[med-svn] [tophat] 01/01: Adpated patches. PLEASE VERIFY - samtools copy looks suspicious!!!!

[Andreas Tille]

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tille pushed a commit to branch master
in repository tophat.

commit ba2e85aca2e1e8aca4546faff0eba2cede7b7baa
Author: Andreas Tille <tille at debian.org>
Date:   Sat Oct 4 21:56:15 2014 +0200

    Adpated patches.  PLEASE VERIFY - samtools copy looks suspicious!!!!
---
 debian/changelog                          |  3 ++-
 debian/patches/fix_build_w_seqan1.4.patch | 19 +-----------------
 debian/patches/fix_includes_path.patch    | 33 +++++++++++--------------------
 3 files changed, 14 insertions(+), 41 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index 37b9482..4576f12 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,6 +1,7 @@
-tophat (2.0.13+dfsg-1) unstable; urgency=medium
+tophat (2.0.13+dfsg-1) UNRELEASED; urgency=medium
 
   * New upstream version
+  * Adapted patches
 
  -- Andreas Tille <tille at debian.org>  Sat, 04 Oct 2014 21:27:24 +0200
 
diff --git a/debian/patches/fix_build_w_seqan1.4.patch b/debian/patches/fix_build_w_seqan1.4.patch
index e9091be..e79efb9 100644
--- a/debian/patches/fix_build_w_seqan1.4.patch
+++ b/debian/patches/fix_build_w_seqan1.4.patch
@@ -3,7 +3,7 @@ Bug-Closed: http://bugs.debian.org/733352
 Descriptions: resolves build failure with seqan 1.4
 --- tophat.orig/src/segment_juncs.cpp
 +++ tophat/src/segment_juncs.cpp
-@@ -2055,10 +2055,13 @@
+@@ -2050,10 +2050,13 @@
      typedef map<uint32_t, IntronMotifs> MotifMap;
      
      MotifMap ims;
@@ -21,20 +21,3 @@ Descriptions: resolves build failure with seqan 1.4
      if (talkative)
          fprintf(stderr, "Collecting potential splice sites in islands\n");
  
-@@ -2602,12 +2605,14 @@
- {
-   const Score<int> globalScore(0, -5, -1, -10);  // (match, mismatch, gapextend, gapopen)
-   Align<String<char> > align;
--  appendValue(rows(align), read);
-   
-+  resize(rows(align), 2);
-+  setSource(row(align, 0), const_cast<seqan::String<char> &>(read));
-+
-   String<char> genomicSequence;
-   assign(genomicSequence, leftReference);
-   append(genomicSequence, rightReference);
--  appendValue(rows(align), genomicSequence);
-+  setSource(row(align, 0), genomicSequence);
-   // int score = globalAlignment(align, globalScore);
- 
-   Row<Align<String<char> > >::Type& row0 = row(align, 0);
diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
index 87c44f8..d5a4c1f 100644
--- a/debian/patches/fix_includes_path.patch
+++ b/debian/patches/fix_includes_path.patch
@@ -1,5 +1,5 @@
 From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
-Date: 2012-01-05
+Date: Andreas Tille <tille at debian.org>  Sat, 04 Oct 2014 21:27:24 +0200
 Subject: Corrected location for samtools .h files 
 
 --- tophat.orig/src/align_status.h
@@ -8,7 +8,7 @@ Subject: Corrected location for samtools .h files
  #include <cassert>
  #include <cstring>
  #include <seqan/sequence.h>
--#include <bam/sam.h>
+-#include <sam.h>
 +#include <samtools/sam.h>
  #include "common.h"
  
@@ -19,8 +19,8 @@ Subject: Corrected location for samtools .h files
  #include <assert.h>
  #include <string>
  
--#include "bam/bam.h"
--#include "bam/sam.h"
+-#include "bam.h"
+-#include "sam.h"
 +#include "samtools/bam.h"
 +#include "samtools/sam.h"
  
@@ -32,7 +32,7 @@ Subject: Corrected location for samtools .h files
  #include <algorithm>
  #include <seqan/sequence.h>
  
--#include <bam/sam.h>
+-#include <sam.h>
 +#include <samtools/sam.h>
  using namespace std;
  
@@ -43,8 +43,8 @@ Subject: Corrected location for samtools .h files
  #include <cstdio>
  #include <string>
  #include <vector>
--#include "bam/bam.h"
--#include "bam/sam.h"
+-#include "bam.h"
+-#include "sam.h"
 +#include "samtools/bam.h"
 +#include "samtools/sam.h"
  
@@ -56,32 +56,21 @@ Subject: Corrected location for samtools .h files
  #include <sstream>
  #include <vector>
  
--#include <bam/bam.h>
--#include <bam/sam.h>
+-#include <bam.h>
+-#include <sam.h>
 +#include <samtools/bam.h>
 +#include <samtools/sam.h>
  
  #include <seqan/sequence.h>
  
---- tophat.orig/ax_bam.m4
-+++ tophat/ax_bam.m4
-@@ -102,7 +102,7 @@
- 
- 	AC_LANG_PUSH(C++)
-      	AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[
--	@%:@include <bam/bam.h>
-+	@%:@include <samtools/bam.h>
- 	]], [[
- 	]])],[
-         AC_MSG_RESULT(yes)
 --- tophat.orig/configure.ac
 +++ tophat/configure.ac
-@@ -93,7 +93,7 @@
+@@ -107,7 +107,7 @@
  	  
  CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
  CXXFLAGS="$CFLAGS"
 -CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS -I./SeqAn-1.3"
 +CXXFLAGS="$CXXFLAGS $BOOST_CPPFLAGS $BAM_CPPFLAGS"
- LDFLAGS="$user_LDFLAGS"
+ LDFLAGS="$BOOST_LDFLAGS $BAM_LDFLAGS $user_LDFLAGS"
  
  AM_INIT_AUTOMAKE([-Wall foreign tar-pax foreign])

-- 
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