This is an automated email from the git hooks/post-receive script. tille pushed a commit to branch master in repository soapdenovo2.
commit b6f362e9fe01e5c8a86fbaa64cc36924289a1ff2 Author: Andreas Tille <[email protected]> Date: Wed Sep 6 10:50:03 2017 +0200 New upstream version --- debian/changelog | 3 +- debian/patches/add_hardening | 65 +++++---- debian/patches/fix_compilation | 8 +- debian/patches/fix_usage_name | 12 +- debian/patches/reproducible | 22 +-- debian/patches/use_debian_zlib | 324 ++++++++++++++++++++--------------------- 6 files changed, 222 insertions(+), 212 deletions(-) diff --git a/debian/changelog b/debian/changelog index 9a6d059..fb575f2 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,5 +1,6 @@ -soapdenovo2 (240+dfsg1-3) UNRELEASED; urgency=medium +soapdenovo2 (241+dfsg-1) UNRELEASED; urgency=medium + * New upstream version * Fix watch file -- Andreas Tille <[email protected]> Fri, 16 Dec 2016 22:32:26 +0100 diff --git a/debian/patches/add_hardening b/debian/patches/add_hardening index 3b2d7eb..b7f6a84 100644 --- a/debian/patches/add_hardening +++ b/debian/patches/add_hardening @@ -7,9 +7,9 @@ Last-Updated: 2013-02-09 --- a/standardPregraph/Makefile +++ b/standardPregraph/Makefile @@ -12,7 +12,11 @@ ifdef debug - CFLAGS= -O0 -g -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 + CFLAGS= -O0 -g -fomit-frame-pointer #-msse4.2 else - CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 + CFLAGS= -O3 -fomit-frame-pointer -w #-msse4.2 +CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS` +CFLAGS+=$(HARDENING_CFLAGS) endif @@ -18,25 +18,25 @@ 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 @@ envTest: +@@ -77,9 +81,10 @@ 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;' -SOAPdenovo: envTest $(OBJS) +#SOAPdenovo: envTest $(OBJS) +SOAPdenovo: - @printf "Linking... \r" + @printf "Linking... \r" - @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) -+ @$(CC) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) - @printf "$(PROG) compilation done.\n"; ++ @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) $(LDFLAGS) + @printf "$(PROG) compilation done. \n" clean: --- a/sparsePregraph/Makefile +++ b/sparsePregraph/Makefile @@ -3,7 +3,11 @@ ifdef debug - CFLAGS= -O0 -g -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 + CFLAGS= -O0 -g -fomit-frame-pointer else - CFLAGS= -O4 -fomit-frame-pointer #-static #-mcrc32 -march=core2 -msse4.1 -msse4.2 + CFLAGS= -O3 -fomit-frame-pointer -w +CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS` +CFLAGS+=$(HARDENING_CFLAGS) endif @@ -45,42 +45,51 @@ Last-Updated: 2013-02-09 DFLAGS= OBJS= build_graph.o build_edge.o multi_threads.o \ -@@ -74,7 +78,7 @@ envTest: +@@ -66,7 +70,7 @@ envTest: - 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"; + pregraph_sparse: clean envTest $(OBJS) + @printf "Linking... \r" +- @$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) ++ @$(CC) $(CFLAGS)$(INCLUDES) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) $(LDFLAGS) + @printf "$(PROG) compilation done. \n" clean: --- a/Makefile +++ b/Makefile -@@ -3,8 +3,13 @@ ifdef debug +@@ -4,7 +4,11 @@ ifdef debug CFLAGS= -O0 -g -fomit-frame-pointer else - CFLAGS= -O4 -fomit-frame-pointer -+CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS` -+CFLAGS+=$(HARDENING_CFLAGS) + CFLAGS= -O3 -fomit-frame-pointer +++CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS` +++CFLAGS+=$(HARDENING_CFLAGS) endif - +LDFLAGS= `dpkg-buildflags --get