[med-svn] [soapdenovo2] 06/09: Imported Debian patch 240+dfsg-1
Sascha Steinbiss
sascha at steinbiss.name
Fri May 27 22:37:08 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository soapdenovo2.
commit 253c9f9caec55dd46eb9fca826f3e79f4c74177f
Merge: ebdcf67 2da3aa4
Author: Olivier Sallou <osallou at debian.org>
Date: Thu Jun 27 16:23:26 2013 +0200
Imported Debian patch 240+dfsg-1
INSTALL | 22 +
MANUAL | 36 +-
Makefile | 76 ++
VERSION | 1 +
debian/changelog | 6 +
debian/compat | 2 +-
debian/control | 9 +-
debian/copyright | 11 +
debian/install | 4 +-
debian/patches/add_hardening | 76 +-
debian/patches/fix_compilation | 40 ++
debian/patches/fix_usage_name | 9 +-
debian/patches/series | 3 +
debian/patches/use_debian_zlib | 228 ++++++
debian/patches/use_libsam | 42 ++
debian/rules | 8 +-
sparsePregraph/Makefile | 16 +-
sparsePregraph/build_graph.cpp | 6 +-
sparsePregraph/build_preArc.cpp | 10 +-
sparsePregraph/change.log | 24 +
sparsePregraph/global.cpp | 2 +-
sparsePregraph/inc/bam.h | 711 -------------------
sparsePregraph/inc/bgzf.h | 136 ----
sparsePregraph/inc/global.h | 2 +-
sparsePregraph/inc/sam.h | 100 ---
sparsePregraph/inc/spinLock.h | 40 --
sparsePregraph/inc/xcurses.h.gch | Bin 0 -> 3154808 bytes
sparsePregraph/inc/zconf.h | 332 ---------
sparsePregraph/inc/zlib.h | 1359 ------------------------------------
sparsePregraph/main.cpp | 11 +
sparsePregraph/multi_threads.cpp | 20 +-
sparsePregraph/pregraph_sparse.cpp | 55 +-
standardPregraph/INSTALL | 35 -
standardPregraph/Makefile | 18 +-
standardPregraph/VERSION | 1 -
standardPregraph/inc/bam.h | 711 -------------------
standardPregraph/inc/bgzf.h | 136 ----
standardPregraph/inc/def.h | 8 +
standardPregraph/inc/sam.h | 100 ---
standardPregraph/inc/zconf.h | 332 ---------
standardPregraph/inc/zlib.h | 1359 ------------------------------------
standardPregraph/iterate.c | 112 ++-
standardPregraph/main.c | 16 +-
standardPregraph/prlHashReads.c | 17 +-
standardPregraph/prlRead2path.c | 10 +-
standardPregraph/read2edge.c | 69 +-
standardPregraph/readseq1by1.c | 22 +-
update.log | 27 +
48 files changed, 880 insertions(+), 5490 deletions(-)
diff --cc debian/changelog
index 9ead6b8,0000000..ac7018f
mode 100644,000000..100644
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,23 -1,0 +1,29 @@@
++soapdenovo2 (240+dfsg-1) unstable; urgency=low
++
++ * New upstream release
++
++ -- Olivier Sallou <osallou at debian.org> Thu, 27 Jun 2013 16:23:26 +0200
++
+soapdenovo2 (223+dfsg-1) unstable; urgency=low
+
+ * debian/copyright:
+ remove .a files from upstream archive (Closes: #705139).
