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@debian.org>
Last-Updated: 2013-08-05
Forwarded: no
--- 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 )
 {
@@ -149,11 +149,11 @@
 
 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();
 }
 
--- 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/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/kmer.c
+++ b/standardPregraph/kmer.c
@@ -498,7 +498,7 @@
   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 );
@@ -810,7 +810,7 @@
   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/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/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/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;
@@ -506,7 +506,7 @@
   fprintf ( outfp, "\n" );
 }
 
-static void getPEreadOnContig ( int t, gzFile *outfp )
+static void getPEreadOnContig ( int t, gzFile outfp )
 {
   int len1, len2, index;
   char orien1, orien2;
@@ -566,7 +566,7 @@
         }
 }*/
 
-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;
@@ -624,7 +624,7 @@
     }
 }
 
-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;
@@ -781,7 +781,7 @@
   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/orderContig.c
+++ b/standardPregraph/orderContig.c
@@ -5545,7 +5545,7 @@
   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 @@
   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/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;