b29f1fbf93c9df5aa65fed050d9f8132dc6a2c73
braney
  Tue Nov 24 14:20:10 2015 -0800
support htslib for sam/bam/cram/tabix support  #14717

diff --git src/hg/inc/hgBam.h src/hg/inc/hgBam.h
index 09a0e63..3e0196d 100644
--- src/hg/inc/hgBam.h
+++ src/hg/inc/hgBam.h
@@ -17,25 +17,29 @@
 
 #ifndef JKSQL_H
 #include "jksql.h"
 #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). */
 
 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... */
 
+#ifdef USE_HTS
+struct samAlignment *bamReadNextSamAlignments(samfile_t *fh, bam_hdr_t *header,  int count, struct lm *lm);
+#else
 struct samAlignment *bamReadNextSamAlignments(samfile_t *fh, int count, struct lm *lm);
+#endif
 /* Read next count alignments in SAM format, allocated in lm.  May return less than
  * count at end of file. */
 
 struct ffAli *bamToFfAli(const bam1_t *bam, struct dnaSeq *target, int targetOffset,
 			 boolean useStrand, char **retQSeq);
 /* Convert from bam to ffAli format.  If retQSeq is non-null, set it to the 
  * query sequence into which ffAli needle pointers point. */
 
 #endif//ndef HGBAM_H