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Fix force genotyping sample ID in header line #446

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Fix force genotyping sample ID in header line #446

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5afaeb5
set sample_id for genotype-vcf mode
ASLeonard Feb 17, 2023
4b4dc9e
replace sample IDs in original header with new ID
ASLeonard Feb 17, 2023
be83341
Merge branch 'fritzsedlazeck:master' into force-genotype-ID
ASLeonard Dec 19, 2023
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2 changes: 1 addition & 1 deletion src/sniffles/sniffles
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Original file line number Diff line number Diff line change
Expand Up @@ -86,7 +86,7 @@ def Sniffles2_Main(config,processes):
if config.vcf == None and config.snf == None:
util.fatal_error_main("Please specify at least one of: --vcf or --snf for output (both may be used at the same time)")

if config.mode=="call_sample":
if config.mode=="call_sample" or config.mode=="genotype-vcf":
if config.sample_id==None:
#config.sample_id,_=os.path.splitext(os.path.basename(config.input))
config.sample_ids_vcf=[(0,"SAMPLE")]
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1 change: 1 addition & 0 deletions src/sniffles/vcf.py
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Original file line number Diff line number Diff line change
Expand Up @@ -314,6 +314,7 @@ def rewrite_genotype(self,svcall):

def rewrite_header_genotype(self,orig_header):
header_lines=orig_header.split("\n")
header_lines[-2] = '\t'.join(header_lines[-2].split()[:9]+[self.config.sample_id])
header_lines.insert(1,'##genotypeFileDate="'+self.config.start_date+'"')
header_lines.insert(1,'##genotypeCommand="'+self.config.command+'"')
header_lines.insert(1,f"##genotypeSource={self.config.version}_{self.config.build}")
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