTACACCCTATGCCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:8:795:871/1 +ACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTGCTCACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:9:489:563/1 +CGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTATAGAGCTTATAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:10:789:865/1 +TACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:11:292:367/1 +CGATGTGAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:12:381:457/1 +TACACCCTATGCCACTCGGCGCAGTACACGACTTCAATAGGGTGTAGGGTCAGCCCGTCCCAGGTTGACGAGCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:13:673:747/1 +GGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAATATTCTCTTATTTGATGCGGACTGGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:14:163:239/1 +CTCCTAAACACTAAACCTGGTTCCGCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:15:69:143/1 +TGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:16:812:888/1 +TCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAGAGAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:17:822:895/1 +ACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAGAGAAACGCACACGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:18:61:138/1 +ACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:19:969:1041/1 +CAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCACTATCGGTCTAGTCTCTGGCACGTCTGACGACTCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:20:880:955/1 +AGAGAAACGCACACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:21:941:1015/1 +AAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCACTATCGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:22:67:141/1 +CCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:23:470:546/1 +GGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:24:482:555/1 +TGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTATAGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:25:714:790/1 +TCATCAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:26:857:932/1 +TATTTTGCTCACGCTAGTCTACCAGAGAAACGCACACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:27:312:386/1 +ACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTTGTACCAAAAGTTACACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:28:26:99/1 +CGGGGGGACGCTACGTGGTATAGCCGGATTACAGCACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:29:307:381/1 +AGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTTGTACCAAAAGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:30:587:661/1 +AACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:31:734:808/1 +GATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:32:657:730/1 +TTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAATATTCTCTTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:33:584:657/1 +AAAAACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:34:239:314/1 +CAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:35:912:987/1 +ATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:36:352:426/1 +AAGAGACCATGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCGGCGCAGTACACGACTTCAATAGGGTGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:37:622:695/1 +GAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:38:514:587/1 +ATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTATAGAGCTTATAGTATGCCCAGTCTGTTTGTTGAAAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:39:1:76/1 +CTTAATTATATATCCAGTACATCAACGGGGGGACGCTACGTGGTATAGCCGGATTACAGCACAGGACCTGACCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:40:406:481/1 +ACACGACTTCAATAGGGTGTAGGGTCAGCCCGTCCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:41:13:88/1 +TCCAGTACATCAACGGGGGGACGCTACGTGGTATAGCCGGATTACAGCACAGGACCTGACCATAATCAGTGATTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:42:246:321/1 +CTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:43:107:181/1 +GCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATGTCTCACGATCATCCATGTCCTCCTAAACACTAAACCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:44:425:500/1 +TAGGGTCAGCCCGTCCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:45:255:329/1 +TTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:46:126:201/1 +CGCGTAAGGCTTCTTATGTCTCACGATCATCCATGTCCTCCTAAACACTAAACCTGGTTCCGCTAAAATGAACCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:47:458:532/1 +ACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:48:352:427/1 +AAGAGACCATGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCGGCGCAGTACACGACTTCAATAGGGTGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:49:303:378/1 +TACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTTGTACCAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:50:640:715/1 +CGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:51:598:672/1 +TTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACTATTTCGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:52:865:938/1 +TCACGCTAGTCTACCAGAGAAACGCACACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:53:938:1012/1 +ACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCACTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:54:237:311/1 +GCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:55:626:701/1 +CCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:56:487:561/1 +TGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTATAGAGCTTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:57:458:533/1 +ACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:58:360:434/1 +ATGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCGGCGCAGTACACGACTTCAATAGGGTGTAGGGTCAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:59:892:966/1 +ACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCCAATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:60:327:402/1 +AACGCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:61:655:728/1 +AGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAATATTCTCTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:62:944:1020/1 +TCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCACTATCGGTCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:63:281:355/1 +GCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:64:876:950/1 +TACCAGAGAAACGCACACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:65:29:103/1 +GGGGACGCTACGTGGTATAGCCGGATTACAGCACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTGGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:66:439:514/1 +CCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:67:843:916/1 +CCTAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAGAGAAACGCACACGGGAGTGGCTGTGTCGTAATCCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:68:48:121/1 +GCCGGATTACAGCACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:69:641:717/1 +GGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:70:448:524/1 +ACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:71:472:545/1 +CCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:72:298:373/1 +GAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTTGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:73:84:158/1 +ATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATGTCTCACGATCATCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:74:473:547/1 +CTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:75:115:190/1 +GGACGTGTCCACGCGTAAGGCTTCTTATGTCTCACGATCATCCATGTCCTCCTAAACACTAAACCTGGTTCCGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:76:803:877/1 +GGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTGCTCACGCTAGTCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:77:241:316/1 +AACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:78:138:213/1 +CTTATGTCTCACGATCATCCATGTCCTCCTAAACACTAAACCTGGTTCCGCTAAAATGAACCGACTATAATAGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:79:845:918/1 +TAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAGAGAAACGCACACGGGAGTGGCTGTGTCGTAATCCATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:80:492:567/1 +TGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTATAGAGCTTATAGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:81:908:983/1 +CGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:82:624:699/1 +AACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:83:235:310/1 +TGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:84:823:896/1 +CCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAGAGAAACGCACACGGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:85:283:358/1 +AGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAAAGAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:86:255:331/1 +TTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:87:72:148/1 +CCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATGTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:88:615:688/1 +GTGCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:89:936:1009/1 +ACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCACTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:90:711:784/1 +TTATCATCAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:91:590:666/1 +TGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:92:747:820/1 +TGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:93:234:309/1 +ATGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:94:325:399/1 +ACAACGCAATAAAAGATCATTCGAGTAAAGAGACCATGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:95:214:287/1 +TAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATTTGTGAGCAGCCGGCTTTGGCAGGCAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:96:155:230/1 +TCCATGTCCTCCTAAACACTAAACCTGGTTCCGCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:97:351:427/1 +AAAGAGACCATGCCGGCTTGTACCAAAAGTTACACCCTATGCCACTCGGCGCAGTACACGACTTCAATAGGGTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:98:734:809/1 +GATGCGGACTGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:99:756:830/1 +TACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:100:266:341/1 +GAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:101:639:714/1 +ACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:102:278:353/1 +TTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:103:265:341/1 +TGAGCAGCCGGCTTTGGCAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:104:394:468/1 +ACTCGGCGCAGTACACGACTTCAATAGGGTGTAGGGTCAGCCCGTCCCAGGTTGACGAGCAACAACGTCCAAAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:105:918:993/1 +TGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCGTACCTCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:106:818:891/1 +GGGTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAGAGAAACGCACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:107:745:818/1 +GGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:108:282:356/1 +CAGGCAGTGTCGATGTGAATTTACCAGAGCACGATATAGCGCCACAACGCAATAAAAGATCATTCGAGTAAAGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:109:942:1016/1 +AGTCCCTCACAAGTTTTCGCCAATGGTCAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCACTATCGGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:110:562:637/1 +AGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:111:778:854/1 +GAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:112:445:519/1 +TTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:113:366:440/1 +GCTTGTACCAAAAGTTACACCCTATGCCACTCGGCGCAGTACACGACTTCAATAGGGTGTAGGGTCAGCCCGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:114:413:488/1 +TTCAATAGGGTGTAGGGTCAGCCCGTCCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:115:564:638/1 +TATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAACGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:116:774:850/1 +CTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:117:101:175/1 +GCTCTAGCTCAGAGGGACGTGTCCACGCGTAAGGCTTCTTATGTCTCACGATCATCCATGTCCTCCTAAACACTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:118:958:1033/1 +TCGCCAATGGTCAATATTGCTTACTCGTACCTCCTGCTCATGTGACCTCACTATCGGTCTAGTCTCTGGCACGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:119:128:203/1 +CGTAAGGCTTCTTATGTCTCACGATCATCCATGTCCTCCTAAACACTAAACCTGGTTCCGCTAAAATGAACCGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:120:860:934/1 +TTTGCTCACGCTAGTCTACCAGAGAAACGCACACGGGAGTGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:121:672:747/1 +CGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAATATTCTCTTATTTGATGCGGACTGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:122:676:750/1 +ACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAATATTCTCTTATTTGATGCGGACTGGGTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:123:188:262/1 +CTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:124:186:260/1 +CGCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:125:647:722/1 +TTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:126:743:818/1 +TGGGTGAGATCGGTACTAATCTCAGACTGAGCTTAGAAGTTGTATCTACATTACAATGAAGGTACGCAATCTGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:127:477:552/1 +CAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAAGTTTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:128:793:868/1 +TTACAATGAAGGTACGCAATCTGTTGGGTACCAAGCAAATTTAGATTGGACCTAAACTACCTTGTATTTTGCTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:129:33:106/1 +ACGCTACGTGGTATAGCCGGATTACAGCACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:130:187:261/1 +GCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGGTATTCCCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:131:681:756/1 +CTCCCGCGGCCTAGATACGGATATACAAATTTATCATCAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:132:899:973/1 +TGGCTGTGTCGTAATCCATTGCGTTGATGGAACGGACACACAAAGTCCCTCACAAGTTTTCGCCAATGGTCAATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:133:472:547/1 +CCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACCTACGGTGATCAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:134:36:111/1 +CTACGTGGTATAGCCGGATTACAGCACAGGACCTGACCATAATCAGTGATTCACTAATCCTCTTGGCTCTAGCTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:135:617:693/1 +GCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACTATTTCGCCGGAACTGACTCCCGCGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:136:832:905/1 +TTTAGATTGGACCTAAACTACCTTGTATTTTGCTCACGCTAGTCTACCAGAGAAACGCACACGGGAGTGGCTGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:137:168:242/1 +AAACACTAAACCTGGTTCCGCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:138:428:503/1 +GGTCAGCCCGTCCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:139:19:92/1 +ACATCAACGGGGGGACGCTACGTGGTATAGCCGGATTACAGCACAGGACCTGACCATAATCAGTGATTCACTAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:140:132:204/1 +AGGCTTCTTATGTCTCACGATCATCCATGTCCTCCTAAACACTAAACCTGGTTCCGCTAAAATGAACCGACTATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:141:538:613/1 +GGTGATCAAGTTTATAGAGCTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATACGGATTATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:142:690:763/1 +CCTAGATACGGATATACAAATTTATCATCAATATTCTCTTATTTGATGCGGACTGGGTGAGATCGGTACTAATCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:143:439:514.dup.2/1 +CCCAGGTTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:144:592:666/1 +CAATAATTAATACGGATTATTGGGTGCAGGGAAACCCTCTGCAACGCACGGACCATTGGCAGGAGTTCGGACTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:145:445:519.dup.2/1 +TTGACGAGCAACAACGTCCAAAACAGGCCTAGCAGAATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:146:530:605/1 +GCACCTACGGTGATCAAGTTTATAGAGCTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAATTAATAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:147:521:595/1 +CGCAGCGCAGCACCTACGGTGATCAAGTTTATAGAGCTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:148:178:250/1 +CCTGGTTCCGCTAAAATGAACCGACTATAATAGTGTTAATTAAACAATAACCCTAGATGGCCAAACAACTGGTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq b/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq new file mode 100644 index 00000000..33460df0 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_insert_codon/reads_2.fq @@ -0,0 +1,592 @@ +@presence_absence1:1:79:154/2 +GTTATTGTTTAATTAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:2:904:979/2 +GATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTACGAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:3:869:942/2 +GACCGATAGTGAGGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACCATTGGCGAAAACTTGTGAGGGACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:4:238:314/2 +AGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:5:202:276/2 +ACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:6:560:635/2 +TTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTGCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:7:321:394/2 +GTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTACTGCGCCGAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:8:795:871/2 +GACTTTGTGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:9:489:563/2 +CGTTGCAGAGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:10:789:865/2 +GTGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:11:292:367/2 +GGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:12:381:457/2 +GCTGCGCTGCGGGTTCATCAGTTTAATATGGCCAAATTCATCGCACGCCATTCTGCTAGGCCTGTTTTGGACGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:13:673:747/2 +ACCCAACAGATTGCGTACCTTCATTGTAATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:14:163:239/2 +GTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAAATGGGAATACCACCAGTTGTTTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:15:69:143/2 +ATTAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:16:812:888/2 +GGCGAAAACTTGTGAGGGACTTTGTGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:17:822:895/2 +GACCATTGGCGAAAACTTGTGAGGGACTTTGTGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:18:61:138/2 +CACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGACATAAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:19:969:1041/2 +TCTATTGTTAAGGTCGCCAGATCTTTAACAGAGGGATTACATGGCTCTACAGCGCCGTGTACGATCTCGAGATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:20:880:955/2 +GTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACCATTGGCGAAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:21:941:1015/2 +AACAGAGGGATTACATGGCTCTACAGCGCCGTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:22:67:141/2 +TAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGACAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:23:470:546/2 +CTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAGCTCTATAAACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:24:482:555/2 +AGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:25:714:790/2 +GCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGCGTACCTTCATTGTAATGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:26:857:932/2 +GAGGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACCATTGGCGAAAACTTGTGAGGGACTTTGTGTGTCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:27:312:386/2 +CGTTGTTGCTCGTCAACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:28:26:99/2 +GTGTTTAGGAGGACATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGACACGTCCCTCTGAGCTAGAGCCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:29:307:381/2 +TTGCTCGTCAACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:30:587:661/2 +TCAAATAAGAGAATATTGATGATAAATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:31:734:808/2 +TCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:32:657:730/2 +CCTTCATTGTAATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:33:584:657/2 +ATAAGAGAATATTGATGATAAATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTCCGAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:34:239:314/2 +AGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:35:912:987/2 +CCGTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:36:352:426/2 +CCAAATTCATCGCACGCCATTCTGCTAGGCCTGTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGGCTGACCCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:37:622:695/2 +GTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGATAAATTTGTATATCCGTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:38:514:587/2 +CCGAACTCCTGCCAATGGTCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:39:1:76/2 +CGTGAGACATAAGAAGCCTTACGCGTGGACACGTCCCTCTGAGCTAGAGCCAAGAGGATTAGTGAATCACTGATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:40:406:481/2 +TCTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCATCAGTTTAATATGGCCAAATTCATCGCACGCCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:41:13:88/2 +GACATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGACACGTCCCTCTGAGCTAGAGCCAAGAGGATTAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:42:246:321/2 +GTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:43:107:181/2 +ATACCACCAGTTGTTTGGCCATCTAGGGTTATTGTTTAATTAACACTATTATAGTCGGTTCATTTTAGCGGAACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:44:425:500/2 +GACTGGGCATACTATAAGCTCTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCATCAGTTTAATATGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:45:255:329/2 +TGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:46:126:201/2 +CCGGCTGCTCACAAATGGGAATACCACCAGTTGTTTGGCCATCTAGGGTTATTGTTTAATTAACACTATTATAGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:47:458:532/2 +CCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAGCTCTATAAACTTGATCACCGTAGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:48:352:427/2 +GCCAAATTCATCGCACGCCATTCTGCTAGGCCTGTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGGCTGACCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:49:303:378/2 +CTCGTCAACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:50:640:715/2 +AGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:51:598:672/2 +CCCAGTCCGCATCAAATAAGAGAATATTGATGATAAATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:52:865:938/2 +GATAGTGAGGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACCATTGGCGAAAACTTGTGAGGGACTTTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:53:938:1012/2 +AGAGGGATTACATGGCTCTACAGCGCCGTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:54:237:311/2 +GTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:55:626:701/2 +AGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGATAAATTTGTATAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:56:487:561/2 +TTGCAGAGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:57:458:533/2 +TCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAGCTCTATAAACTTGATCACCGTAGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:58:360:434/2 +TAATATGGCCAAATTCATCGCACGCCATTCTGCTAGGCCTGTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:59:892:966/2 +AGTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:60:327:402/2 +CTAGGCCTGTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTACTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:61:655:728/2 +TTCATTGTAATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:62:944:1020/2 +TCTTTAACAGAGGGATTACATGGCTCTACAGCGCCGTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:63:281:355/2 +CCCTACACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:64:876:950/2 +AGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACCATTGGCGAAAACTTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:65:29:103/2 +TTTAGTGTTTAGGAGGACATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGACACGTCCCTCTGAGCTAGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:66:439:514/2 +TTTTTCAACAAACAGACTGGGCATACTATAAGCTCTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:67:843:916/2 +GAGGTACGAGTAAGCAATATTGACCATTGGCGAAAACTTGTGAGGGACTTTGTGTGTCCGTTCCATCAACGCAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:68:48:121/2 +CATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:69:641:717/2 +GTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:70:448:524/2 +ATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAGCTCTATAAACTTGATCACCGTAGGTGCTGCGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:71:472:545/2 +TGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAGCTCTATAAACTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:72:298:373/2 +CAACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:73:84:158/2 +TAGGGTTATTGTTTAATTAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:74:473:547/2 +CCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAGCTCTATAAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:75:115:190/2 +CAAATGGGAATACCACCAGTTGTTTGGCCATCTAGGGTTATTGTTTAATTAACACTATTATAGTCGGTTCATTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:76:803:877/2 +GTGAGGGACTTTGTGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:77:241:316/2 +ATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:78:138:213/2 +TGCCTGCCAAAGCCGGCTGCTCACAAATGGGAATACCACCAGTTGTTTGGCCATCTAGGGTTATTGTTTAATTAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:79:845:918/2 +AGGAGGTACGAGTAAGCAATATTGACCATTGGCGAAAACTTGTGAGGGACTTTGTGTGTCCGTTCCATCAACGCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:80:492:567/2 +CGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:81:908:983/2 +GTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTACG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:82:624:699/2 +CTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGATAAATTTGTATATCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:83:235:310/2 +TGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:84:823:896/2 +TGACCATTGGCGAAAACTTGTGAGGGACTTTGTGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:85:283:358/2 +TGACCCTACACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:86:255:331/2 +ACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:87:72:148/2 +GTTTAATTAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTTAGTGTTTAGGAGGACATGGATGATCGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:88:615:688/2 +ATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGATAAATTTGTATATCCGTATCTAGGCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:89:936:1009/2 +GGGATTACATGGCTCTACAGCGCCGTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:90:711:784/2 +TACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTGCGTACCTTCATTGTAATGTAGATAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:91:590:666/2 +CCGCATCAAATAAGAGAATATTGATGATAAATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:92:747:820/2 +CGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:93:234:309/2 +GTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:94:325:399/2 +GGCCTGTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGGCTGACCCTACACCCTATTGAAGTCGTGTACTGCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:95:214:287/2 +ATGGTCTCTTTACTCGAATGATCTTTTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:96:155:230/2 +TAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAAATGGGAATACCACCAGTTGTTTGGCCATCTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:97:351:427/2 +GCCAAATTCATCGCACGCCATTCTGCTAGGCCTGTTTTGGACGTTGTTGCTCGTCAACCTGGGACGGGCTGACCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:98:734:809/2 +CTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCCAACAGATTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:99:756:830/2 +CAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAATT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:100:266:341/2 +GAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:101:639:714/2 +GATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:102:278:353/2 +CTACACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:103:265:341/2 +GAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTCTCTTTACTCGAATGA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:104:394:468/2 +TCACCGTAGGTGCTGCGCTGCGGGTTCATCAGTTTAATATGGCCAAATTCATCGCACGCCATTCTGCTAGGCCTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:105:918:993/2 +ACAGCGCCGTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:106:818:891/2 +ATTGGCGAAAACTTGTGAGGGACTTTGTGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCCCGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:107:745:818/2 +TGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:108:282:356/2 +ACCCTACACCCTATTGAAGTCGTGTACTGCGCCGAGTGGCATAGGGTGTAACTTTTGGTACAAGCCGGCATGGTC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:109:942:1016/2 +TAACAGAGGGATTACATGGCTCTACAGCGCCGTGTACGATCTCGAGATTGAGTCGTCAGACGTGCCAGAGACTAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:110:562:637/2 +AATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:111:778:854/2 +CCATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:112:445:519/2 +TGCAGTTTTTCAACAAACAGACTGGGCATACTATAAGCTCTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:113:366:440/2 +TCAGTTTAATATGGCCAAATTCATCGCACGCCATTCTGCTAGGCCTGTTTTGGACGTTGTTGCTCGTCAACCTGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:114:413:488/2 +TATAAGCTCTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCATCAGTTTAATATGGCCAAATTCATCGC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:115:564:638/2 +AAATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:116:774:850/2 +CAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:117:101:175/2 +CCAGTTGTTTGGCCATCTAGGGTTATTGTTTAATTAACACTATTATAGTCGGTTCATTTTAGCGGAACCAGGTTT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:118:958:1033/2 +TAAGGTCGCCAGATCTTTAACAGAGGGATTACATGGCTCTACAGCGCCGTGTACGATCTCGAGATTGAGTCGTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:119:128:203/2 +AGCCGGCTGCTCACAAATGGGAATACCACCAGTTGTTTGGCCATCTAGGGTTATTGTTTAATTAACACTATTATA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:120:860:934/2 +GTGAGGTCACATGAGCAGGAGGTACGAGTAAGCAATATTGACCATTGGCGAAAACTTGTGAGGGACTTTGTGTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:121:672:747/2 +ACCCAACAGATTGCGTACCTTCATTGTAATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:122:676:750/2 +GGTACCCAACAGATTGCGTACCTTCATTGTAATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:123:188:262/2 +TTATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:124:186:260/2 +ATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:125:647:722/2 +GTAATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:126:743:818/2 +TGTGCGTTTCTCTGGTAGACTAGCGTGAGCAAAATACAAGGTAGTTTAGGTCCAATCTAAATTTGCTTGGTACCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:127:477:552/2 +GTTTCCCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAGCTCTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:128:793:868/2 +TTTGTGTGTCCGTTCCATCAACGCAATGGATTACGACACAGCCACTCCCGTGTGCGTTTCTCTGGTAGACTAGCG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:129:33:106/2 +AGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGACACGTCCCTCTGAGCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:130:187:261/2 +TATTGCGTTGTGGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:131:681:756/2 +TTGCTTGGTACCCAACAGATTGCGTACCTTCATTGTAATGTAGATACAACTTCTAAGCTCAGTCTGAGATTAGTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:132:899:973/2 +GAGATTGAGTCGTCAGACGTGCCAGAGACTAGACCGATAGTGAGGTCACATGAGCAGGAGGTACGAGTAAGCAAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:133:472:547/2 +CCTGCACCCAATAATCCGTATTAATTATTGCAGTTTTTCAACAAACAGACTGGGCATACTATAAGCTCTATAAAC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:134:36:111/2 +GAACCAGGTTTAGTGTTTAGGAGGACATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGACACGTCCCTCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:135:617:693/2 +CTGAGATTAGTACCGATCTCACCCAGTCCGCATCAAATAAGAGAATATTGATGATAAATTTGTATATCCGTATCT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:136:832:905/2 +AAGCAATATTGACCATTGGCGAAAACTTGTGAGGGACTTTGTGTGTCCGTTCCATCAACGCAATGGATTACGACA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:137:168:242/2 +ATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAAATGGGAATACCACCAGTTGT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:138:428:503/2 +ACAGACTGGGCATACTATAAGCTCTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCATCAGTTTAATAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:139:19:92/2 +GGAGGACATGGATGATCGTGAGACATAAGAAGCCTTACGCGTGGACACGTCCCTCTGAGCTAGAGCCAAGAGGAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:140:132:204/2 +AAGCCGGCTGCTCACAAATGGGAATACCACCAGTTGTTTGGCCATCTAGGGTTATTGTTTAATTAACACTATTAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:141:538:613/2 +GCGGGAGTCAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTGCGTTGCAGAGGGTTTCCCTGCACCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:142:690:763/2 +TCTAAATTTGCTTGGTACCCAACAGATTGCGTACCTTCATTGTAATGTAGATACAACTTCTAAGCTCAGTCTGAG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:143:439:514.dup.2/2 +TTTTTCAACAAACAGACTGGGCATACTATAAGCTCTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGGTTCAT ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:144:592:666/2 +CCGCATCAAATAAGAGAATATTGATGATAAATTTGTATATCCGTATCTAGGCCGCGGGAGTCAGTTCCGGCGAAA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:145:445:519.dup.2/2 +TGCAGTTTTTCAACAAACAGACTGGGCATACTATAAGCTCTATAAACTTGATCACCGTAGGTGCTGCGCTGCGGG ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:146:530:605/2 +CAGTTCCGGCGAAATAGTCCGAACTCCTGCCAATGGTCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAATCC ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:147:521:595/2 +GAAATAGTCCGAACTCCTGCCAATGGTCCGTGCGTTGCAGAGGGTTTCCCTGCACCCAATAATCCGTATTAATTA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII +@presence_absence1:148:178:250/2 +GGCGCTATATCGTGCTCTGGTAAATTCACATCGACACTGCCTGCCAAAGCCGGCTGCTCACAAATGGGAATACCA ++ +IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII diff --git a/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa b/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa new file mode 100644 index 00000000..be619452 --- /dev/null +++ b/ariba/tests/data/cluster_test_full_run_insert_codon/references.fa @@ -0,0 +1,3 @@ +>presence_absence1 +ATGGCGTGCGATGAATTTGGCCATATTAAACTGATGAACCCGCAGCGCAGCACC +TACGGTGATCAAGTTTATAGTATGCCCAGTCTGTTTGTTGAAAAACTGCAATAA From 332c71ff603006cc90deb9edfe34ad4689c15c23 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Wed, 12 Oct 2016 13:27:39 +0100 Subject: [PATCH 14/16] Add mash sketch file --- ariba/tests/data/clusters_test_dummy_db.fa.msh | Bin 0 -> 504 bytes 1 file changed, 0 insertions(+), 0 deletions(-) create mode 100644 ariba/tests/data/clusters_test_dummy_db.fa.msh diff --git a/ariba/tests/data/clusters_test_dummy_db.fa.msh b/ariba/tests/data/clusters_test_dummy_db.fa.msh new file mode 100644 index 0000000000000000000000000000000000000000..a208432e72e590b33b30ded9cc2cb42661fc8e92 GIT binary patch literal 504 zcmZQzU|_HVVh~^kLQx2lVL=-slm($Uz!W3H6)1fZNNWKxNR>Yjvj8y@13Qp}0BaZn zjTQv*g@71Db0Nv`0@=1mR#qU%ftdE1Cq%U7HL2ovxcl>ym{_$JU6AM$zkIxU3{Mvr`#k_!s z(#a1sU)?{+TDABS`*KC~=E=HW=lF7XE?A`WaV}qYYu%DvIVD;<${Z)=3aHknjd9yfBDtL zmI($MKBe8BG)d|IOoz}1A6MVH_rB)gqnmq}`}m&Ud!~H)k=X@~>mRLcRM*RfxqJ(E z^Ij4ckn%&{&wO>RNd6D66W5;SS8V$6;{GI6+lAae%L`nJj$Y#b4GL0NtS|%Fj?V5O Hpzs6$P`s!x literal 0 HcmV?d00001 From d3acd0c2c69c1b15cc5e466c450368ee8c432b62 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Wed, 12 Oct 2016 13:28:03 +0100 Subject: [PATCH 15/16] Check mash sketch file is present --- ariba/clusters.py | 3 +++ ariba/tests/clusters_test.py | 1 + 2 files changed, 4 insertions(+) diff --git a/ariba/clusters.py b/ariba/clusters.py index 993a78b6..f2eac5a7 100644 --- a/ariba/clusters.py +++ b/ariba/clusters.py @@ -76,6 +76,9 @@ def __init__(self, self.extern_progs = extern_progs self.clusters_tsv = os.path.abspath(os.path.join(refdata_dir, '02.cdhit.clusters.tsv')) self.all_ref_seqs_fasta = os.path.abspath(os.path.join(refdata_dir, '02.cdhit.all.fa')) + mash_file = self.all_ref_seqs_fasta + '.msh' + if not os.path.exists(mash_file): + raise Error('Error! Mash file ' + mash_file + ' not found.\nThe likely cause is that prepareref was run using an old version of ariba.\nIf this is the case, please rerun ariba preparef.') if version_report_lines is None: self.version_report_lines = [] diff --git a/ariba/tests/clusters_test.py b/ariba/tests/clusters_test.py index 61d09296..10561298 100644 --- a/ariba/tests/clusters_test.py +++ b/ariba/tests/clusters_test.py @@ -24,6 +24,7 @@ def setUp(self): self.refdata_dir = 'tmp.RefData' os.mkdir(self.refdata_dir) shutil.copyfile(os.path.join(data_dir, 'clusters_test_dummy_db.fa'), os.path.join(self.refdata_dir, '02.cdhit.all.fa')) + shutil.copyfile(os.path.join(data_dir, 'clusters_test_dummy_db.fa.msh'), os.path.join(self.refdata_dir, '02.cdhit.all.fa.msh')) shutil.copyfile(os.path.join(data_dir, 'clusters_test_dummy_db.tsv'), os.path.join(self.refdata_dir, '01.filter.check_metadata.tsv')) with open(os.path.join(self.refdata_dir, '00.info.txt'), 'w') as f: print('genetic_code\t11', file=f) From ebd2baa5fe07cd577a6f79be24da8f3cdcca60b9 Mon Sep 17 00:00:00 2001 From: Martin Hunt Date: Wed, 12 Oct 2016 13:29:14 +0100 Subject: [PATCH 16/16] Version bump 2.3.0 --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 416b0f43..dc7533f8 100644 --- a/setup.py +++ b/setup.py @@ -55,7 +55,7 @@ setup( ext_modules=[minimap_mod, fermilite_mod, vcfcall_mod], name='ariba', - version='2.2.5', + version='2.3.0', description='ARIBA: Antibiotic Resistance Identification By Assembly', packages = find_packages(), package_data={'ariba': ['test_run_data/*']},