625a9fdc7a5620695b4c507f23335cc4cc8724d1
angie
  Fri Feb 11 14:43:00 2011 -0800
MLQ #2810 (error compiling uscs genome browser): fixing a couplefunction declarations in USE_BAM=0 code, that would have been
caught by compiling with the environment variable USE_BAM=0.

diff --git src/hg/lib/bamFile.c src/hg/lib/bamFile.c
index a3aceff..e8fd1f0 100644
--- src/hg/lib/bamFile.c
+++ src/hg/lib/bamFile.c
@@ -799,31 +799,31 @@
 /* Return file name from table.  If table has a seqName column, then grab the
  * row associated with bamSeqName (which is not nec. in chromInfo, e.g.
  * bam file might have '1' not 'chr1'). */
 {
 errAbort(COMPILE_WITH_SAMTOOLS, "bamFileNameFromTable");
 return NULL;
 }
 
 boolean bamFileExists(char *bamFileName)
 /* Return TRUE if we can successfully open the bam file and its index file. */
 {
 warn(COMPILE_WITH_SAMTOOLS, "bamFileExists");
 return FALSE;
 }
 
-samfile_t *bamOpen(char *bamFileName)
+samfile_t *bamOpen(char *fileOrUrl, char **retBamFileName)
 /* Return an open bam file, dealing with some FUSE caching if need be. */
 {
 errAbort(COMPILE_WITH_SAMTOOLS, "bamOpen");
 return FALSE;
 }
 
 void bamClose(samfile_t **pSamFile)
 /* Close down a samefile_t */
 {
 errAbort(COMPILE_WITH_SAMTOOLS, "bamClose");
 }
 
 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,
@@ -832,31 +832,31 @@
  * 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.  */
 {
 errAbort(COMPILE_WITH_SAMTOOLS, "bamFetch");
 }
 
 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... */
 {
 errAbort(COMPILE_WITH_SAMTOOLS, "bamFetchSamAlignment");
 return NULL;
 }
 
-struct samAlignment *bamReadNextSamAlignments(struct samfile_t *fh, int count, struct lm *lm)
+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. */
 {
 errAbort(COMPILE_WITH_SAMTOOLS, "bamReadNextSamAlignments");
 return NULL;
 }
 
 boolean bamIsRc(const bam1_t *bam)
 /* Return TRUE if alignment is on - strand. */
 {
 errAbort(COMPILE_WITH_SAMTOOLS, "bamIsRc");
 return FALSE;
 }
 
 void bamGetSoftClipping(const bam1_t *bam, int *retLow, int *retHigh, int *retClippedQLen)