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/hg/lib/knetUdc.c src/hg/lib/knetUdc.c
deleted file mode 100644
index 25c8229..0000000
--- src/hg/lib/knetUdc.c
+++ /dev/null
@@ -1,87 +0,0 @@
-/* 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