+ debian/patches:
+ update patches after lib removal
+ debian/control:
+ add bam and aio lib dependencies
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 10 Apr 2013 17:27:22 +0200
+
+soapdenovo2 (223-2) unstable; urgency=low
+
+ * debian/copyright:
+ Update copyright years and content,
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 09 Feb 2013 13:02:55 +0100
+
+soapdenovo2 (223-1) unstable; urgency=low
+
+ * Initial release (Closes: #700160)
+
+ -- Olivier Sallou <osallou at debian.org> Sat, 09 Feb 2013 10:40:45 +0100
diff --cc debian/compat
index 45a4fb7,0000000..ec63514
mode 100644,000000..100644
--- a/debian/compat
+++ b/debian/compat
@@@ -1,1 -1,0 +1,1 @@@
- 8
++9
diff --cc debian/control
index 03e0d6c,0000000..cc1e908
mode 100644,000000..100644
--- a/debian/control
+++ b/debian/control
@@@ -1,24 -1,0 +1,23 @@@
+Source: soapdenovo2
+Section: science
+Priority: optional
- Build-Depends: debhelper (>= 8), hardening-includes, zlib1g-dev, libbam-dev, libaio-dev
++Build-Depends: debhelper (>= 9), hardening-includes, zlib1g-dev, libbam-dev, libaio-dev
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
- DM-Upload-Allowed: yes
- Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/soap/soapdenovo2/trunk/
- Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/soap/soapdenovo2/
- Standards-Version: 3.9.3
++Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/soap/soapdenovo2/trunk/
++Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/soap/soapdenovo2/
++Standards-Version: 3.9.4
+Homepage: http://soap.genomics.org.cn/soapdenovo.html
+
+Package: soapdenovo2
+Architecture: any-amd64 any-ppc64 any-ia64
+#Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}, zlib1g
+Description: short-read assembly method to build de novo draft assembly
+ SOAPdenovo is a novel short-read assembly method that can build a de novo draft
+ assembly for the human-sized genomes. The program is specially designed to
+ assemble Illumina GA short reads.
+ .
+ It creates new opportunities for building reference
+ sequences and carrying out accurate analyses of unexplored genomes in a cost
+ effective way.
diff --cc debian/copyright
index 9d90db9,0000000..1f8ee66
mode 100644,000000..100644
--- a/debian/copyright
+++ b/debian/copyright
@@@ -1,87 -1,0 +1,98 @@@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: soapdenovo
+Source: http://soap.genomics.org.cn/soapdenovo.html
+Files-Excluded:
+ standardPregraph/*.a
++ standardPregraph/inc/sam.h
++ standardPregraph/inc/bam.h
++ standardPregraph/inc/bgzf.h
++ sparsePregraph/inc/sam.h
++ sparsePregraph/inc/bam.h
++ sparsePregraph/inc/bgzf.h
++ standardPregraph/inc/zlib.h
++ standardPregraph/inc/zconf.h
++ sparsePregraph/inc/zlib.h
++ sparsePregraph/inc/zconf.h
++ standardPregraph/inc/*.so
+ sparsePregraph/*.a
+
+Files: standardPregraph/inc/bam.h standardPregraph/inc/faidx.h sparsePregraph/inc/bam.h sparsePregraph/inc/faidx.h
+Copyright: 2008 Genome Research Ltd (GRL)
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+Files: standardPregraph/inc/faidx.h sparsePregraph/inc/faidx.h
+Copyright: 2008 Broad Institute / Massachusetts Institute of Technology
+License: MIT
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.
