[med-svn] samtools 02/03: Removed patch; issue solved upstream.

[Charles Plessy]

This is an automated email from the git hooks/post-receive script.

plessy pushed a commit to branch debian/unstable
in repository samtools.

commit c12f4f35b82b40a6b3d44236a89c543bac210bd9
Author: Charles Plessy <plessy at debian.org>
Date:   Thu Dec 24 14:07:10 2015 +0900

    Removed patch; issue solved upstream.
    
    https://github.com/samtools/samtools/pull/286
---
 debian/patches/fix_segfault_with_small_ref.patch | 54 ------------------------
 debian/patches/series                            |  1 -
 2 files changed, 55 deletions(-)

diff --git a/debian/patches/fix_segfault_with_small_ref.patch b/debian/patches/fix_segfault_with_small_ref.patch
deleted file mode 100644
index 9304c6a..0000000
--- a/debian/patches/fix_segfault_with_small_ref.patch
+++ /dev/null
@@ -1,54 +0,0 @@
-Description: Fix segfault if position is outside of the reference sequence length
-Origin: Don Armstrong <don at donarmstrong.com>
-Forwarded: https://github.com/samtools/samtools/pull/286
-
-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;
-+    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
-                 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, 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;
--        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, 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);
--            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/patches/series b/debian/patches/series
index 02347fd..dd5a9b1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
-fix_segfault_with_small_ref.patch
 dynamic-build.patch
 i386-build.patch
 mayhem.patch

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/samtools.git