* set mapQ as 20 if it equals 255
#define CALL_ETA 0.03f
#define CALL_MAX 256
#define CALL_DEFTHETA 0.83f
+#define DEF_MAPQ 20
#define CAP_DIST 25
seqQ = is_indel? (p->aux>>8&0xff) : 99;
if (q < bca->min_baseQ) continue;
if (q > seqQ) q = seqQ;
- mapQ = p->b->core.qual < bca->capQ? p->b->core.qual : bca->capQ;
+ mapQ = p->b->core.qual < 255? p->b->core.qual : DEF_MAPQ; // special case for mapQ==255
+ mapQ = mapQ < bca->capQ? mapQ : bca->capQ;
if (q > mapQ) q = mapQ;
if (q > 63) q = 63;
if (q < 4) q = 4;
#endif
#ifndef PACKAGE_VERSION
-#define PACKAGE_VERSION "0.1.12-7 (r888)"
+#define PACKAGE_VERSION "0.1.12-8 (r889)"
#endif
int bam_taf2baf(int argc, char *argv[]);