[med-svn] [soapdenovo2] 07/08: Refresh patches
Andreas Tille
tille at debian.org
Sun Dec 4 17:08:50 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository soapdenovo2.
commit 83349de319a95b6302d555616cb46d211d67814c
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 4 18:01:06 2016 +0100
Refresh patches
---
debian/patches/add_hardening | 12 ++++++------
debian/patches/fix_compilation | 4 ++--
debian/patches/fix_usage_name | 3 +--
debian/patches/reproducible | 10 +++++-----
debian/patches/use_debian_zlib | 42 +++++++++++++++++++++---------------------
debian/patches/use_libsam | 6 +++---
6 files changed, 38 insertions(+), 39 deletions(-)
diff --git a/debian/patches/add_hardening b/debian/patches/add_hardening
index e7c7d90..3b2d7eb 100644
--- a/debian/patches/add_hardening
+++ b/debian/patches/add_hardening
@@ -6,7 +6,7 @@ Author: Olivier Sallou <osallou at debian.org>
Last-Updated: 2013-02-09
--- a/standardPregraph/Makefile
+++ b/standardPregraph/Makefile
-@@ -12,7 +12,11 @@
+@@ -12,7 +12,11 @@ ifdef debug
CFLAGS= -O0 -g -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
else
CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
@@ -18,7 +18,7 @@ Last-Updated: 2013-02-09
DFLAGS=
OBJS= arc.o attachPEinfo.o bubble.o check.o compactEdge.o \
concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o \
-@@ -87,9 +91,10 @@
+@@ -87,9 +91,10 @@ envTest:
@test $(GCCVERSIONMAJOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;'
@test $(GCCVERSIONMINOR) == 1 || sh -c 'echo "GCC version lower than 4.4.0";false;'
@@ -33,7 +33,7 @@ Last-Updated: 2013-02-09
clean:
--- a/sparsePregraph/Makefile
+++ b/sparsePregraph/Makefile
-@@ -3,7 +3,11 @@
+@@ -3,7 +3,11 @@ ifdef debug
CFLAGS= -O0 -g -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
else
CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
@@ -45,7 +45,7 @@ Last-Updated: 2013-02-09
DFLAGS=
OBJS= build_graph.o build_edge.o multi_threads.o \
-@@ -74,7 +78,7 @@
+@@ -74,7 +78,7 @@ envTest:
pregraph_sparse: clean envTest $(OBJS)
@printf "Linking... \r"
@@ -56,7 +56,7 @@ Last-Updated: 2013-02-09
clean:
--- a/Makefile
+++ b/Makefile
-@@ -3,8 +3,13 @@
+@@ -3,8 +3,13 @@ ifdef debug
CFLAGS= -O0 -g -fomit-frame-pointer
else
CFLAGS= -O4 -fomit-frame-pointer
@@ -70,7 +70,7 @@ Last-Updated: 2013-02-09
SUBDIRS = sparsePregraph standardPregraph
PROG= SOAPdenovo-63mer SOAPdenovo-127mer
INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc -I/usr/include/x86_64-linux-gnu
-@@ -64,11 +69,11 @@
+@@ -64,11 +69,11 @@ else
SOAPdenovo-63mer:
@cd sparsePregraph;make 63mer=1;cd ..;
@cd standardPregraph;make 63mer=1;cd ..;
diff --git a/debian/patches/fix_compilation b/debian/patches/fix_compilation
index 1cce216..6a3499c 100644
--- a/debian/patches/fix_compilation
+++ b/debian/patches/fix_compilation
@@ -8,7 +8,7 @@ Author: Olivier Sallou <osallou at debian.org>
