[med-svn] [tophat] 04/04: New upstream version

Mon Jul 20 09:28:16 UTC 2015

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tille pushed a commit to branch master
in repository tophat.

commit 7f849394b182bc4b7925f62f40f68253c72f5bf6
Author: Andreas Tille <tille at debian.org>
Date:   Sat Jul 18 17:42:34 2015 +0200

    New upstream version
---
 debian/changelog                             |  6 ++++++
 debian/patches/bashism_in_shell_script.patch |  4 ++--
 debian/patches/fix_build_w_seqan1.4.patch    |  6 +++---
 debian/patches/fix_includes_path.patch       | 28 ++++++++++++++--------------
 debian/patches/hardening4samtools.patch      |  6 +++---
 5 files changed, 28 insertions(+), 22 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index c52f9ac..2002ae9 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+tophat (2.1.0+dfsg-1) UNRELEASED; urgency=medium
+
+  * New upstream version
+
+ -- Andreas Tille <tille at debian.org>  Sat, 18 Jul 2015 17:42:10 +0200
+
 tophat (2.0.14+dfsg-1) unstable; urgency=medium
 
   * Imported Upstream version 2.0.14+dfsg
diff --git a/debian/patches/bashism_in_shell_script.patch b/debian/patches/bashism_in_shell_script.patch
index 268dd08..5943ca8 100644
--- a/debian/patches/bashism_in_shell_script.patch
+++ b/debian/patches/bashism_in_shell_script.patch
@@ -1,8 +1,8 @@
 Description: Remove bashism from shell script
 Bug-Closed: http://bugs.debian.org/671813
 Author: Andreas Tille <tille at debian.org>
---- tophat.orig/src/tophat2.in
-+++ tophat/src/tophat2.in
+--- a/src/tophat2.in
++++ b/src/tophat2.in
 @@ -1,9 +1,9 @@
  #!/bin/bash
  prefix="__PREFIX__"
diff --git a/debian/patches/fix_build_w_seqan1.4.patch b/debian/patches/fix_build_w_seqan1.4.patch
index f767aae..7ab7c5a 100644
--- a/debian/patches/fix_build_w_seqan1.4.patch
+++ b/debian/patches/fix_build_w_seqan1.4.patch
@@ -1,9 +1,9 @@
 Description: Resolves build failure with seqan 1.4
 Bug-Closed: http://bugs.debian.org/733352
 Author: Manuel Holtgrewe <manuel.holtgrewe at fu-berlin.de>
---- tophat.orig/src/segment_juncs.cpp
-+++ tophat/src/segment_juncs.cpp
-@@ -2050,10 +2050,13 @@
+--- 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;
diff --git a/debian/patches/fix_includes_path.patch b/debian/patches/fix_includes_path.patch
index 734c572..94ec400 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>
---- tophat.orig/src/align_status.h
-+++ tophat/src/align_status.h
+--- a/src/align_status.h
++++ b/src/align_status.h
 @@ -14,7 +14,7 @@
  #include <cassert>
  #include <cstring>
@@ -12,8 +12,8 @@ From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
  #include "common.h"
  
  #include "bwt_map.h"
---- tophat.orig/src/bam2fastx.cpp
-+++ tophat/src/bam2fastx.cpp
+--- a/src/bam2fastx.cpp
++++ b/src/bam2fastx.cpp
 @@ -5,8 +5,8 @@
  #include <assert.h>
  #include <string>
@@ -25,8 +25,8 @@ From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
  
  using namespace std;
  
---- tophat.orig/src/bwt_map.h
-+++ tophat/src/bwt_map.h
+--- a/src/bwt_map.h
++++ b/src/bwt_map.h
 @@ -16,7 +16,7 @@
  #include <algorithm>
  #include <seqan/sequence.h>
@@ -36,9 +36,9 @@ From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
  using namespace std;
  
  #include "common.h"
---- tophat.orig/src/common.h
-+++ tophat/src/common.h
-@@ -15,8 +15,8 @@
+--- a/src/common.h
++++ b/src/common.h
+@@ -16,8 +16,8 @@
  #include <cstdio>
  #include <string>
  #include <vector>
@@ -49,8 +49,8 @@ From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
  
  #define MAX_READ_LEN 1024
  
---- tophat.orig/src/map2gtf.h
-+++ tophat/src/map2gtf.h
+--- a/src/map2gtf.h
++++ b/src/map2gtf.h
 @@ -20,8 +20,8 @@
  #include <sstream>
  #include <vector>
@@ -62,9 +62,9 @@ From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
  
  #include <seqan/sequence.h>
  
---- tophat.orig/configure.ac
-+++ tophat/configure.ac
-@@ -105,7 +105,7 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -105,7 +105,7 @@ AS_IF([test "x$enable_debug" = xyes],
  	  
  CFLAGS="${generic_CFLAGS} ${ext_CFLAGS} ${user_CFLAGS} ${debug_CFLAGS}"
  CXXFLAGS="$CFLAGS"
diff --git a/debian/patches/hardening4samtools.patch b/debian/patches/hardening4samtools.patch
index cf37497..ea04e09 100644
--- a/debian/patches/hardening4samtools.patch
+++ b/debian/patches/hardening4samtools.patch
@@ -1,8 +1,8 @@
 Description: Hardening for samtools
 Subject: add hardening flags to embedded copy of samtools
 Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
---- tophat.orig/src/samtools-0.1.18/Makefile
-+++ tophat/src/samtools-0.1.18/Makefile
+--- a/src/samtools-0.1.18/Makefile
++++ b/src/samtools-0.1.18/Makefile
 @@ -1,5 +1,7 @@
  CC=			gcc
 -CFLAGS=		-g -Wall -O2 #-m64 #-arch ppc
@@ -12,7 +12,7 @@ Author: Alex Mestiashvili <alex at biotec.tu-dresden.de>
  DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
  KNETFILE_O=	knetfile.o
  LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
-@@ -41,7 +43,7 @@
+@@ -41,7 +43,7 @@ libbam.a:$(LOBJS)
  		$(AR) -csru $@ $(LOBJS)
  
  samtools_0.1.18:lib-recur $(AOBJS)

-- 
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