[med-svn] [tophat] 01/01: Commit Diane's patch

[Andreas Tille]

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tille pushed a commit to branch master
in repository tophat.

commit 27fe383b4b3c5f11bdc86bc2751c871f572bcef6
Author: Andreas Tille <tille at debian.org>
Date:   Fri Apr 11 23:46:18 2014 +0200

    Commit Diane's patch
---
 debian/patches/bashism_in_shell_script.patch |  4 ++--
 debian/patches/const_ness_part1.patch        | 22 ++++++++++++++++++++++
 debian/patches/fix_includes_path.patch       | 24 ++++++++++++------------
 debian/patches/series                        |  1 +
 4 files changed, 37 insertions(+), 14 deletions(-)

diff --git a/debian/patches/bashism_in_shell_script.patch b/debian/patches/bashism_in_shell_script.patch
index d93b0b8..602e1d8 100644
--- a/debian/patches/bashism_in_shell_script.patch
+++ b/debian/patches/bashism_in_shell_script.patch
@@ -2,8 +2,8 @@ Author: Andreas Tille <tille at debian.org>
 Bug-Closed: http://bugs.debian.org/671813
 Descriptions: Remove bashism from shell script
 
---- a/src/tophat2.in
-+++ b/src/tophat2.in
+--- tophat.orig/src/tophat2.in
++++ tophat/src/tophat2.in
 @@ -1,9 +1,9 @@
  #!/bin/bash
  prefix="__PREFIX__"
diff --git a/debian/patches/const_ness_part1.patch b/debian/patches/const_ness_part1.patch
new file mode 100644
index 0000000..6255c3c
--- /dev/null
+++ b/debian/patches/const_ness_part1.patch
@@ -0,0 +1,22 @@
+Author: Diane Trout <diane at ghic.org>
+Last-Update: Thu, 10 Apr 2014 15:29:38 -0700
+Description: The patch deals with one of the compile errors in Bug #733352.
+ I don't know if just hiding the const modifier is better than pushing
+ const-ness further into tophat.
+ .
+ Unfortunately the next const error I get is even worse. Const-ness seems to
+ get flipped between appendValue and trying to create a seqan::Gaps...
+
+--- tophat.orig/src/segment_juncs.cpp
++++ tophat/src/segment_juncs.cpp
+@@ -2056,8 +2056,8 @@
+     
+     MotifMap ims;
+ 	
+-    seqan::DnaStringReverseComplement rev_donor_dinuc(donor_dinuc);
+-    seqan::DnaStringReverseComplement rev_acceptor_dinuc(acceptor_dinuc);
++    seqan::DnaStringReverseComplement rev_donor_dinuc(const_cast<DnaString&>(donor_dinuc));
++    seqan::DnaStringReverseComplement rev_acceptor_dinuc(const_cast<DnaString&>(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 0fb35ff..337b5c2 100644
--- a/debian/patches/fix_includes_path.patch
+++ b/debian/patches/fix_includes_path.patch
@@ -2,8 +2,8 @@ From: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
 Date: 2012-01-05
 Subject: Corrected location for samtools .h files 
 
---- 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>
@@ -13,8 +13,8 @@ Subject: Corrected location for samtools .h files
  #include "common.h"
  
  #include "bwt_map.h"
---- a/src/bam2fastx.cpp
-+++ b/src/bam2fastx.cpp
+--- tophat.orig/src/bam2fastx.cpp
++++ tophat/src/bam2fastx.cpp
 @@ -5,8 +5,8 @@
  #include <assert.h>
  #include <string>
@@ -26,8 +26,8 @@ Subject: Corrected location for samtools .h files
  
  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>
@@ -37,8 +37,8 @@ Subject: Corrected location for samtools .h files
  using namespace std;
  
  #include "common.h"
---- a/src/common.h
-+++ b/src/common.h
+--- tophat.orig/src/common.h
++++ tophat/src/common.h
 @@ -15,8 +15,8 @@
  #include <cstdio>
  #include <string>
@@ -50,8 +50,8 @@ Subject: Corrected location for samtools .h files
  
  #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>
@@ -63,8 +63,8 @@ Subject: Corrected location for samtools .h files
  
  #include <seqan/sequence.h>
  
---- a/ax_bam.m4
-+++ b/ax_bam.m4
+--- tophat.orig/ax_bam.m4
++++ tophat/ax_bam.m4
 @@ -102,7 +102,7 @@
  
  	AC_LANG_PUSH(C++)
diff --git a/debian/patches/series b/debian/patches/series
index 18fe133..8b5c581 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 fix_includes_path.patch
 bashism_in_shell_script.patch
+const_ness_part1.patch

-- 
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