src/hg/lib/knetUdc.c 1.1

Index: src/hg/lib/knetUdc.c
===================================================================
RCS file: src/hg/lib/knetUdc.c
diff -N src/hg/lib/knetUdc.c
--- /dev/null	1 Jan 1970 00:00:00 -0000
+++ src/hg/lib/knetUdc.c	24 Feb 2010 01:10:24 -0000	1.1
@@ -0,0 +1,84 @@
+/* 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);
+AllocVar(kf);
+kf->udcf = udcFileOpen((char *)filename, udcCacheDir);
+verbose(2, "kuOpen: returning %lld\n", (long 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(%lld, buf, %lld)\n", (long 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(%lld, %lld)\n", (long long)(fp->udcf), offset);
+udcSeek(fp->udcf, offset);
+return 0;
+}
+
+static off_t kuTell(knetFile *fp)
+/* Tell current offset in file. */
+{
+verbose(2, "udcTell(%lld)\n", (long long)(fp->udcf));
+return udcTell(fp->udcf);
+}
+
+static int kuClose(knetFile *fp)
+/* Close and free fp->udcf. */
+{
+verbose(2, "udcClose(%lld)\n", (long 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