Last-Updated: 2013-08-05
--- a/sparsePregraph/pregraph_sparse.cpp
+++ b/sparsePregraph/pregraph_sparse.cpp
-@@ -32,6 +32,7 @@
+@@ -34,6 +34,7 @@
#include "seq_util.h"
#include "convert_soapdenovo.h"
@@ -29,7 +29,7 @@ Last-Updated: 2013-08-05
unsigned char threadID;
--- a/Makefile
+++ b/Makefile
-@@ -7,7 +7,7 @@
+@@ -7,7 +7,7 @@ endif
SUBDIRS = sparsePregraph standardPregraph
PROG= SOAPdenovo-63mer SOAPdenovo-127mer
diff --git a/debian/patches/fix_usage_name b/debian/patches/fix_usage_name
index b5d8640..8b89886 100644
--- a/debian/patches/fix_usage_name
+++ b/debian/patches/fix_usage_name
@@ -7,7 +7,7 @@ Author: Olivier Sallou <osallou at debian.org>
Last-Updated: 2013-02-09
--- a/standardPregraph/main.c
+++ b/standardPregraph/main.c
-@@ -104,7 +104,7 @@
+@@ -104,7 +104,7 @@ int main ( int argc, char ** argv )
static void display_usage ()
{
@@ -16,4 +16,3 @@ Last-Updated: 2013-02-09
fprintf ( stderr, " pregraph construct kmer-graph\n" );
fprintf ( stderr, " sparse_pregraph construct sparse kmer-graph\n");
fprintf ( stderr, " contig eliminate errors and output contigs\n" );
-
diff --git a/debian/patches/reproducible b/debian/patches/reproducible
index 211dad3..1bd699a 100644
--- a/debian/patches/reproducible
+++ b/debian/patches/reproducible
@@ -4,7 +4,7 @@ Description: Enable reproducible build
--- a/sparsePregraph/Makefile
+++ b/sparsePregraph/Makefile
-@@ -6,6 +6,7 @@
+@@ -6,6 +6,7 @@ CFLAGS= -O4 -fomit-frame-pointer
CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
CFLAGS+=$(HARDENING_CFLAGS)
endif
@@ -14,7 +14,7 @@ Description: Enable reproducible build
--- a/sparsePregraph/main.cpp
+++ b/sparsePregraph/main.cpp
-@@ -5,7 +5,7 @@
+@@ -5,7 +5,7 @@ extern "C" int call_pregraph_sparse ( in
int main ( int argc, char ** argv )
{
@@ -25,7 +25,7 @@ Description: Enable reproducible build
--- a/sparsePregraph/pregraph_sparse.cpp
+++ b/sparsePregraph/pregraph_sparse.cpp
-@@ -45,7 +45,7 @@
+@@ -47,7 +47,7 @@ static void display_pregraph_usage();
/*
int main ( int argc, char ** argv )
{
@@ -36,7 +36,7 @@ Description: Enable reproducible build
--- a/standardPregraph/Makefile
+++ b/standardPregraph/Makefile
-@@ -34,6 +34,7 @@
+@@ -34,6 +34,7 @@ SUBDIRS= .
LIBPATH= -L/lib64 -L/usr/lib64 -L./inc
LIBS= -pthread -lz -lm
EXTRA_FLAGS=
@@ -46,7 +46,7 @@ Description: Enable reproducible build
ifeq (,$(findstring $(shell uname -m), x86_64 ppc64 ia64))
--- a/standardPregraph/main.c
+++ b/standardPregraph/main.c
-@@ -59,7 +59,7 @@
+@@ -59,7 +59,7 @@ Return:
int main ( int argc, char ** argv )
{
crc32c_Init();
diff --git a/debian/patches/use_debian_zlib b/debian/patches/use_debian_zlib
index 2fec460..e1b6f54 100644
--- a/debian/patches/use_debian_zlib
+++ b/debian/patches/use_debian_zlib
@@ -8,7 +8,7 @@ Last-Updated: 2013-08-05
Forwaded: no
--- a/standardPregraph/prlRead2Ctg.c
+++ b/standardPregraph/prlRead2Ctg.c
-@@ -424,7 +424,7 @@
