c571aeb65d3c0ee76bea06111aa9b0fff4d198b1
aamp
  Sat Jul 16 09:07:15 2011 -0700
deleted anything udcFUSE-related
diff --git src/inc/bamFile.h src/inc/bamFile.h
index 080b6a4..02f39b6 100644
--- src/inc/bamFile.h
+++ src/inc/bamFile.h
@@ -22,39 +22,39 @@
     "TARGET=_BLANK>http://samtools.sourceforge.net</A>) and recompile kent/src with " \
     "USE_BAM=1 in your environment " \
     "(see <A HREF=\"http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables\" " \
     "TARGET=_BLANK>http://genomewiki.ucsc.edu/index.php/Build_Environment_Variables</A>)."
 
 #endif // USE_BAM
 
 #ifndef DNASEQ_H
 #include "dnaseq.h"
 #endif
 
 #ifndef DYSTRING_H
 #include "dystring.h"
 #endif
 
-boolean bamFileExistsUdc(char *bamFileName, char *udcFuseRoot);
+boolean bamFileExists(char *bamFileName);
 /* Return TRUE if we can successfully open the bam file and its index file. */
 
-samfile_t *bamOpenUdc(char *fileOrUrl, char **retBamFileName, char *udcFuseRoot);
+samfile_t *bamOpen(char *fileOrUrl, char **retBamFileName);
 /* Return an open bam file, dealing with FUSE caching if need be. 
  * Return parameter if NON-null will return the file name after FUSing */
 
-void bamFetchUdc(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,
-	samfile_t **pSamFile, char *udcFuseRoot);
+void bamFetch(char *fileOrUrl, char *position, bam_fetch_f callbackFunc, void *callbackData,
+	samfile_t **pSamFile);
 /* Open the .bam file, fetch items in the seq:start-end position range,
  * and call callbackFunc on each bam item retrieved from the file plus callbackData.
  * This handles BAM files with "chr"-less sequence names, e.g. from Ensembl. 
  * The pSamFile parameter is optional.  If non-NULL it will be filled in, just for
  * the benefit of the callback function, with the open samFile.  */
 
 void bamClose(samfile_t **pSamFile);
 /* Close down a samefile_t */
 
 boolean bamIsRc(const bam1_t *bam);
 /* Return TRUE if alignment is on - strand. */
 
 INLINE int bamUnpackCigarElement(unsigned int packed, char *retOp)
 /* Given an unsigned int containing a number of bases and an offset into an
  * array of BAM-enhanced-CIGAR ASCII characters (operations), store operation