05c89b00677e24821ea01e20b95f2c1b0263b1f4
aamp
  Sat Jul 16 08:48:52 2011 -0700
removed open, fetch, exists functions to make way for removing udcFUSE stuff
diff --git src/hg/inc/hgBam.h src/hg/inc/hgBam.h
index 9dd8768..65c9937 100644
--- src/hg/inc/hgBam.h
+++ src/hg/inc/hgBam.h
@@ -9,41 +9,30 @@
 #endif
 
 #ifdef USE_BAM
 
 #ifndef SAMALIGNMENT_H
 #include "samAlignment.h"
 #endif
 
 #endif
 
 char *bamFileNameFromTable(struct sqlConnection *conn, char *table, char *bamSeqName);
 /* Return file name from table.  If table has a seqName column, then grab the 
  * row associated with bamSeqName (which can be e.g. '1' not 'chr1' if that is the
  * case in the bam file). */
 
-boolean bamFileExists(char *bamFileName);
-/* Return TRUE if we can successfully open the bam file and its index file. */
-
-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.  */
-
 struct samAlignment *bamFetchSamAlignment(char *fileOrUrl, char *chrom, int start, int end,
 	struct lm *lm);
 /* Fetch region as a list of samAlignments - which is more or less an unpacked
  * bam record.  Results is allocated out of lm, since it tends to be large... */
 
 struct samAlignment *bamReadNextSamAlignments(samfile_t *fh, int count, struct lm *lm);
 /* Read next count alignments in SAM format, allocated in lm.  May return less than
  * count at end of file. */
 
 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 */
 
 struct ffAli *bamToFfAli(const bam1_t *bam, struct dnaSeq *target, int targetOffset,
 			 boolean useStrand, char **retQSeq);