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commit 253c9f9caec55dd46eb9fca826f3e79f4c74177f Merge: ebdcf67 2da3aa4 Author: Olivier Sallou <[email protected]> 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 <[email protected]> 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 <[email protected]> Wed, 10 Apr 2013 17:27:22 +0200 + +soapdenovo2 (223-2) unstable; urgency=low + + * debian/copyright: + Update copyright years and content, + + -- Olivier Sallou <[email protected]> Sat, 09 Feb 2013 13:02:55 +0100 + +soapdenovo2 (223-1) unstable; urgency=low + + * Initial release (Closes: #700160) + + -- Olivier Sallou <[email protected]> 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 <[email protected]> +Uploaders: Olivier Sallou <[email protected]> - 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 <[email protected]> +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 <[email protected]> +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 <[email protected]> ++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 <[email protected]> +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/[email protected] ++Author: Olivier Sallou <[email protected]> ++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 <[email protected]> ++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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/soapdenovo2.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
