[med-svn] r14352 - in trunk/packages/soap/soapdenovo2/trunk/debian: . patches
Olivier Sallou
osallou at alioth.debian.org
Mon Aug 5 14:58:04 UTC 2013
Author: osallou
Date: 2013-08-05 14:58:04 +0000 (Mon, 05 Aug 2013)
New Revision: 14352
Added:
trunk/packages/soap/soapdenovo2/trunk/debian/patches/use_debian_zlib
trunk/packages/soap/soapdenovo2/trunk/debian/patches/use_libsam
Modified:
trunk/packages/soap/soapdenovo2/trunk/debian/copyright
trunk/packages/soap/soapdenovo2/trunk/debian/patches/series
Log:
add patches to use debian libs and get compilation
Modified: trunk/packages/soap/soapdenovo2/trunk/debian/copyright
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/copyright 2013-08-05 12:55:59 UTC (rev 14351)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/copyright 2013-08-05 14:58:04 UTC (rev 14352)
@@ -3,6 +3,12 @@
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
Modified: trunk/packages/soap/soapdenovo2/trunk/debian/patches/series
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/series 2013-08-05 12:55:59 UTC (rev 14351)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/series 2013-08-05 14:58:04 UTC (rev 14352)
@@ -1,3 +1,5 @@
+use_libsam
fix_compilation
fix_usage_name
add_hardening
+use_debian_zlib
Added: trunk/packages/soap/soapdenovo2/trunk/debian/patches/use_debian_zlib
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/use_debian_zlib (rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/use_debian_zlib 2013-08-05 14:58:04 UTC (rev 14352)
@@ -0,0 +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();
+ }
+
Added: trunk/packages/soap/soapdenovo2/trunk/debian/patches/use_libsam
===================================================================
--- trunk/packages/soap/soapdenovo2/trunk/debian/patches/use_libsam (rev 0)
+++ trunk/packages/soap/soapdenovo2/trunk/debian/patches/use_libsam 2013-08-05 14:58:04 UTC (rev 14352)
@@ -0,0 +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>
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