This is an automated email from the git hooks/post-receive script. plessy pushed a commit to branch debian/unstable in repository samtools.
commit 1091aab090d557e3891bf99e3d1271ffd852dc4c Author: Charles Plessy <[email protected]> Date: Mon Jun 15 21:46:58 2015 +0900 Refreshed fuzzy patches. --- debian/patches/dynamic-build.patch | 8 +++++--- debian/patches/fix_segfault_with_small_ref.patch | 16 +++++++++------- 2 files changed, 14 insertions(+), 10 deletions(-) diff --git a/debian/patches/dynamic-build.patch b/debian/patches/dynamic-build.patch index 569ca87..b49b4a3 100644 --- a/debian/patches/dynamic-build.patch +++ b/debian/patches/dynamic-build.patch @@ -2,9 +2,11 @@ Description: disable inclusion of accessory makefile needed for static build Forwarded: https://github.com/samtools/samtools/issues/275 Author: Charles Plessy ---- a/Makefile -+++ b/Makefile -@@ -82,7 +82,7 @@ +Index: samtools/Makefile +=================================================================== +--- samtools.orig/Makefile ++++ samtools/Makefile +@@ -83,7 +83,7 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS) # Adjust $(HTSDIR) to point to your top-level htslib directory HTSDIR = ../htslib diff --git a/debian/patches/fix_segfault_with_small_ref.patch b/debian/patches/fix_segfault_with_small_ref.patch index 466098a..9304c6a 100644 --- a/debian/patches/fix_segfault_with_small_ref.patch +++ b/debian/patches/fix_segfault_with_small_ref.patch @@ -2,9 +2,11 @@ Description: Fix segfault if position is outside of the reference sequence lengt Origin: Don Armstrong <[email protected]> Forwarded: https://github.com/samtools/samtools/pull/286 ---- a/bam_plcmd.c -+++ b/bam_plcmd.c -@@ -127,6 +127,7 @@ +Index: samtools/bam_plcmd.c +=================================================================== +--- samtools.orig/bam_plcmd.c ++++ samtools/bam_plcmd.c +@@ -129,6 +129,7 @@ typedef struct { hts_itr_t *iter; bam_hdr_t *h; int ref_id; @@ -12,7 +14,7 @@ Forwarded: https://github.com/samtools/samtools/pull/286 char *ref; const mplp_conf_t *conf; } mplp_aux_t; -@@ -172,6 +173,11 @@ +@@ -174,6 +175,11 @@ static int mplp_func(void *data, bam1_t qual[i] = qual[i] > 31? qual[i] - 31 : 0; } has_ref = (ma->ref && ma->ref_id == b->core.tid)? 1 : 0; @@ -24,7 +26,7 @@ Forwarded: https://github.com/samtools/samtools/pull/286 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) { -@@ -419,7 +425,11 @@ +@@ -435,7 +441,11 @@ static int mpileup(mplp_conf_t *conf, in 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; @@ -36,8 +38,8 @@ Forwarded: https://github.com/samtools/samtools/pull/286 + } } else ref_tid = -1, ref = 0; - // begin pileup -@@ -442,7 +452,11 @@ + // init pileup +@@ -459,7 +469,11 @@ static int mpileup(mplp_conf_t *conf, in 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); -- 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