+
+
+Files: *
+Copyright: 2008-2012 BGI-Shenzhen
+License: GPL-3+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
+Files: debian/*
+Copyright: 2012 Olivier Sallou <osallou at debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
diff --cc debian/install
index 7d2fc41,0000000..8b68e12
mode 100644,000000..100644
--- a/debian/install
+++ b/debian/install
@@@ -1,2 -1,0 +1,2 @@@
- standardPregraph/SOAPdenovo-63mer usr/bin/
- standardPregraph/SOAPdenovo-127mer usr/bin/
++SOAPdenovo-63mer usr/bin/
++SOAPdenovo-127mer usr/bin/
diff --cc debian/patches/add_hardening
index 8b27d1d,0000000..e7c7d90
mode 100644,000000..100644
--- a/debian/patches/add_hardening
+++ b/debian/patches/add_hardening
@@@ -1,30 -1,0 +1,86 @@@
+Subject: add fortify flags
+Description: Makefile does not load CFLAGS
+ from env, add extra flags for debian fortify
+Forwarded: no
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-02-09
+--- a/standardPregraph/Makefile
++++ b/standardPregraph/Makefile
- @@ -8,7 +8,11 @@
- CC= gcc
- #GCCVERSIONMAJOR := $(shell expr `$(CC) -dumpversion | cut -f1 -d.` \>= 4)
- #GCCVERSIONMINOR := $(shell expr `$(CC) -dumpversion | cut -f2 -d.` \>= 4)
- -CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
- +CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2
- +CFLAGS += `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
++@@ -12,7 +12,11 @@
++ 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
+++CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
++CFLAGS+=$(HARDENING_CFLAGS)
- +LDFLAGS = `dpkg-buildflags --get LDFLAGS`
++ endif
+++LDFLAGS= `dpkg-buildflags --get LDFLAGS`
++LDFLAGS+=$(HARDENING_LDFLAGS)
+ DFLAGS=
+ OBJS= arc.o attachPEinfo.o bubble.o check.o compactEdge.o \
+ concatenateEdge.o connect.o contig.o cutTipPreGraph.o cutTip_graph.o \
- @@ -83,7 +87,7 @@
++@@ -87,9 +91,10 @@
++ @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;'
+
- SOAPdenovo: envTest $(OBJS)
++-SOAPdenovo: envTest $(OBJS)
+++#SOAPdenovo: envTest $(OBJS)
+++SOAPdenovo:
+ @printf "Linking... \r"
+- @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
++ @$(CC) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
+ @printf "$(PROG) compilation done.\n";
+
+ clean:
++--- a/sparsePregraph/Makefile
+++++ b/sparsePregraph/Makefile
++@@ -3,7 +3,11 @@
++ 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
+++CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
+++CFLAGS+=$(HARDENING_CFLAGS)
++ endif
+++LDFLAGS= `dpkg-buildflags --get LDFLAGS`
+++LDFLAGS+=$(HARDENING_LDFLAGS)
++
++ DFLAGS=
++ OBJS= build_graph.o build_edge.o multi_threads.o \
++@@ -74,7 +78,7 @@
++
++ pregraph_sparse: clean envTest $(OBJS)
++ @printf "Linking... \r"
++- #@$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
+++ #@$(CC) $(LDFLAGS) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS)
++ @printf "$(PROG) compilation done.\n";
++
++ clean:
++--- a/Makefile
+++++ b/Makefile
++@@ -3,8 +3,13 @@
++ CFLAGS= -O0 -g -fomit-frame-pointer
++ else
++ CFLAGS= -O4 -fomit-frame-pointer
+++CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS`
+++CFLAGS+=$(HARDENING_CFLAGS)
++ endif
++
+++LDFLAGS= `dpkg-buildflags --get LDFLAGS`
+++LDFLAGS+=$(HARDENING_LDFLAGS)
+++
++ 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 @@
++ SOAPdenovo-63mer:
++ @cd sparsePregraph;make 63mer=1;cd ..;
++ @cd standardPregraph;make 63mer=1;cd ..;
++- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
+++ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LDFLAGS) $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer
++ SOAPdenovo-127mer:
++ @cd sparsePregraph;make 127mer=1;cd ..;
++ @cd standardPregraph;make 127mer=1;cd ..;
++- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
+++ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LDFLAGS) $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer
++ clean:
++ @cd sparsePregraph;make clean;cd ..;
++ @cd standardPregraph;make clean;cd ..;
diff --cc debian/patches/fix_compilation
index 0000000,0000000..1cce216
new file mode 100644
--- /dev/null
+++ b/debian/patches/fix_compilation
@@@ -1,0 -1,0 +1,40 @@@
++Subject: Fails to compile, usleep unknown
++Description: code from upstream fails to compile.
++ An include is missing.
