[med-svn] samtools 05/07: Refreshed fuzzy patches.

[Charles Plessy]

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

commit 1091aab090d557e3891bf99e3d1271ffd852dc4c
Author: Charles Plessy <plessy at debian.org>
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 <don at donarmstrong.com>
 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);

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