[med-svn] [rna-star] 06/07: Update patches
Andreas Tille
tille at debian.org
Thu May 19 16:16:38 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository rna-star.
commit cc4e99e3fce15c11fc9349be43fd22d751edc6b8
Author: Andreas Tille <tille at debian.org>
Date: Thu May 19 18:06:43 2016 +0200
Update patches
---
debian/patches/compilationstuff.patch | 31 ---------------------
debian/patches/donotuse_own_htslib.patch | 48 +++++++++++---------------------
debian/patches/mips_shm_noreserve.patch | 6 ++--
debian/patches/series | 1 -
4 files changed, 19 insertions(+), 67 deletions(-)
diff --git a/debian/patches/compilationstuff.patch b/debian/patches/compilationstuff.patch
deleted file mode 100644
index cbf80d4..0000000
--- a/debian/patches/compilationstuff.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-Author: Steffen Moeller <moeller at debian.org>,
-Last-Changed: Thu, 29 Jan 2015 14:18:44 +0100
-Description: Setting some compile options, fix some gcc errors
-
-Index: rna-star/source/Parameters.h
-===================================================================
---- rna-star.orig/source/Parameters.h
-+++ rna-star/source/Parameters.h
-@@ -61,7 +61,7 @@ class Parameters {
- int readFilesIndex;
- uint32 readFilesN;
- vector <string> readFilesIn, readFilesInTmp;
-- vector <vector <string>> readFilesNames;
-+ vector <vector <string> > readFilesNames;
- uint readNmates;
- string readMatesLengthsIn;
- vector <string> readFilesCommand;
-Index: rna-star/source/STAR.cpp
-===================================================================
---- rna-star.orig/source/STAR.cpp
-+++ rna-star/source/STAR.cpp
-@@ -386,7 +386,7 @@ int main(int argInN, char* argIn[]) {
- vector <string> bamBinNamesV;
- for (uint32 ibin=0; ibin<nBins; ibin++) {
-
-- bamBinNamesV.push_back(P->outBAMsortTmpDir+"/b"+to_string((uint) ibin));
-+ bamBinNamesV.push_back(P->outBAMsortTmpDir+"/b"+std::to_string((uint) ibin));
- struct stat buffer;
- if (stat (bamBinNamesV.back().c_str(), &buffer) != 0) {//check if file exists
- bamBinNamesV.pop_back();
-
diff --git a/debian/patches/donotuse_own_htslib.patch b/debian/patches/donotuse_own_htslib.patch
index f274ea7..2eeb604 100644
--- a/debian/patches/donotuse_own_htslib.patch
+++ b/debian/patches/donotuse_own_htslib.patch
@@ -2,10 +2,8 @@ Author: Steffen Moeller <moeller at debian.org>,
Last-Changed: Thu, 29 Jan 2015 14:18:44 +0100
Description: Use Debian packaged htslib
-Index: rna-star/source/Makefile
-===================================================================
---- rna-star.orig/source/Makefile
-+++ rna-star/source/Makefile
+--- a/source/Makefile
++++ b/source/Makefile
@@ -12,17 +12,17 @@ CXXFLAGSextra ?=
CXX ?= g++
@@ -77,10 +75,8 @@ Index: rna-star/source/Makefile
parametersDefault.xxd: parametersDefault
xxd -i parametersDefault > parametersDefault.xxd
-Index: rna-star/source/bamRemoveDuplicates.cpp
-===================================================================
---- rna-star.orig/source/bamRemoveDuplicates.cpp
-+++ rna-star/source/bamRemoveDuplicates.cpp
+--- a/source/bamRemoveDuplicates.cpp
++++ b/source/bamRemoveDuplicates.cpp
@@ -1,7 +1,7 @@
#include <unordered_map>
#include "bamRemoveDuplicates.h"
@@ -90,10 +86,8 @@ Index: rna-star/source/bamRemoveDuplicates.cpp
#include "IncludeDefine.h"
#include SAMTOOLS_BGZF_H
#include "ErrorWarning.h"
-Index: rna-star/source/bam_cat.c
-===================================================================
---- rna-star.orig/source/bam_cat.c
-+++ rna-star/source/bam_cat.c
+--- a/source/bam_cat.c
++++ b/source/bam_cat.c
@@ -52,8 +52,8 @@ THE SOFTWARE.
