From efc2b2337caed7b7a042800f8e08f01f502e0184 Mon Sep 17 00:00:00 2001 From: martinghunt Date: Thu, 28 Jul 2016 10:00:24 +0000 Subject: [PATCH] Add -l 15 to fermilite assemblies --- ariba/tests/cluster_test.py | 8 ++++---- third_party/fermi-lite-0.1/fml-asm_ariba.cpp | 1 + 2 files changed, 5 insertions(+), 4 deletions(-) diff --git a/ariba/tests/cluster_test.py b/ariba/tests/cluster_test.py index 5d4b6c45..1d4d1854 100644 --- a/ariba/tests/cluster_test.py +++ b/ariba/tests/cluster_test.py @@ -184,12 +184,12 @@ def test_full_run_ok_presence_absence(self): c.run() expected = [ - 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t1\tSNP\tp\tA10V\t1\tA10V\tNONSYN\t28\t28\tC\t83\t83\tT\t22\t.\t22\tpresence_absence1:1:0:A10V:.:Ref has wild, reads have variant so report\tGeneric description of presence_absence1', - 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t0\t.\tp\t.\t0\t.\tSYN\t53\t53\tT\t108\t108\tC\t32\t.\t32\t.\tGeneric description of presence_absence1', + 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tA10V\t1\tA10V\tNONSYN\t28\t28\tC\t83\t83\tT\t22\t.\t22\tpresence_absence1:1:0:A10V:.:Ref has wild, reads have variant so report\tGeneric description of presence_absence1', + 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t0\t.\tp\t.\t0\t.\tSYN\t53\t53\tT\t108\t108\tC\t32\t.\t32\t.\tGeneric description of presence_absence1', - 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tC;G;C\t62\t64\tC;G;C\t18;17;17\t.;.;.\t18;17;17\tpresence_absence1:1:0:R3S:.:Ref and assembly have wild type\tGeneric description of presence_absence1', + 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tR3S\t0\t.\t.\t7\t9\tC;G;C\t62\t64\tC;G;C\t18;17;17\t.;.;.\t18;17;17\tpresence_absence1:1:0:R3S:.:Ref and assembly have wild type\tGeneric description of presence_absence1', - 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t158\t17.4\t1\tSNP\tp\tI5A\t1\t.\t.\t13\t15\tG;C;G\t68\t70\tG;C;G\t18;20;20\t.;.;.\t18;20;20\tpresence_absence1:1:0:I5A:.:Ref and reads have variant so report\tGeneric description of presence_absence1', + 'presence_absence1\t1\t0\t539\t64\tcluster_name\t96\t96\t97.92\tcluster_name.scaffold.1\t213\t15.0\t1\tSNP\tp\tI5A\t1\t.\t.\t13\t15\tG;C;G\t68\t70\tG;C;G\t18;20;20\t.;.;.\t18;20;20\tpresence_absence1:1:0:I5A:.:Ref and reads have variant so report\tGeneric description of presence_absence1', ] self.assertEqual(expected, c.report_lines) diff --git a/third_party/fermi-lite-0.1/fml-asm_ariba.cpp b/third_party/fermi-lite-0.1/fml-asm_ariba.cpp index e4114f65..8d529761 100644 --- a/third_party/fermi-lite-0.1/fml-asm_ariba.cpp +++ b/third_party/fermi-lite-0.1/fml-asm_ariba.cpp @@ -143,6 +143,7 @@ int assemble(char *readsFile, char *fastaOut, char* logfileOut) bseq1_t *seqs; fml_opt_init(&opt); opt.max_cnt = 10000; + opt.min_asm_ovlp = 15; std::vector minCounts; minCounts.push_back(4); minCounts.push_back(8);