+@@ -424,7 +424,7 @@ static void locate1read ( int t )
}
}
@@ -17,7 +17,7 @@ Forwaded: no
{
int len = lenBuffer[t];
int index;
-@@ -500,7 +500,7 @@
+@@ -500,7 +500,7 @@ static void output1Nread ( int t, FILE *
fprintf ( outfp, "\n" );
}
@@ -26,7 +26,7 @@ Forwaded: no
{
int len1, len2, index;
char orien1, orien2;
-@@ -560,7 +560,7 @@
+@@ -560,7 +560,7 @@ static void getPEreadOnContig(int t,FILE
}
}*/
@@ -35,7 +35,7 @@ Forwaded: no
{
int read1, read2;
char orientation;
-@@ -618,7 +618,7 @@
+@@ -618,7 +618,7 @@ static void recordLongRead ( FILE * outf
}
}
@@ -44,7 +44,7 @@ Forwaded: no
{
int t, ctgId;
boolean rd1gap, rd2gap;
-@@ -773,7 +773,7 @@
+@@ -773,7 +773,7 @@ void prlRead2Ctg ( char * libfile, char
long long i;
char * src_name, *next_name, name[256];
FILE * fo2;
@@ -55,7 +55,7 @@ Forwaded: no
pthread_t threads[thrd_num];
--- a/standardPregraph/prlReadFillGap.c
+++ b/standardPregraph/prlReadFillGap.c
-@@ -104,7 +104,7 @@
+@@ -104,7 +104,7 @@ static void convertIndex ()
free ( ( void * ) length_array );
}
@@ -64,7 +64,7 @@ Forwaded: no
{
long long readCounter = 0;
-@@ -206,7 +206,7 @@
+@@ -206,7 +206,7 @@ static long long getRead1by1 ( FILE * fp
static boolean loadReads4gap ( char * graphfile )
{
FILE * fp1, *fp2;
@@ -75,7 +75,7 @@ Forwaded: no
--- a/standardPregraph/output_pregraph.c
+++ b/standardPregraph/output_pregraph.c
-@@ -85,7 +85,7 @@
+@@ -85,7 +85,7 @@ void output_vertex ( char * outfile )
fclose ( fp );
}
@@ -86,7 +86,7 @@ Forwaded: no
gzprintf ( fp, ">length %d,", edge->length );
--- a/standardPregraph/orderContig.c
+++ b/standardPregraph/orderContig.c
-@@ -5072,7 +5072,7 @@
+@@ -5072,7 +5072,7 @@ void PE2Links ( char * infile )
char name[256], *line;
FILE * fp1;
FILE * linkF;
@@ -97,7 +97,7 @@ Forwaded: no
unsigned int j;
--- a/standardPregraph/node2edge.c
+++ b/standardPregraph/node2edge.c
-@@ -37,8 +37,8 @@
+@@ -37,8 +37,8 @@ static int edge_c, edgeCounter;
static preEDGE temp_edge; // for temp use in merge_V2()
static char edge_seq[100000]; //use this static 'edge_seq ' as an temp seq in merge_V2() for speed ..
@@ -108,7 +108,7 @@ Forwaded: no
static int check_iden_kmerList ( STACK * stack1, STACK * stack2 );
//for stack
-@@ -60,7 +60,7 @@
+@@ -60,7 +60,7 @@ Return:
*************************************************/
void kmer2edges ( char * outfile )
{
@@ -117,7 +117,7 @@ Forwaded: no
char temp[256];
sprintf ( temp, "%s.edge.gz", outfile );
fp = gzopen ( temp, "w" );
-@@ -234,7 +234,7 @@
+@@ -234,7 +234,7 @@ Output:
Return:
0.
*************************************************/
@@ -126,7 +126,7 @@ Forwaded: no
{
int node_c, palindrome;
unsigned char flag;
-@@ -363,7 +363,7 @@
+@@ -363,7 +363,7 @@ Output:
Return:
None.
*************************************************/
@@ -135,7 +135,7 @@ Forwaded: no
{
int i = 0;
kmer_t * node1;
-@@ -427,7 +427,7 @@
+@@ -427,7 +427,7 @@ Output:
Return:
None.