#include <stdlib.h>
#include <unistd.h>
@@ -105,10 +99,8 @@ Index: rna-star/source/bam_cat.c
#include <cstring>
#define BUF_SIZE 0x10000
-Index: rna-star/source/signalFromBAM.h
-===================================================================
---- rna-star.orig/source/signalFromBAM.h
-+++ rna-star/source/signalFromBAM.h
+--- a/source/signalFromBAM.h
++++ b/source/signalFromBAM.h
@@ -1,6 +1,6 @@
#ifndef CODE_signalFromBAM
#define CODE_signalFromBAM
@@ -117,10 +109,8 @@ Index: rna-star/source/signalFromBAM.h
#include <fstream>
#include <string>
#include "Stats.h"
-Index: rna-star/source/IncludeDefine.h
-===================================================================
---- rna-star.orig/source/IncludeDefine.h
-+++ rna-star/source/IncludeDefine.h
+--- a/source/IncludeDefine.h
++++ b/source/IncludeDefine.h
@@ -28,8 +28,8 @@
#define ERROR_OUT string ( __FILE__ ) +":"+ to_string ( (uint) __LINE__ ) +":"+ string ( __FUNCTION__ )
@@ -132,10 +122,8 @@ Index: rna-star/source/IncludeDefine.h
using namespace std;
-Index: rna-star/source/BAMfunctions.cpp
-===================================================================
---- rna-star.orig/source/BAMfunctions.cpp
-+++ rna-star/source/BAMfunctions.cpp
+--- a/source/BAMfunctions.cpp
++++ b/source/BAMfunctions.cpp
@@ -1,5 +1,5 @@
#include "BAMfunctions.h"
-#include "htslib/htslib/kstring.h"
@@ -143,10 +131,8 @@ Index: rna-star/source/BAMfunctions.cpp
string bam_cigarString (bam1_t *b) {//output CIGAR string
// kstring_t strK;
-Index: rna-star/source/STAR.cpp
-===================================================================
---- rna-star.orig/source/STAR.cpp
-+++ rna-star/source/STAR.cpp
+--- a/source/STAR.cpp
++++ b/source/STAR.cpp
@@ -26,7 +26,7 @@
#include "sjdbInsertJunctions.h"
#include "bam_cat.h"
@@ -156,10 +142,8 @@ Index: rna-star/source/STAR.cpp
#include "parametersDefault.xxd"
-Index: rna-star/source/bam_cat.h
-===================================================================
---- rna-star.orig/source/bam_cat.h
-+++ rna-star/source/bam_cat.h
+--- a/source/bam_cat.h
++++ b/source/bam_cat.h
@@ -1,7 +1,7 @@
#ifndef CODE_bam_cat
#define CODE_bam_cat
diff --git a/debian/patches/mips_shm_noreserve.patch b/debian/patches/mips_shm_noreserve.patch
index 30da5bf..36ae29b 100644
--- a/debian/patches/mips_shm_noreserve.patch
+++ b/debian/patches/mips_shm_noreserve.patch
@@ -5,8 +5,8 @@ Description: resolves build issue for mipsel, until this issue gets fixed in gli
--- a/source/IncludeDefine.h
+++ b/source/IncludeDefine.h
-@@ -38,6 +38,10 @@ using namespace std;
- #define SHM_NORESERVE 0
+@@ -42,6 +42,10 @@ using namespace std;
+ #define SHM_NORESERVE 010000
#endif
+#if defined(__mips__) && !defined(SHM_NORESERVE)
@@ -14,5 +14,5 @@ Description: resolves build issue for mipsel, until this issue gets fixed in gli
+#endif
+
typedef int8_t int8;
- typedef uint8_t uint8;
+ typedef uint8_t uint8;
diff --git a/debian/patches/series b/debian/patches/series
index 2d31638..4abc50b 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,2 @@
donotuse_own_htslib.patch
-compilationstuff.patch
mips_shm_noreserve.patch
--
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