From 35dc3eb9daaba941e91acbd9c4302afcb54eabf4 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Sat, 13 Nov 2010 02:36:27 +0000 Subject: [PATCH] * samtools-0.1.9-13 (r819) * fixed a bug in pileup given refskip --- bam_maqcns.c | 4 ++-- bamtk.c | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/bam_maqcns.c b/bam_maqcns.c index 2f3fc08..4fbc6c6 100644 --- a/bam_maqcns.c +++ b/bam_maqcns.c @@ -154,7 +154,7 @@ glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam const bam_pileup1_t *p = pl + i; uint32_t q, x = 0, qq; uint16_t y = 0; - if (p->is_del || (p->b->core.flag&BAM_FUNMAP)) continue; + if (p->is_del || p->is_refskip || (p->b->core.flag&BAM_FUNMAP)) continue; q = (uint32_t)bam1_qual(p->b)[p->qpos]; if (q < bm->min_baseQ) continue; x |= (uint32_t)bam1_strand(p->b) << 18 | q << 8 | p->b->core.qual; @@ -166,7 +166,7 @@ glf1_t *bam_maqcns_glfgen(int _n, const bam_pileup1_t *pl, uint8_t ref_base, bam y |= q << 5; qq = bam1_seqi(bam1_seq(p->b), p->qpos); q = bam_nt16_nt4_table[qq? qq : ref_base]; - if (!p->is_del && q < 4) x |= 1 << 21 | q << 16, y |= q; + if (!p->is_del && !p->is_refskip && q < 4) x |= 1 << 21 | q << 16, y |= q; bm->aux->info16[n] = y; bm->aux->info[n++] = x; } diff --git a/bamtk.c b/bamtk.c index 428e9ed..1bbc4c0 100644 --- a/bamtk.c +++ b/bamtk.c @@ -9,7 +9,7 @@ #endif #ifndef PACKAGE_VERSION -#define PACKAGE_VERSION "0.1.9-12 (r818)" +#define PACKAGE_VERSION "0.1.9-13 (r819)" #endif int bam_taf2baf(int argc, char *argv[]); -- 2.39.2