src/hg/lib/knetUdc.c 1.3

Index: src/hg/lib/knetUdc.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/lib/knetUdc.c,v
retrieving revision 1.2
retrieving revision 1.3
diff -b -B -U 1000000 -r1.2 -r1.3
--- src/hg/lib/knetUdc.c	3 Mar 2010 02:19:44 -0000	1.2
+++ src/hg/lib/knetUdc.c	10 Mar 2010 23:52:06 -0000	1.3
@@ -1,84 +1,87 @@
 /* knetUdc -- install udc i/o functions in knetfile interface in samtools. */
 /* As of 2/23/10, the KNETFILE_HOOKS extension is a UCSC-local modification of samtools. */
 
 #if (defined USE_BAM && defined KNETFILE_HOOKS)
 
 #include "common.h"
 #include "udc.h"
 #include "knetUdc.h"
 #include "knetfile.h"
 
 static char const rcsid[] = "$Id$";
 
 struct knetFile_s {
     struct udcFile *udcf;
 }; // typedef'd to knetFile in knetfile.h
 
 static char *udcCacheDir = NULL;
 
 static knetFile *kuOpen(const char *filename, const char *mode)
 /* Open the given filename with mode which must be "r". */
 {
-knetFile *kf = NULL;
 if (!sameOk((char *)mode, "r"))
     errAbort("mode passed to kuOpen must be 'r' not '%s'", mode);
+struct udcFile *udcf = udcFileMayOpen((char *)filename, udcCacheDir);
+if (udcf == NULL)
+    return NULL;
+knetFile *kf = NULL;
 AllocVar(kf);
-kf->udcf = udcFileOpen((char *)filename, udcCacheDir);
+kf->udcf = udcf;
 verbose(2, "kuOpen: returning %lu\n", (unsigned long)(kf->udcf));
 return kf;
 }
 
 static knetFile *kuDopen(int fd, const char *mode)
 /* Open from a file descriptor -- not necessary for our use of samtools. */
 {
 errAbort("kuDopen not implemented");
 return NULL;
 }
 
 static off_t kuRead(knetFile *fp, void *buf, off_t len)
 /* Read len bytes into buf, return amount actually read. */
 {
 verbose(2, "udcRead(%lu, buf, %lld)\n", (unsigned long)(fp->udcf), (long long)len);
 return (off_t)udcRead(fp->udcf, buf, (int)len);
 }
 
 static off_t kuSeek(knetFile *fp, int64_t off, int whence)
 /* Seek to off according to whence (but don't waste time with samtools' SEEK_END to
  * check empty record at end of file.  Don't be fooled by the off_t return type --
  * it's 0 for OK, non-0 for fail. */
 {
 bits64 offset;
 if (whence == SEEK_SET)
     offset = off;
 else if (whence == SEEK_CUR)
     offset = off+ udcTell(fp->udcf);
 else
     return -1;
 verbose(2, "udcSeek(%lu, %lld)\n", (unsigned long)(fp->udcf), offset);
 udcSeek(fp->udcf, offset);
 return 0;
 }
 
 static off_t kuTell(knetFile *fp)
 /* Tell current offset in file. */
 {
 verbose(2, "udcTell(%lu)\n", (unsigned long)(fp->udcf));
 return udcTell(fp->udcf);
 }
 
 static int kuClose(knetFile *fp)
 /* Close and free fp->udcf. */
 {
 verbose(2, "udcClose(%lu)\n", (unsigned long)(fp->udcf));
 udcFileClose(&(fp->udcf));
 return 0;
 }
 
 void knetUdcInstall()
 /* install udc i/o functions in knetfile interface in Heng Li's samtools lib. */
 {
 // maybe init udcCacheDir from hg.conf?
 knet_init_alt(kuOpen, kuDopen, kuRead, kuSeek, kuTell, kuClose);
 }
 
 #endif//def USE_BAM && KNETFILE_HOOKS