Mercurial > repos > jjohnson > defuse
changeset 32:8027fc53f3f9
Fix formatting error in defuse_results_to_vcf.py
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 06 Sep 2013 08:13:22 -0500 |
| parents | 7c0d935bd205 |
| children | 3e3ebdecb0e1 |
| files | defuse_results_to_vcf.py |
| diffstat | 1 files changed, 2 insertions(+), 2 deletions(-) [+] |
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--- a/defuse_results_to_vcf.py Tue Sep 03 10:59:43 2013 -0500 +++ b/defuse_results_to_vcf.py Fri Sep 06 08:13:22 2013 -0500 @@ -258,8 +258,8 @@ info1 = [svtype,'MATEID=%s' % mate_id2] + info info2 = [svtype,'MATEID=%s' % mate_id1] + info qual = int(float(fields[columns.index('probability')]) * 255) if columns.index('probability') else '.' - vcf1 = '%s\t%d\t%s\t%s\t%s\t%s\t%d\t%s'% (gene_chromosome1,genomic_break_pos1, mate_id1, ref1, alt1, qual, filt, ';'.join(info1) ) - vcf2 = '%s\t%d\t%s\t%s\t%s\t%s\t%d\t%s'% (gene_chromosome2,genomic_break_pos2, mate_id2, ref2, alt2, qual, filt, ';'.join(info2) ) + vcf1 = '%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s'% (gene_chromosome1,genomic_break_pos1, mate_id1, ref1, alt1, qual, filt, ';'.join(info1) ) + vcf2 = '%s\t%d\t%s\t%s\t%s\t%s\t%s\t%s'% (gene_chromosome2,genomic_break_pos2, mate_id2, ref2, alt2, qual, filt, ';'.join(info2) ) add_vcf_line(gene_chromosome1,genomic_break_pos1,mate_id1,vcf1) add_vcf_line(gene_chromosome2,genomic_break_pos2,mate_id2,vcf2) write_vcf()