From c1e9248358a76e932de6f21039e56dbca9950dae Mon Sep 17 00:00:00 2001 From: Heng Li Date: Wed, 15 Dec 2010 16:28:16 +0000 Subject: [PATCH] * samtools-0.1.12-12 (r889) * set mapQ as 20 if it equals 255 --- bam2bcf.c | 4 +++- bamtk.c | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/bam2bcf.c b/bam2bcf.c index 08120fc..46f534e 100644 --- a/bam2bcf.c +++ b/bam2bcf.c @@ -11,6 +11,7 @@ extern void ks_introsort_uint32_t(size_t n, uint32_t a[]); #define CALL_ETA 0.03f #define CALL_MAX 256 #define CALL_DEFTHETA 0.83f +#define DEF_MAPQ 20 #define CAP_DIST 25 @@ -63,7 +64,8 @@ int bcf_call_glfgen(int _n, const bam_pileup1_t *pl, int ref_base, bcf_callaux_t 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; diff --git a/bamtk.c b/bamtk.c index 7e72b4e..64ed4de 100644 --- a/bamtk.c +++ b/bamtk.c @@ -9,7 +9,7 @@ #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[]); -- 2.39.2