[med-svn] [bcftools] 02/03: Update patches as they were applied upstream

[Graham Inggs]

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ginggs pushed a commit to branch master
in repository bcftools.

commit 13f2347656778a412d8d295ec0bf785960502aec
Author: Graham Inggs <ginggs at debian.org>
Date:   Fri Nov 10 14:44:13 2017 +0200

    Update patches as they were applied upstream
---
 debian/changelog                               |  1 +
 debian/patches/fix-test_vcf_query.patch        | 18 ++++++++++++++----
 debian/patches/test-regidx-unsigned-char.patch |  1 +
 3 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 95641a9..b9670e8 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,7 @@
 bcftools (1.5-4) UNRELEASED; urgency=medium
 
   * Add debian/clean to fix FTBFSx2
+  * Update patches as they were applied upstream
 
  -- Graham Inggs <ginggs at debian.org>  Fri, 10 Nov 2017 12:41:15 +0000
 
diff --git a/debian/patches/fix-test_vcf_query.patch b/debian/patches/fix-test_vcf_query.patch
index 584f8b0..3134b18 100644
--- a/debian/patches/fix-test_vcf_query.patch
+++ b/debian/patches/fix-test_vcf_query.patch
@@ -2,17 +2,27 @@ Description: Fix test_vcf_query on 32-bit architectures
  Introduced by upstream commit:
  https://github.com/samtools/bcftools/commit/25d042b833987d32e5de1fc3a109d357c4d0f738
 Forwarded: https://github.com/samtools/bcftools/pull/701
+Applied-Upstream: https://github.com/samtools/bcftools/commit/e436c3d0fb26614505fb02297a21a5ede1961723
 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
+Last-Update 2017-11-09
+--- a/vcfnorm.c
++++ b/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
++    char *end = seq + nseq;
      while ( *seq && seq<end )
      {
          char c = toupper(*seq);
+@@ -326,7 +326,7 @@
+     {
+         if ( line->d.allele[i][0]=='<' ) return ERR_SYMBOLIC;  // symbolic allele
+         if ( line->d.allele[i][0]=='*' ) return ERR_SPANNING_DELETION;  // spanning deletion
+-        if ( has_non_acgtn(line->d.allele[i],0) )
++        if ( has_non_acgtn(line->d.allele[i],line->shared.l) )
+         {
+             if ( args->check_ref==CHECK_REF_EXIT )
+                 error("Non-ACGTN alternate allele at %s:%d .. REF_SEQ:'%s' vs VCF:'%s'\n", bcf_seqname(args->hdr,line),line->pos+1,ref,line->d.allele[i]);
diff --git a/debian/patches/test-regidx-unsigned-char.patch b/debian/patches/test-regidx-unsigned-char.patch
index 28625cf..685bfce 100644
--- a/debian/patches/test-regidx-unsigned-char.patch
+++ b/debian/patches/test-regidx-unsigned-char.patch
@@ -3,6 +3,7 @@ Description: Fix test-regidx argument parsing on archs with unsigned char
 Author: Adrian Bunk <bunk at debian.org>
 Bug-Debian: https://bugs.debian.org/865060
 Forwarded: https://github.com/samtools/bcftools/pull/700
+Applied-Upstream: https://github.com/samtools/bcftools/commit/9d83925bcb1eed867288bcd6441e863a51349c2d
 
 --- a/test/test-regidx.c
 +++ b/test/test-regidx.c

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