LDFLAGS` +LDFLAGS+=$(HARDENING_LDFLAGS) -+ - SUBDIRS = sparsePregraph standardPregraph - PROG= SOAPdenovo-63mer SOAPdenovo-127mer - INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc -I/usr/include/x86_64-linux-gnu -@@ -64,11 +69,11 @@ else + + SUBDIRS = sparsePregraph standardPregraph fusion + PROG= SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion +@@ -46,20 +50,20 @@ ifdef debug + SOAPdenovo-63mer: + @cd sparsePregraph;make 63mer=1 debug=1;cd ..; + @cd standardPregraph;make 63mer=1 debug=1;cd ..; +- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer ++ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer $(LDFLAGS) + SOAPdenovo-127mer: + @cd sparsePregraph;make 127mer=1 debug=1;cd ..; + @cd standardPregraph;make 127mer=1 debug=1;cd ..; +- @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer ++ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer $(LDFLAGS) + else SOAPdenovo-63mer: @cd sparsePregraph;make 63mer=1;cd ..; @cd standardPregraph;make 63mer=1;cd ..; - @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer -+ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LDFLAGS) $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer ++ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-63mer $(LDFLAGS) SOAPdenovo-127mer: @cd sparsePregraph;make 127mer=1;cd ..; @cd standardPregraph;make 127mer=1;cd ..; - @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer -+ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LDFLAGS) $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer ++ @$(CC) sparsePregraph/*.o standardPregraph/*.o $(LIBPATH) $(LIBS) $(EXTRA_FLAGS) -o SOAPdenovo-127mer $(LDFLAGS) + endif + clean: - @cd sparsePregraph;make clean;cd ..; - @cd standardPregraph;make clean;cd ..; diff --git a/debian/patches/fix_compilation b/debian/patches/fix_compilation index 6a3499c..cd682fb 100644 --- a/debian/patches/fix_compilation +++ b/debian/patches/fix_compilation @@ -26,13 +26,13 @@ Last-Updated: 2013-08-05 + typedef struct parameter { - unsigned char threadID; + unsigned char threadID; --- a/Makefile +++ b/Makefile -@@ -7,7 +7,7 @@ endif +@@ -8,7 +8,7 @@ endif - SUBDIRS = sparsePregraph standardPregraph - PROG= SOAPdenovo-63mer SOAPdenovo-127mer + SUBDIRS = sparsePregraph standardPregraph fusion + PROG= SOAPdenovo-63mer SOAPdenovo-127mer SOAPdenovo-fusion -INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc +INCLUDES= -I./sparsePregraph/inc -I./standardPregraph/inc -I/usr/include/x86_64-linux-gnu diff --git a/debian/patches/fix_usage_name b/debian/patches/fix_usage_name index 8b89886..29c4054 100644 --- a/debian/patches/fix_usage_name +++ b/debian/patches/fix_usage_name @@ -7,12 +7,12 @@ Author: Olivier Sallou <[email protected]> Last-Updated: 2013-02-09 --- a/standardPregraph/main.c +++ b/standardPregraph/main.c -@@ -104,7 +104,7 @@ int main ( int argc, char ** argv ) +@@ -105,7 +105,7 @@ int main ( int argc, char **argv ) 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, " sparse_pregraph construct sparse kmer-graph\n"); - fprintf ( stderr, " contig eliminate errors and output contigs\n" ); +- 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, " 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 1bd699a..7d02468 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 @@ CFLAGS= -O4 -fomit-frame-pointer +@@ -6,6 +6,7 @@ CFLAGS= -O3 -fomit-frame-pointer CFLAGS+= `dpkg-buildflags --get CFLAGS` `dpkg-buildflags --get CPPFLAGS` CFLAGS+=$(HARDENING_CFLAGS) endif @@ -16,11 +16,11 @@ Description: Enable reproducible