++ Mail has been sent upstream and question posted to
++ their google group but got no answer.
++Forwarded: no
++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 @@
++ #include "seq_util.h"
++ #include "convert_soapdenovo.h"
++
+++#include <unistd.h>
++
++ static int LOAD_GRAPH = 0, BUILD_DBG = 1, BUILD_EDGES = 1, BUILD_PREARCS = 1;
++ //static int run_mode=0;
++--- a/sparsePregraph/inc/multi_threads.h
+++++ b/sparsePregraph/inc/multi_threads.h
++@@ -24,6 +24,8 @@
++ #define _MULTI_THREADS_H
++ #include "stdinc.h"
++
+++#include <unistd.h>
+++
++ typedef struct parameter
++ {
++ unsigned char threadID;
++--- a/Makefile
+++++ b/Makefile
++@@ -7,7 +7,7 @@
++
++ SUBDIRS = sparsePregraph standardPregraph
++ PROG= SOAPdenovo-63mer SOAPdenovo-127mer
++-INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc
+++INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc -I/usr/include/x86_64-linux-gnu
++
++ LIBPATH= -L/lib64 -L/usr/lib64 -L./sparsePregraph/inc -L./standardPregraph/inc
++ LIBS= -pthread -lz -lm
diff --cc debian/patches/fix_usage_name
index fd20ec7,0000000..b5d8640
mode 100644,000000..100644
--- a/debian/patches/fix_usage_name
+++ b/debian/patches/fix_usage_name
@@@ -1,18 -1,0 +1,19 @@@
+Subject: update binary name
+Description: usage show SOAPdenovo binary name
+ while generated binaries are kmer dependent.
+ Debian modification to lowercase applied too.
+Forwarded: no
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-02-09
+--- a/standardPregraph/main.c
++++ b/standardPregraph/main.c
- @@ -99,7 +99,7 @@
++@@ -104,7 +104,7 @@
+
+ static void display_usage ()
+ {
+- fprintf ( stderr, "\nUsage: SOAPdenovo <command> [option]\n" );
++ fprintf ( stderr, "\nUsage: soapdenovo2-63mer/soapdenovo2-127mer <command> [option]\n" );
- fprintf ( stderr, " pregraph construct kmer-graph\n" );
- fprintf ( stderr, " contig eliminate errors and output contigs\n" );
- fprintf ( stderr, " map map reads to contigs\n" );
++ 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 --cc debian/patches/series
index 8666706,0000000..a2efd1d
mode 100644,000000..100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@@ -1,2 -1,0 +1,5 @@@
++use_libsam
++fix_compilation
+fix_usage_name
+add_hardening
++use_debian_zlib
diff --cc debian/patches/use_debian_zlib
index 0000000,0000000..2fec460
new file mode 100644
--- /dev/null
+++ b/debian/patches/use_debian_zlib
@@@ -1,0 -1,0 +1,228 @@@
++Subject: use Debian zlib library
++Description: Debian library is more recent than the one embedded upstream.
++ Its API changed and code needs to be updated to use this version.
