[med-svn] [tophat] 04/06: Refresh and delete patches

[Alex Mestiashvili]

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malex-guest pushed a commit to branch master
in repository tophat.

commit 12a2deb539ff3a493383b2c6508a94e724e36309
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Mar 17 14:28:43 2016 +0100

    Refresh and delete patches
    
    Remove:
     -fix_build_w_seqan1.4.patch: Upstream switched to seqan-1.4
     -bashism_in_shell_script.patch: No file to patch in the new version
    Update and refresh fix_includes_path.patch
---
 debian/patches/bashism_in_shell_script.patch | 17 ----------------
 debian/patches/fix_build_w_seqan1.4.patch    | 23 ---------------------
 debian/patches/fix_includes_path.patch       | 30 ++++++++++++++--------------
 debian/patches/series                        |  2 --
 4 files changed, 15 insertions(+), 57 deletions(-)

diff --git a/debian/patches/bashism_in_shell_script.patch b/debian/patches/bashism_in_shell_script.patch
deleted file mode 100644
index 5943ca8..0000000
--- a/debian/patches/bashism_in_shell_script.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-Description: Remove bashism from shell script
-Bug-Closed: http://bugs.debian.org/671813
-Author: Andreas Tille <tille at debian.org>
---- a/src/tophat2.in
-+++ b/src/tophat2.in
-@@ -1,9 +1,9 @@
- #!/bin/bash
- prefix="__PREFIX__"
- pbin=""
--if [[ -z $prefix ]]; then
-+if [ "$prefix" = "" ]; then
-    fl=$(readlink $0)
--   if [[ -z $fl ]]; then
-+   if [ "$fl" = "" ]; then
-      pbin=$(dirname $0)
-    else
-      pbin=$(dirname $fl)
diff --git a/debian/patches/fix_build_w_seqan1.4.patch b/debian/patches/fix_build_w_seqan1.4.patch
deleted file mode 100644
index 7ab7c5a..0000000
--- a/debian/patches/fix_build_w_seqan1.4.patch
+++ /dev/null
@@ -1,23 +0,0 @@
-Description: Resolves build failure with seqan 1.4
-Bug-Closed: http://bugs.debian.org/733352
-Author: Manuel Holtgrewe <manuel.holtgrewe at fu-berlin.de>
---- a/src/segment_juncs.cpp
-+++ b/src/segment_juncs.cpp
-@@ -2050,10 +2050,13 @@ void juncs_from_ref_segs(RefSequenceTabl
-     typedef map<uint32_t, IntronMotifs> MotifMap;
-     
-     MotifMap ims;
--	
--    seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
--    seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
--    
-+
-+    typedef seqan::ModifiedString<
-+                    seqan::ModifiedString<seqan::DnaString const, seqan::ModView<seqan::FunctorComplement<seqan::Dna> > >,  
-+                    seqan::ModReverse>   ConstDnaStringReverseComplement;
-+    ConstDnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
-+    ConstDnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
-+     
-     if (talkative)
-         fprintf(stderr, "Collecting potential splice sites in islands\n");
- 
diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
index 94ec400..b4341f7 100644
--- a/debian/patches/fix_includes_path.patch
+++ b/debian/patches/fix_includes_path.patch
@@ -1,8 +1,8 @@
 Description: Fix_includes_path
 Subject: Corrected location for samtools .h files 
 From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
---- a/src/align_status.h
-+++ b/src/align_status.h
+--- tophat.orig/src/align_status.h
++++ tophat/src/align_status.h
 @@ -14,7 +14,7 @@
  #include <cassert>
  #include <cstring>
@@ -12,9 +12,9 @@ From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
  #include "common.h"
  
  #include "bwt_map.h"
---- a/src/bam2fastx.cpp
-+++ b/src/bam2fastx.cpp
-@@ -5,8 +5,8 @@
+--- tophat.orig/src/bam2fastx.cpp
++++ tophat/src/bam2fastx.cpp
+@@ -13,8 +13,8 @@
  #include <assert.h>
  #include <string>
  
@@ -25,8 +25,8 @@ From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
  
  using namespace std;
  
---- a/src/bwt_map.h
-+++ b/src/bwt_map.h
+--- tophat.orig/src/bwt_map.h
++++ tophat/src/bwt_map.h
 @@ -16,7 +16,7 @@
  #include <algorithm>
  #include <seqan/sequence.h>
@@ -36,8 +36,8 @@ From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
  using namespace std;
  
  #include "common.h"
---- a/src/common.h
-+++ b/src/common.h
+--- tophat.orig/src/common.h
++++ tophat/src/common.h
 @@ -16,8 +16,8 @@
  #include <cstdio>
  #include <string>
@@ -49,8 +49,8 @@ From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
  
  #define MAX_READ_LEN 1024
  
---- a/src/map2gtf.h
-+++ b/src/map2gtf.h
+--- tophat.orig/src/map2gtf.h
++++ tophat/src/map2gtf.h
 @@ -20,8 +20,8 @@
  #include <sstream>
  #include <vector>
@@ -62,13 +62,13 @@ From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
  
  #include <seqan/sequence.h>
  
---- a/configure.ac
-+++ b/configure.ac
-@@ -105,7 +105,7 @@ AS_IF([test "x$enable_debug" = xyes],
+--- tophat.orig/configure.ac
++++ tophat/configure.ac
+@@ -105,7 +105,7 @@
  	  
  CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
  CXXFLAGS="$CFLAGS"
--CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.3"
+-CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS -I./SeqAn-1.4.2"
 +CXXFLAGS="$CXXFLAGS $BAM_CPPFLAGS $BOOST_CPPFLAGS"
  LDFLAGS="$BAM_LDFLAGS $BOOST_LDFLAGS $user_LDFLAGS"
  
diff --git a/debian/patches/series b/debian/patches/series
index cb80a65..3f22e5f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,2 @@
-fix_build_w_seqan1.4.patch
 fix_includes_path.patch
-bashism_in_shell_script.patch
 hardening4samtools.patch

-- 
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