Commit e80e4429 by CosteaPaul

fix overhanging mismatches

parent eef3fe39
......@@ -541,7 +541,12 @@ int main(int argc, char *argv[])
} else {
++entireChr[pp];
pp = pp + ((*cigar) >> BAM_CIGAR_SHIFT);
--entireChr[pp];
if (pp >= chrSize) {//These are mismatches that actually hang over the end. Silly mapper!
//fprintf(stderr,"you are fucked %d %d\n",pp,chrSize);
--entireChr[chrSize-1];
} else {
--entireChr[pp];
}
}
++cigar;
}
......
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