2e75814ac8468bdfb14d01cabe7455b63154a64b
kent
  Thu Feb 10 16:59:09 2011 -0800
Adding example lines to BAM schema page in table browser.  Pushing forward on getting identifiers to work there, but still a ways to go.  (It no longer bombs at the paste identifiers page, but it does shortly thereafter.)
diff --git src/hg/inc/bamFile.h src/hg/inc/bamFile.h
index a7cea23..e80e231 100644
--- src/hg/inc/bamFile.h
+++ src/hg/inc/bamFile.h
@@ -47,30 +47,41 @@
 /* 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 */
+
+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 
  * char into *retOp (retOp must not be NULL) and return the number of bases. */
 {
 #ifdef USE_BAM
 // decoding lifted from samtools bam.c bam_format1(), long may it remain stable:
 #define BAM_DOT_C_OPCODE_STRING "MIDNSHP"
 int n = packed>>BAM_CIGAR_SHIFT;
 int opcode = packed & BAM_CIGAR_MASK;
 if (opcode >= strlen(BAM_DOT_C_OPCODE_STRING))
     errAbort("bamUnpackCigarElement: unrecognized opcode %d. "