11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/lib/knetUdc.c src/lib/knetUdc.c
index 0b85438..a711a5b 100644
--- src/lib/knetUdc.c
+++ src/lib/knetUdc.c
@@ -1,49 +1,34 @@
 /* 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. */
 
 /* Copyright (C) 2014 The Regents of the University of California 
  * See README in this or parent directory for licensing information. */
 
-#if ((defined USE_BAM || defined USE_TABIX) && defined KNETFILE_HOOKS)
 
 #include "common.h"
 #include "udc.h"
 #include "knetUdc.h"
-#ifdef USE_HTS
 #include "htslib/knetfile.h"
-#else
-#include "knetfile.h"
-
-
-struct knetFile_s {
-    struct udcFile *udcf;
-}; // typedef'd to knetFile in knetfile.h
-#endif
 
 static char *udcCacheDir = NULL;
 
 static knetFile *kuOpen(const char *filename, const char *mode)
 /* Open the given filename with mode which must be "r". */
 {
-#ifdef USE_HTS
 if (!(sameOk((char *)mode, "r") || sameOk((char *)mode, "rb")))
     errAbort("mode passed to kuOpen must be 'r' or 'rb' not '%s'", mode);
-#else
-if (!sameOk((char *)mode, "r"))
-    errAbort("mode passed to kuOpen must be 'r' not '%s'", mode);
-#endif
 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;
@@ -84,23 +69,15 @@
 /* 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);
 }
 
 
-#else// no (USE_BAM || USE_TABIX) && KNETFILE_HOOKS
-
-void knetUdcInstall()
-/* Required libs aren't installed; do nothing. */
-{
-}
-
-#endif