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Change Haplotype field data type from "Integer" to "Character" in VCF header #2

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Change Haplotype field data type from "Integer" to "Character" in VCF header #2

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bc15752
Change HS (haplotype) field from Integer to character in VCFs heterog…
ajw2329 Mar 14, 2024
c7ff9f1
Merge pull request #1 from ajw2329/ajw2329-patch-1
ajw2329 Mar 14, 2024
a797f38
Update heterogenesis_varincorp.py -- augment substitutions with all I…
ajw2329 Mar 11, 2025
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26 changes: 21 additions & 5 deletions heterogenesis_varincorp.py
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Original file line number Diff line number Diff line change
Expand Up @@ -146,7 +146,7 @@ def writevcffile(directory,prefix,clo,combvcfs,prochro):
file.write('##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">\n')
file.write('##FORMAT=<ID=AF,Number=A,Type=Float,Description="Alt allele frequency">\n')
file.write('##FORMAT=<ID=TC,Number=1,Type=Integer,Description="Total copies of alt allele">\n')
file.write('##FORMAT=<ID=HS,Number=1,Type=Integer,Description="Haplotypes">\n')
file.write('##FORMAT=<ID=HS,Number=1,Type=Character,Description="Haplotypes">\n')
file.write('##FORMAT=<ID=HC,Number=.,Type=Integer,Description="Total copies of alt allele per haplotype">\n')
file.write('##FORMAT=<ID=CN,Number=2,Type=Integer,Description="Copy number at position">\n')
file.write('#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t'+clo+'\n')
Expand Down Expand Up @@ -252,10 +252,26 @@ def invert(forward):
substitutions['g']='c'
substitutions['N']='N'
substitutions['n']='n'
substitutions['R']='R'
substitutions['r']='r'
substitutions['M']='M'
substitutions['m']='m'
substitutions['R']='Y'
substitutions['Y']='R'
substitutions['y']='r'
substitutions['r']='y'
substitutions['S']='S'
substitutions['s']='s'
substitutions['W']='W'
substitutions['w']='w'
substitutions['K']='M'
substitutions['M']='K'
substitutions['k']='m'
substitutions['m']='k'
substitutions['B']='V'
substitutions['V']='B'
substitutions['b']='v'
substitutions['v']='b'
substitutions['D']='H'
substitutions['H']='D'
substitutions['d']='h'
substitutions['h']='d'
for i in forward[::-1]:
reverse.append(substitutions[i])
return reverse
Expand Down