[med-svn] samtools 03/03: 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 5c4ca0b5309fa25e1ecd6790ad6eec269a75789f
Author: Charles Plessy <plessy at debian.org>
Date:   Thu Dec 24 14:09:58 2015 +0900

    Removed patch; issue solved upstream.
    
    https://github.com/samtools/samtools/issues/305
---
 debian/patches/i386-build.patch | 48 -----------------------------------------
 debian/patches/series           |  1 -
 2 files changed, 49 deletions(-)

diff --git a/debian/patches/i386-build.patch b/debian/patches/i386-build.patch
deleted file mode 100644
index 4e43bf0..0000000
--- a/debian/patches/i386-build.patch
+++ /dev/null
@@ -1,48 +0,0 @@
-Description: Fix build on i386
- This is a backport of the upstream patch linked below because the patch from
- this commit did not cleanly apply.
-Origin: upstream, https://github.com/samtools/samtools/commit/5c3b72714acf36506a2ad8429927b502ac8966c1
-Bug: https://github.com/samtools/samtools/issues/305
-Applied-Upstream: https://github.com/samtools/samtools/commit/5c3b72714acf36506a2ad8429927b502ac8966c1
-Last-Update: 2015-09-13
---- samtools.orig/bam2bcf.h
-+++ samtools/bam2bcf.h
-@@ -56,7 +56,8 @@
-     int capQ, min_baseQ;
-     int openQ, extQ, tandemQ; // for indels
-     uint32_t min_support, max_support; // for collecting indel candidates
--    float min_frac, max_frac; // for collecting indel candidates
-+    double min_frac; // for collecting indel candidates
-+    float max_frac; // for collecting indel candidates
-     int per_sample_flt; // indel filtering strategy
-     int *ref_pos, *alt_pos, npos, *ref_mq, *alt_mq, *ref_bq, *alt_bq, *fwd_mqs, *rev_mqs, nqual; // for bias tests
-     // for internal uses
---- samtools.orig/bam2bcf_indel.c
-+++ samtools/bam2bcf_indel.c
-@@ -26,6 +26,7 @@
- #include <assert.h>
- #include <ctype.h>
- #include <string.h>
-+#include <float.h>
- #include "htslib/sam.h"
- #include "bam2bcf.h"
- #include "kprobaln.h"
-@@ -199,7 +200,7 @@
-                 j = bam_cigar2qlen(p->b->core.n_cigar, bam_get_cigar(p->b));
-                 if (j > max_rd_len) max_rd_len = j;
-             }
--            float frac = (float)na/nt;
-+            double frac = (double)na/nt;
-             if ( !indel_support_ok && na >= bca->min_support && frac >= bca->min_frac )
-                 indel_support_ok = 1;
-             if ( na > bca->max_support && frac > 0 ) bca->max_support = na, bca->max_frac = frac;
-@@ -217,7 +218,8 @@
-             if (aux[i] != aux[i-1]) ++n_types;
-         // Taking totals makes it hard to call rare indels
-         if ( !bca->per_sample_flt )
--            indel_support_ok = ( (float)n_alt / n_tot < bca->min_frac || n_alt < bca->min_support ) ? 0 : 1;
-+            indel_support_ok = ( (float)n_alt / n_tot < bca->min_frac
-+                                 || n_alt < bca->min_support ) ? 0 : 1;
-         if ( n_types == 1 || !indel_support_ok ) { // then skip
-             free(aux); return -1;
-         }
diff --git a/debian/patches/series b/debian/patches/series
index dd5a9b1..3347f33 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
 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