*************************************************/
@@ -146,7 +146,7 @@ Forwaded: no
preEDGE * newedge;
--- a/standardPregraph/loadPreGraph.c
+++ b/standardPregraph/loadPreGraph.c
-@@ -449,7 +449,7 @@
+@@ -449,7 +449,7 @@ void loadEdge ( char * graphfile )
{
char c, name[256], line[1024], str[32];
char * tightSeq = NULL;
@@ -157,7 +157,7 @@ Forwaded: no
int linelen;
--- a/standardPregraph/kmer.c
+++ b/standardPregraph/kmer.c
-@@ -483,7 +483,7 @@
+@@ -483,7 +483,7 @@ void print_kmer ( FILE * fp, Kmer kmer,
fprintf ( fp, "%c", c );
}
@@ -166,7 +166,7 @@ Forwaded: no
{
gzprintf ( fp, "%llx %llx %llx %llx", kmer.high1, kmer.low1, kmer.high2, kmer.low2 );
gzprintf ( fp, "%c", c );
-@@ -795,7 +795,7 @@
+@@ -795,7 +795,7 @@ void print_kmer ( FILE * fp, Kmer kmer,
fprintf ( fp, "%c", c );
}
@@ -177,7 +177,7 @@ Forwaded: no
gzprintf ( fp, "%c", c );
--- a/standardPregraph/attachPEinfo.c
+++ b/standardPregraph/attachPEinfo.c
-@@ -492,7 +492,7 @@
+@@ -492,7 +492,7 @@ int connectByPE_grad ( FILE * fp, int pe
Return:
Loaded alignment record number.
*************************************************/
@@ -188,7 +188,7 @@ Forwaded: no
int pre_pos, pos, flag, PE, count = 0, Total_PE = 0;
--- a/standardPregraph/inc/extfunc.h
+++ b/standardPregraph/inc/extfunc.h
-@@ -79,10 +79,10 @@
+@@ -79,10 +79,10 @@ extern void loadPEgrads ( char * infile
extern int putInsertS ( long long readid, int size, int * currGrads );
extern int getInsertS ( long long readid, int * readlen );
extern int connectByPE_grad ( FILE * fp, int peGrad, char * line );
@@ -203,7 +203,7 @@ Forwaded: no
extern void prlLoadPath ( char * graphfile );
--- a/standardPregraph/hashFunction.c
+++ b/standardPregraph/hashFunction.c
-@@ -82,7 +82,7 @@
+@@ -82,7 +82,7 @@ static int crc_table[256] =
};
typedef int ( *CRC32CFunctionPtr ) ( uint32_t, const char *, size_t );
@@ -212,7 +212,7 @@ Forwaded: no
static uint32_t cpuid ( uint32_t functionInput )
{
-@@ -145,11 +145,11 @@
+@@ -145,11 +145,11 @@ CRC32CFunctionPtr detectBestCRC32C()
ubyte8 hash_kmer ( Kmer kmer )
{
diff --git a/debian/patches/use_libsam b/debian/patches/use_libsam
index 43f075a..e2883b7 100644
--- a/debian/patches/use_libsam
+++ b/debian/patches/use_libsam
@@ -5,7 +5,7 @@ Last-Updated: 2013-08-05
Forwarded: no
--- a/sparsePregraph/Makefile
+++ b/sparsePregraph/Makefile
-@@ -10,7 +10,7 @@
+@@ -10,7 +10,7 @@ OBJS= build_graph.o build_edge.o multi_
build_preArc.o pregraph_sparse.o io_func.o\
global.o convert_soapdenovo.o
PROG=
@@ -16,7 +16,7 @@ Forwarded: no
LIBS= -pthread -lz -L./inc
--- a/sparsePregraph/inc/stdinc.h
+++ b/sparsePregraph/inc/stdinc.h
-@@ -39,4 +39,4 @@
+@@ -40,4 +40,4 @@ using namespace std;
@@ -24,7 +24,7 @@ Forwarded: no
+#include <stdbool.h>
--- a/standardPregraph/Makefile
+++ b/standardPregraph/Makefile
-@@ -25,7 +25,7 @@
+@@ -25,7 +25,7 @@ OBJS= arc.o attachPEinfo.o bubble.o che
readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \
cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o
PROG= SOAPdenovo-63mer
--
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