[med-svn] [bcftools] 01/04: Incorporate lost changes from 1.4-3

[Afif Elghraoui]

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commit 2d2d47a4228b092d88910eb074356f586470c529
Author: Afif Elghraoui <afif at debian.org>
Date:   Thu Oct 12 00:05:25 2017 -0400

    Incorporate lost changes from 1.4-3
    
    1.5-1 was made to follow immediately from 1.4-2, so missed
    an important change made in 1.4-3.
    
    Closes: #868958
---
 debian/changelog                        |  8 ++++++++
 debian/patches/fix-test_vcf_query.patch | 18 ++++++++++++++++++
 debian/patches/series                   |  1 +
 3 files changed, 27 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index 3bed8ba..4bcc001 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -20,6 +20,14 @@ bcftools (1.5-1~exp1) experimental; urgency=medium
 
  -- Afif Elghraoui <afif at debian.org>  Tue, 08 Aug 2017 12:35:44 -0400
 
+bcftools (1.4.1-3) unstable; urgency=medium
+
+  * Team upload.
+  * Incorporate patches from Ubuntu to fix FTBFS on some 32-bit archs.
+  * Fix autopkgtests by ensuring presence of all deps.
+
+ -- Sascha Steinbiss <satta at debian.org>  Sat, 29 Jul 2017 10:38:27 +0200
+
 bcftools (1.4.1-2) unstable; urgency=medium
 
   * Team upload
diff --git a/debian/patches/fix-test_vcf_query.patch b/debian/patches/fix-test_vcf_query.patch
new file mode 100644
index 0000000..9fad479
--- /dev/null
+++ b/debian/patches/fix-test_vcf_query.patch
@@ -0,0 +1,18 @@
+Description: Fix test_vcf_query on 32-bit architectures
+ Introduced by upstream commit:
+ https://github.com/samtools/bcftools/commit/25d042b833987d32e5de1fc3a109d357c4d0f738
+Forwarded: not-yet
+Bug-Debian: https://bugs.debian.org/868958
+Author: Graham Inggs <ginggs at debian.org>
+Last-Update 2017-07-21
+--- bcftools.orig/vcfnorm.c
++++ bcftools/vcfnorm.c
+@@ -94,7 +94,7 @@
+ }
+ static inline int has_non_acgtn(char *seq, int nseq)
+ {
+-    char *end = nseq ? seq + nseq : seq + UINT32_MAX;   // arbitrary large number
++    char *end = nseq ? seq + nseq : seq + (UINT32_MAX >> 2);   // arbitrary large number
+     while ( *seq && seq<end )
+     {
+         char c = toupper(*seq);
diff --git a/debian/patches/series b/debian/patches/series
index b4ead10..a6429f0 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@
 # destdir.patch
 tests-pluginpath.patch
 test-regidx-unsigned-char.patch
+fix-test_vcf_query.patch

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