++ See more info here:
++ http://www.postgresql.org/message-id/1329988571.6474.9.camel@vanquo.pezone.net
++Author: Olivier Sallou <osallou at debian.org>
++Last-Updated: 2013-08-05
++Forwaded: no
++--- a/standardPregraph/prlRead2Ctg.c
+++++ b/standardPregraph/prlRead2Ctg.c
++@@ -424,7 +424,7 @@
++ }
++ }
++
++-static void output1read_gz ( int t, gzFile * outfp, gzFile * outfp2, char orien, int dhflag )
+++static void output1read_gz ( int t, gzFile outfp, gzFile outfp2, char orien, int dhflag )
++ {
++ int len = lenBuffer[t];
++ int index;
++@@ -500,7 +500,7 @@
++ fprintf ( outfp, "\n" );
++ }
++
++-static void getPEreadOnContig ( int t, gzFile * outfp )
+++static void getPEreadOnContig ( int t, gzFile outfp )
++ {
++ int len1, len2, index;
++ char orien1, orien2;
++@@ -560,7 +560,7 @@
++ }
++ }*/
++
++-static void getReadIngap ( int t, int insSize, gzFile * outfp1, gzFile * outfp2, boolean readOne )
+++static void getReadIngap ( int t, int insSize, gzFile outfp1, gzFile outfp2, boolean readOne )
++ {
++ int read1, read2;
++ char orientation;
++@@ -618,7 +618,7 @@
++ }
++ }
++
++-static void recordAlldgn ( gzFile * outfp, int * insSizeArr, gzFile * outfp1, gzFile * outfp2, gzFile * outfp4 )
+++static void recordAlldgn ( gzFile outfp, int * insSizeArr, gzFile outfp1, gzFile outfp2, gzFile outfp4 )
++ {
++ int t, ctgId;
++ boolean rd1gap, rd2gap;
++@@ -773,7 +773,7 @@
++ long long i;
++ char * src_name, *next_name, name[256];
++ FILE * fo2;
++- gzFile * fo, *outfp1 = NULL, *outfp2 = NULL, *outfp3 = NULL, *outfp4 = NULL;
+++ gzFile fo, outfp1 = NULL, outfp2 = NULL, outfp3 = NULL, outfp4 = NULL;
++ int maxReadNum, libNo, prevLibNo, insSize = 0;
++ boolean flag, pairs = 1;
++ pthread_t threads[thrd_num];
++--- a/standardPregraph/prlReadFillGap.c
+++++ b/standardPregraph/prlReadFillGap.c
++@@ -104,7 +104,7 @@
++ free ( ( void * ) length_array );
++ }
++
++-static long long getRead1by1_gz ( gzFile * fp, DARRAY * readSeqInGap )
+++static long long getRead1by1_gz ( gzFile fp, DARRAY * readSeqInGap )
++ {
++ long long readCounter = 0;
++
++@@ -206,7 +206,7 @@
++ static boolean loadReads4gap ( char * graphfile )
++ {
++ FILE * fp1, *fp2;
++- gzFile * fp;
+++ gzFile fp;
++ char name[1024];
++ long long readCounter;
++
++--- a/standardPregraph/output_pregraph.c
+++++ b/standardPregraph/output_pregraph.c
++@@ -85,7 +85,7 @@
++ fclose ( fp );
++ }
++
++-void output_1edge ( preEDGE * edge, gzFile * fp )
+++void output_1edge ( preEDGE * edge, gzFile fp )
++ {
++ int i;
++ gzprintf ( fp, ">length %d,", edge->length );
++--- a/standardPregraph/orderContig.c
+++++ b/standardPregraph/orderContig.c
++@@ -5072,7 +5072,7 @@
++ char name[256], *line;
++ FILE * fp1;
++ FILE * linkF;
++- gzFile * fp2;
+++ gzFile fp2;
++ int i;
++ int flag = 0;
++ unsigned int j;
++--- a/standardPregraph/node2edge.c
+++++ b/standardPregraph/node2edge.c
++@@ -37,8 +37,8 @@
++ 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 ..
++
++-static void make_edge ( gzFile * fp );
++-static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, gzFile * fp );
+++static void make_edge ( gzFile fp );
+++static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, gzFile fp );
++ static int check_iden_kmerList ( STACK * stack1, STACK * stack2 );
++
++ //for stack
++@@ -60,7 +60,7 @@
++ *************************************************/
++ void kmer2edges ( char * outfile )
++ {
++- gzFile * fp;
+++ gzFile fp;
++ char temp[256];
++ sprintf ( temp, "%s.edge.gz", outfile );
++ fp = gzopen ( temp, "w" );
++@@ -234,7 +234,7 @@
++ Return:
++ 0.
