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Made some changes to README.md file
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Changed write_output code in vcf generator script version 4
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sayantansls committed Sep 13, 2020
1 parent 40e14f1 commit 84c2ce7
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -31,7 +31,7 @@ For the input file and output vcf format, check the examples at - /vcf-generator

## Limitations

1. The script only consumes genomic HGVS nomenclature, not cDNA or protein nomenclature.
The script only consumes genomic HGVS nomenclature, not cDNA or protein nomenclature.

*The limitations are currently being worked on and will be resolved in future versions*

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5 changes: 3 additions & 2 deletions src/vcf_generator/version4/vcf_generator_ver4.py
Original file line number Diff line number Diff line change
Expand Up @@ -147,8 +147,9 @@ def toString(self):
self.vcf_format, self.sample));

def writeEntry(self):
write_output = '{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}\t{}'.format(self.chrom, self.pos, self.vcf_id, self.ref, self.alt, \
self.qual, self.vcf_filter, self.info, self.vcf_format, self.sample)
write_output = '{chrom}\t{pos}\t{id}\t{ref}\t{alt}\t{qual}\t{filter}\t{info}\t{format}\t{sample}'.format(chrom=self.chrom, \
pos=self.pos, id=self.vcf_id, ref=self.ref, alt=self.alt, qual=self.qual, filter=self.vcf_filter, info=self.info, \
format=self.vcf_format, sample=self.sample)
return write_output

# Datamodel(object) that defines the File Entry (an entry from the input file)
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