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Handle zero-depth genotypes in allele-balance filtering #665

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Handle zero-depth genotypes in allele-balance filtering #665

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4 changes: 3 additions & 1 deletion abcCallGenotypes.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -168,7 +168,9 @@ void abcCallGenotypes::getGeno(funkyPars *pars){
int geno_Depth = pars->counts[s][i*4] + pars->counts[s][i*4+1] + pars->counts[s][i*4+2] + pars->counts[s][i*4+3];
int mm_Depth = pars->counts[s][i*4+pars->major[s]] + pars->counts[s][i*4+pars->minor[s]];

if(mm_Depth * 1.0 / geno_Depth < geno_minMM)
// A zero-depth genotype has no allele-balance evidence and must remain
// missing rather than producing a NaN through division by zero.
if(geno_Depth == 0 || mm_Depth * 1.0 / geno_Depth < geno_minMM)
maxGeno=-1;


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