++ *************************************************/
++-static int startEdgeFromNode ( kmer_t * node1, gzFile * fp )
+++static int startEdgeFromNode ( kmer_t * node1, gzFile fp )
++ {
++ int node_c, palindrome;
++ unsigned char flag;
++@@ -363,7 +363,7 @@
++ Return:
++ None.
++ *************************************************/
++-void make_edge ( gzFile * fp )
+++void make_edge ( gzFile fp )
++ {
++ int i = 0;
++ kmer_t * node1;
++@@ -427,7 +427,7 @@
++ Return:
++ None.
++ *************************************************/
++-static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, gzFile * fp )
+++static void merge_linearV2 ( char bal_edge, STACK * nStack, int count, gzFile fp )
++ {
++ int length, char_index;
++ preEDGE * newedge;
++--- a/standardPregraph/loadPreGraph.c
+++++ b/standardPregraph/loadPreGraph.c
++@@ -449,7 +449,7 @@
++ {
++ char c, name[256], line[1024], str[32];
++ char * tightSeq = NULL;
++- gzFile * fp;
+++ gzFile fp;
++ Kmer from_kmer, to_kmer;
++ int n = 0, i, length, cvg, index = -1, bal_ed, edgeno;
++ int linelen;
++--- a/standardPregraph/kmer.c
+++++ b/standardPregraph/kmer.c
++@@ -483,7 +483,7 @@
++ fprintf ( fp, "%c", c );
++ }
++
++-void print_kmer_gz ( gzFile * fp, Kmer kmer, char c )
+++void print_kmer_gz ( gzFile fp, Kmer kmer, char c )
++ {
++ gzprintf ( fp, "%llx %llx %llx %llx", kmer.high1, kmer.low1, kmer.high2, kmer.low2 );
++ gzprintf ( fp, "%c", c );
++@@ -795,7 +795,7 @@
++ fprintf ( fp, "%c", c );
++ }
++
++-void print_kmer_gz ( gzFile * fp, Kmer kmer, char c )
+++void print_kmer_gz ( gzFile fp, Kmer kmer, char c )
++ {
++ gzprintf ( fp, "%llx %llx", kmer.high, kmer.low );
++ gzprintf ( fp, "%c", c );
++--- a/standardPregraph/attachPEinfo.c
+++++ b/standardPregraph/attachPEinfo.c
++@@ -492,7 +492,7 @@
++ Return:
++ Loaded alignment record number.
++ *************************************************/
++-int connectByPE_grad_gz ( gzFile * fp, int peGrad, char * line )
+++int connectByPE_grad_gz ( gzFile fp, int peGrad, char * line )
++ {
++ long long pre_readno, readno, minno, maxno;
++ 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 @@
++ 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 );
++-extern int connectByPE_grad_gz ( gzFile * fp, int peGrad, char * line );
+++extern int connectByPE_grad_gz ( gzFile fp, int peGrad, char * line );
++ extern void PEgradsScaf ( char * infile );
++ extern void reorderAnnotation ( char * infile, char * outfile );
++-extern void output_1edge ( preEDGE * edge, gzFile * fp );
+++extern void output_1edge ( preEDGE * edge, gzFile fp );
++ extern void prlRead2edge ( char * libfile, char * outfile );
++ extern void annotFileTrans ( char * infile, char * outfile );
++ extern void prlLoadPath ( char * graphfile );
++--- a/standardPregraph/hashFunction.c
+++++ b/standardPregraph/hashFunction.c
++@@ -82,7 +82,7 @@
++ };
++
++ typedef int ( *CRC32CFunctionPtr ) ( uint32_t, const char *, size_t );
++-static CRC32CFunctionPtr crc32;
+++static CRC32CFunctionPtr s_crc32;
++
++ static uint32_t cpuid ( uint32_t functionInput )
++ {
++@@ -145,11 +145,11 @@
++
++ ubyte8 hash_kmer ( Kmer kmer )
++ {
++- return ( crc32 ( 0, ( char * ) &kmer, sizeof ( Kmer ) ) );
+++ return ( s_crc32 ( 0, ( char * ) &kmer, sizeof ( Kmer ) ) );
++ }
++
++ void crc32c_Init()
++ {
++- crc32 = detectBestCRC32C();
+++ s_crc32 = detectBestCRC32C();
++ }
++
diff --cc debian/patches/use_libsam
index 0000000,0000000..43f075a
new file mode 100644
--- /dev/null
+++ b/debian/patches/use_libsam
@@@ -1,0 -1,0 +1,42 @@@
++Subject: upstream copies libsam headers
++Description: use Debian libraries instead of embedded headers
++Author: Olivier Sallou <osallou at debian.org>
++Last-Updated: 2013-08-05
++Forwarded: no
++--- a/sparsePregraph/Makefile
+++++ b/sparsePregraph/Makefile
++@@ -10,7 +10,7 @@
++ build_preArc.o pregraph_sparse.o io_func.o\
++ global.o convert_soapdenovo.o
++ PROG=
++-INCLUDES= -I./inc
+++INCLUDES= -I./inc -I/usr/include/samtools
++ SUBDIRS= .
