This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch debian/unstable in repository samtools.
commit c789e05419a795fa01a162aa84419f856d5385b8 Author: Charles Plessy <[email protected]> Date: Mon Jun 15 22:03:26 2015 +0900 Current changelog. --- Makefile | 2 +- bam_plcmd.c | 18 ++++++++++++++++-- debian/changelog | 3 +++ debian/patches/series | 1 + 4 files changed, 21 insertions(+), 3 deletions(-) diff --git a/Makefile b/Makefile index bf7fd25..e39ee72 100644 --- a/Makefile +++ b/Makefile @@ -83,7 +83,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) $(BUILT_TEST_PROGRAMS) # Adjust $(HTSDIR) to point to your top-level htslib directory HTSDIR = ../htslib -include $(HTSDIR)/htslib.mk +-include $(HTSDIR)/htslib.mk HTSLIB = $(HTSDIR)/libhts.a BGZIP = $(HTSDIR)/bgzip diff --git a/bam_plcmd.c b/bam_plcmd.c index d574cca..b23a0cc 100644 --- a/bam_plcmd.c +++ b/bam_plcmd.c @@ -129,6 +129,7 @@ typedef struct { hts_itr_t *iter; bam_hdr_t *h; int ref_id; + int ref_len; char *ref; const mplp_conf_t *conf; } mplp_aux_t; @@ -174,6 +175,11 @@ static int mplp_func(void *data, bam1_t *b) qual[i] = qual[i] > 31? qual[i] - 31 : 0; } has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0; + if (has_ref && (ma->ref_len <= b->core.pos)) { // exclude reads outside of the reference sequence + fprintf(stderr,"[%s] Skipping because %d is outside of %d [ref:%d]\n",__func__,b->core.pos,ma->ref_len,ma->ref_id); + skip = 1; + continue; + } skip = 0; if (has_ref && (ma->conf->flag&MPLP_REALN)) bam_prob_realn_core(b, ma->ref, (ma->conf->flag & MPLP_REDO_BAQ)? 7 : 3); if (has_ref && ma->conf->capQ_thres > 10) { @@ -435,7 +441,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) if (tid0 >= 0 && conf->fai) { // region is set ref = faidx_fetch_seq(conf->fai, h->target_name[tid0], 0, 0x7fffffff, &ref_len); ref_tid = tid0; - for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid0; + for (i = 0; i < n; ++i) { + data[i]->ref = ref; + data[i]->ref_id = tid0; + data[i]->ref_len = ref_len; + } } else ref_tid = -1, ref = 0; // init pileup @@ -459,7 +469,11 @@ static int mpileup(mplp_conf_t *conf, int n, char **fn) if (tid != ref_tid) { free(ref); ref = 0; if (conf->fai) ref = faidx_fetch_seq(conf->fai, h->target_name[tid], 0, 0x7fffffff, &ref_len); - for (i = 0; i < n; ++i) data[i]->ref = ref, data[i]->ref_id = tid; + for (i = 0; i < n; ++i) { + data[i]->ref = ref; + data[i]->ref_id = tid; + data[i]->ref_len = ref_len; + } ref_tid = tid; } if (conf->flag & MPLP_BCF) { diff --git a/debian/changelog b/debian/changelog index eba0d37..db75c9c 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,8 +1,11 @@ samtools (1.2-1) UNRELEASED; urgency=medium a5f28a0 Merge tag '1.2' into debian/unstable + c542e84 Build-depend on libhts-dev 1.2. 6c2d9cd Build-depend and recommend libio-pty-perl. (Needed for the regression tests.) + 23e44a4 Removed fix_coverage_cap.patch, obsoleted by -d option. + 1091aab Refreshed fuzzy patches. -- Charles Plessy <[email protected]> Thu, 25 Sep 2014 21:39:37 +0900 diff --git a/debian/patches/series b/debian/patches/series index dda8ba0..4b093e4 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,2 +1,3 @@ fix_segfault_with_small_ref.patch dynamic-build.patch +debian-changes -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