build +++ b/sparsePregraph/main.cpp @@ -5,7 +5,7 @@ extern "C" int call_pregraph_sparse ( in - int main ( int argc, char ** argv ) + int main ( int argc, char **argv ) { -- fprintf ( stderr, "\nVersion 1.0.3: released on July 13th, 2012\nCompile %s\t%s\n\n", __DATE__, __TIME__ ); -+ fprintf ( stderr, "\nVersion 1.0.3: released on July 13th, 2012\nCompile %s\t%s\n\n", BDATE, BTIME ); - call_pregraph_sparse ( argc, argv ); +- fprintf ( stderr, "\nVersion 1.0.3: released on July 13th, 2012\nCompile %s\t%s\n\n", __DATE__, __TIME__ ); ++ fprintf ( stderr, "\nVersion 1.0.3: released on July 13th, 2012\nCompile %s\t%s\n\n", BDATE, BTIME ); + call_pregraph_sparse ( argc, argv ); } --- a/sparsePregraph/pregraph_sparse.cpp @@ -47,11 +47,11 @@ Description: Enable reproducible build --- a/standardPregraph/main.c +++ b/standardPregraph/main.c @@ -59,7 +59,7 @@ Return: - int main ( int argc, char ** argv ) + int main ( int argc, char **argv ) { - crc32c_Init(); -- fprintf ( stderr, "\nVersion 2.04: released on July 13th, 2012\nCompile %s\t%s\n", __DATE__, __TIME__ ); -+ fprintf ( stderr, "\nVersion 2.04: released on July 13th, 2012\nCompile %s\t%s\n", BDATE, BTIME ); - argc--; - argv++; + crc32c_Init(); +- fprintf ( stderr, "\nVersion 2.04: released on July 13th, 2012\nCompile %s\t%s\n", __DATE__, __TIME__ ); ++ fprintf ( stderr, "\nVersion 2.04: released on July 13th, 2012\nCompile %s\t%s\n", BDATE, BTIME ); + argc--; + argv++; diff --git a/debian/patches/use_debian_zlib b/debian/patches/use_debian_zlib index e1b6f54..6456e93 100644 --- a/debian/patches/use_debian_zlib +++ b/debian/patches/use_debian_zlib @@ -6,223 +6,223 @@ Description: Debian library is more recent than the one embedded upstream. 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 locate1read ( int t ) - } - } +--- a/standardPregraph/hashFunction.c ++++ b/standardPregraph/hashFunction.c +@@ -82,7 +82,7 @@ static int crc_table[256] = + }; --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 @@ static void output1Nread ( int t, FILE * - fprintf ( outfp, "\n" ); - } + typedef int ( *CRC32CFunctionPtr ) ( uint32_t, const char *, size_t ); +-static CRC32CFunctionPtr crc32; ++static CRC32CFunctionPtr s_crc32; --static void getPEreadOnContig ( int t, gzFile * outfp ) -+static void getPEreadOnContig ( int t, gzFile outfp ) + static uint32_t cpuid ( uint32_t functionInput ) { - int len1, len2, index; - char orien1, orien2; -@@ -560,7 +560,7 @@ static void getPEreadOnContig(int t,FILE - } - }*/ +@@ -149,11 +149,11 @@ CRC32CFunctionPtr detectBestCRC32C() --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 ) + ubyte8 hash_kmer ( Kmer kmer ) { - int read1, read2; - char orientation; -@@ -618,7 +618,7 @@ static void recordLongRead ( FILE * outf - } +- return ( crc32 ( 0, ( char * ) &kmer, sizeof ( Kmer ) ) ); ++ return ( s_crc32 ( 0, ( char * ) &kmer, sizeof ( Kmer ) ) ); } --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 @@ void prlRead2Ctg ( char * libfile, char - 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 @@ static void convertIndex () - free ( ( void * ) length_array ); + void crc32c_Init() + { +- crc32 = detectBestCRC32C(); ++ s_crc32 = detectBestCRC32C(); } --static long long getRead1by1_gz ( gzFile * fp, DARRAY * readSeqInGap ) -+static long long getRead1by1_gz ( gzFile fp, DARRAY * readSeqInGap ) +--- a/standardPregraph/inc/extfunc.h ++++ b/standardPregraph/inc/extfunc.h +@@ -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 ); +-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/attachPEinfo.c ++++ b/standardPregraph/attachPEinfo.c +@@ -492,7 +492,7 @@ int connectByPE_grad ( FILE *fp, int peG + 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 readCounter = 0; + long long pre_readno, readno, minno, maxno; + int pre_pos, pos, flag, PE, count = 0, Total_PE = 0; +--- a/standardPregraph/kmer.c ++++ b/standardPregraph/kmer.c +@@ -498,7 +498,7 @@ void print_kmer ( FILE *fp, Kmer kmer, c + fprintf ( fp, "%c", c ); + } -@@ -206,7 +206,7 @@ static long long getRead1by1 ( FILE * fp - static boolean loadReads4gap ( char * graphfile ) +-void print_kmer_gz ( gzFile *fp, Kmer kmer, char c ) ++void print_kmer_gz ( gzFile fp, Kmer kmer, char c ) { - 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 @@ void output_vertex ( char * outfile ) - fclose ( fp ); + gzprintf ( fp, "%llx %llx %llx %llx", kmer.high1, kmer.low1, kmer.high2, kmer.low2 ); + gzprintf ( fp, "%c", c ); +@@ -810,7 +810,7 @@ void print_kmer ( FILE *fp, Kmer kmer, c + fprintf ( fp, "%c", c ); } --void output_1edge ( preEDGE * edge, gzFile * fp ) -+void output_1edge ( preEDGE * edge, gzFile fp ) +-void print_kmer_gz ( gzFile *fp, Kmer kmer, char c ) ++void print_kmer_gz ( gzFile fp, Kmer kmer, char c ) { - int i; - gzprintf ( fp, ">length %d,", edge->length ); ---- a/standardPregraph/orderContig.c -+++ b/standardPregraph/orderContig.c -@@ -5072,7 +5072,7 @@ void PE2Links ( char * infile ) - char name[256], *line; - FILE * fp1; - FILE * linkF; -- gzFile * fp2; -+ gzFile fp2; - int i; - int flag = 0; - unsigned int j; + gzprintf ( fp, "%llx %llx", kmer.high, kmer.low ); + gzprintf ( fp, "%c", c ); +--- a/standardPregraph/loadPreGraph.c ++++ b/standardPregraph/loadPreGraph.c +@@ -449,7 +449,7 @@ void loadEdge ( char *graphfile ) + { + 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/node2edge.c +++ b/standardPregraph/node2edge.c @@ -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 .. --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 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 ); ++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 @@ Return: *************************************************/ - void kmer2edges ( char * outfile ) + void kmer2edges ( char *outfile ) { -- gzFile * fp; -+ gzFile fp; - char temp[256]; - sprintf ( temp, "%s.edge.gz", outfile ); - fp = gzopen ( temp, "w" ); +- gzFile *fp; ++ gzFile fp; + char temp[256]; + sprintf ( temp, "%s.edge.gz", outfile ); + fp = gzopen ( temp, "w" ); @@ -234,7 +234,7 @@ Output: Return: 0. *************************************************/ --static int startEdgeFromNode ( kmer_t * node1, gzFile * fp ) -+static int startEdgeFromNode ( kmer_t * node1, gzFile fp ) +-static int startEdgeFromNode ( kmer_t *node1, gzFile *fp ) ++static int startEdgeFromNode ( kmer_t *node1, gzFile fp ) { - int node_c, palindrome; - unsigned char flag; + int node_c, palindrome; + unsigned char flag; @@ -363,7 +363,7 @@ Output: Return: None. *************************************************/ --void make_edge ( gzFile * fp ) +-void make_edge ( gzFile *fp ) +void make_edge ( gzFile fp ) { - int i = 0; - kmer_t * node1; + int i = 0; + kmer_t *node1; @@ -427,7 +427,7 @@ Output: 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 ) +-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 @@ void loadEdge ( char * graphfile ) - { - 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 @@ void print_kmer ( FILE * fp, Kmer kmer, - fprintf ( fp, "%c", c ); + int length, char_index; + preEDGE *newedge; +--- a/standardPregraph/prlRead2Ctg.c ++++ b/standardPregraph/prlRead2Ctg.c +@@ -424,7 +424,7 @@ static void locate1read ( int t ) + } } --void print_kmer_gz ( gzFile * fp, Kmer kmer, char c ) -+void print_kmer_gz ( gzFile fp, Kmer kmer, char c ) +-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 ) { - gzprintf ( fp, "%llx %llx %llx %llx", kmer.high1, kmer.low1, kmer.high2, kmer.low2 ); - gzprintf ( fp, "%c", c ); -@@ -795,7 +795,7 @@ void print_kmer ( FILE * fp, Kmer kmer, - fprintf ( fp, "%c", c ); + int len = lenBuffer[t]; + int index; +@@ -506,7 +506,7 @@ static void output1Nread ( int t, FILE * + fprintf ( outfp, "\n" ); } --void print_kmer_gz ( gzFile * fp, Kmer kmer, char c ) -+void print_kmer_gz ( gzFile fp, Kmer kmer, char c ) +-static void getPEreadOnContig ( int t, gzFile *outfp ) ++static void getPEreadOnContig ( int t, gzFile outfp ) { - gzprintf ( fp, "%llx %llx", kmer.high, kmer.low ); - gzprintf ( fp, "%c", c ); ---- a/standardPregraph/attachPEinfo.c -+++ b/standardPregraph/attachPEinfo.c -@@ -492,7 +492,7 @@ int connectByPE_grad ( FILE * fp, int pe - 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 ) + int len1, len2, index; + char orien1, orien2; +@@ -566,7 +566,7 @@ static void getPEreadOnContig(int t,FILE + } + }*/ + +-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 ) { - 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 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 ); --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 @@ static int crc_table[256] = - }; + int read1, read2; + char orientation; +@@ -624,7 +624,7 @@ static void recordLongRead ( FILE *outfp + } + } - typedef int ( *CRC32CFunctionPtr ) ( uint32_t, const char *, size_t ); --static CRC32CFunctionPtr crc32; -+static CRC32CFunctionPtr s_crc32; +-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; +@@ -781,7 +781,7 @@ void prlRead2Ctg ( char *libfile, char * + 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/orderContig.c ++++ b/standardPregraph/orderContig.c +@@ -5544,7 +5544,7 @@ void PE2Links ( char *infile ) + char name[256], *line; + FILE *fp1; + FILE *linkF; +- gzFile *fp2; ++ gzFile fp2; + int i; + int flag = 0; + unsigned int j; +--- a/standardPregraph/output_pregraph.c ++++ b/standardPregraph/output_pregraph.c +@@ -85,7 +85,7 @@ void output_vertex ( char *outfile ) + fclose ( fp ); + } - static uint32_t cpuid ( uint32_t functionInput ) +-void output_1edge ( preEDGE *edge, gzFile *fp ) ++void output_1edge ( preEDGE *edge, gzFile fp ) { -@@ -145,11 +145,11 @@ CRC32CFunctionPtr detectBestCRC32C() + int i; + gzprintf ( fp, ">length %d,", edge->length ); +--- a/standardPregraph/prlReadFillGap.c ++++ b/standardPregraph/prlReadFillGap.c +@@ -104,7 +104,7 @@ static void convertIndex () + free ( ( void * ) length_array ); + } - ubyte8 hash_kmer ( Kmer kmer ) +-static long long getRead1by1_gz ( gzFile *fp, DARRAY *readSeqInGap ) ++static long long getRead1by1_gz ( gzFile fp, DARRAY *readSeqInGap ) { -- return ( crc32 ( 0, ( char * ) &kmer, sizeof ( Kmer ) ) ); -+ return ( s_crc32 ( 0, ( char * ) &kmer, sizeof ( Kmer ) ) ); - } + long long readCounter = 0; - void crc32c_Init() +@@ -206,7 +206,7 @@ static long long getRead1by1 ( FILE *fp, + static boolean loadReads4gap ( char *graphfile ) { -- crc32 = detectBestCRC32C(); -+ s_crc32 = detectBestCRC32C(); - } + FILE *fp1, *fp2; +- gzFile *fp; ++ gzFile fp; + char name[1024]; + long long readCounter; -- 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