++ LIBPATH= -L/usr/lib64
++ LIBS= -pthread -lz -L./inc
++--- a/sparsePregraph/inc/stdinc.h
+++++ b/sparsePregraph/inc/stdinc.h
++@@ -39,4 +39,4 @@
++
++
++
++-
+++#include <stdbool.h>
++--- a/standardPregraph/Makefile
+++++ b/standardPregraph/Makefile
++@@ -25,7 +25,7 @@
++ readseq1by1.o scaffold.o searchPath.o seq.o splitReps.o \
++ cutTip_graph2.o linearEdge.o kmerhash.o read2edge.o iterate.o
++ PROG= SOAPdenovo-63mer
++-INCLUDES= -Iinc
+++INCLUDES= -Iinc -I/usr/include/samtools
++ SUBDIRS= .
++ LIBPATH= -L/lib64 -L/usr/lib64 -L./inc
++ LIBS= -pthread -lz -lm
++--- a/standardPregraph/inc/stdinc.h
+++++ b/standardPregraph/inc/stdinc.h
++@@ -32,3 +32,4 @@
++ #include "types.h"
++ #include <aio.h>
++ #include <errno.h>
+++#include <stdbool.h>
diff --cc debian/rules
index 0478a1a,0000000..bc351d6
mode 100755,000000..100755
--- a/debian/rules
+++ b/debian/rules
@@@ -1,34 -1,0 +1,34 @@@
+#!/usr/bin/make -f
+# -*- makefile -*-
+export DEB_BUILD_HARDENING=1
+export DEB_BUILD_HARDENING_FORTIFY=1
+
+include /usr/share/hardening-includes/hardening.make
+
+CFLAGS=$(shell dpkg-buildflags --get CFLAGS)
+LDFLAGS=$(shell dpkg-buildflags --get LDFLAGS)
+CFLAGS+=$(HARDENING_CFLAGS)
+CXXFLAGS+=$(HARDENING_CXXFLAGS)
+LDFLAGS+=$(HARDENING_LDFLAGS)
+
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+%:
+ dh $@
+
- override_dh_auto_build:
- cd standardPregraph && make 63mer=1
- cd standardPregraph && make 127mer=1
++#override_dh_auto_build:
++# cd standardPregraph && make 63mer=1
++# cd standardPregraph && make 127mer=1
+# cd sparsePregraph && make
- dh_auto_build
++# dh_auto_build
+
+override_dh_install:
+ dh_install
+ cd debian/soapdenovo2/usr/bin/;rename 's/SOAPdenovo/soapdenovo2/' SOAP*
+
+override_dh_clean:
+ cd standardPregraph && make 63mer=1 clean && make 127mer=1 clean
+ cd sparsePregraph && make clean
+ dh_clean
--
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