* samtools-0.1.12-12 (r889)

 * set mapQ as 20 if it equals 255

diff --git a/bam2bcf.c b/bam2bcf.c
index 08120fc46c2a3902e01582b45de0659d4b333eb6..46f534ee7553182f790384921c8c667417838b75 100644 (file)
--- 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 7e72b4e8f67e012747925c7302cea05c031f8a80..64ed4de4df8029c48c52313214cb056c2d4ee088 100644 (file)
--- 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[]);