[med-svn] [soapdenovo2] 03/03: New upstream version
Andreas Tille
tille at debian.org
Wed Sep 6 08:50:54 UTC 2017
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 <tille at debian.org>
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 <tille at debian.org> 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 <osallou at debian.org>
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 <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 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;
--
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