16439684a0ecc75ede242ded740c51cf1f60c8a4
angie
  Tue Feb 22 11:36:43 2011 -0800
Feature #2820 (tabix: add as optional linked library in kent/src):Added lineFile wrapper on tabix: lineFileOnTabix to open; then
lineFileNext and its derivatives work as usual.
lineFileSetTabixRegion seeks to the given position range, and
subsequent lineFileNext's return lines in that position range.
lineFileSeek is not supported -- tabix doesn't have linear offsets
but rather a block number and offset which are packed into 64 bits.
Line numbers are not known after calls to lineFileSetTabixRegion.

diff --git src/lib/knetUdc.c src/lib/knetUdc.c
new file mode 100644
index 0000000..25c8229
--- /dev/null
+++ src/lib/knetUdc.c
@@ -0,0 +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: knetUdc.c,v 1.3 2010/03/10 23:52:06 angie Exp $";
+
+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". */
+{
+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 = 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