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bug fix summary when no samtools alt #131

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merged 2 commits into from
Aug 22, 2016
Merged

bug fix summary when no samtools alt #131

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47d5904
Catch when samtools vars were ND
Aug 22, 2016
c157d8d
Version bump 2.2.3
Aug 22, 2016
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2 changes: 1 addition & 1 deletion ariba/summary_cluster_variant.py
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Expand Up @@ -33,7 +33,7 @@ def _has_nonsynonymous(cls, data_dict):

@classmethod
def _get_het_percent(cls, data_dict):
if data_dict['gene'] == '1' or data_dict['ref_ctg_effect'] != 'SNP' or data_dict['smtls_alt_nt'] == '.' or ';' in data_dict['smtls_alt_nt']:
if data_dict['gene'] == '1' or data_dict['ref_ctg_effect'] != 'SNP' or data_dict['smtls_alt_nt'] == '.' or ';' in data_dict['smtls_alt_nt'] or data_dict['smtls_alt_depth'] == 'ND':
return None
else:
nucleotides = [data_dict['ctg_nt']] + data_dict['smtls_alt_nt'].split(',')
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2 changes: 1 addition & 1 deletion setup.py
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Expand Up @@ -51,7 +51,7 @@
setup(
ext_modules=[minimap_mod, fermilite_mod],
name='ariba',
version='2.2.2',
version='2.2.3',
description='ARIBA: Antibiotic Resistance Identification By Assembly',
packages = find_packages(),
package_data={'ariba': ['test_run_data/*']},
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