[med-svn] samtools 02/05: Add patch to fix building on i386

[Afif Elghraoui]

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afif-guest pushed a commit to branch debian/unstable
in repository samtools.

commit eb56918001cda9174a4d7078d91d171e158772d7
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sun Sep 13 18:51:50 2015 -0700

    Add patch to fix building on i386
---
 debian/patches/i386-build.patch | 48 +++++++++++++++++++++++++++++++++++++++++
 debian/patches/series           |  1 +
 2 files changed, 49 insertions(+)

diff --git a/debian/patches/i386-build.patch b/debian/patches/i386-build.patch
new file mode 100644
index 0000000..4e43bf0
--- /dev/null
+++ b/debian/patches/i386-build.patch
@@ -0,0 +1,48 @@
+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 dda8ba0..b9ad524 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 fix_segfault_with_small_ref.patch
 dynamic-build.patch
+i386-build.patch

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