3377b968b5f797ef07f454f5a5fb125668f6c2e4
braney
  Tue May 10 12:10:55 2016 -0700
fix a problem that shows up if neither samtabix or htslib are installed

diff --git src/hg/lib/hgBam.c src/hg/lib/hgBam.c
index 6565075..9d5ab91 100644
--- src/hg/lib/hgBam.c
+++ src/hg/lib/hgBam.c
@@ -261,40 +261,53 @@
 return helper.samList;
 }
 
 #else
 // If we're not compiling with samtools, make stub routines so compile won't fail:
 
 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 is not nec. in chromInfo, e.g.
  * bam file might have '1' not 'chr1'). */
 {
 errAbort(COMPILE_WITH_SAMTOOLS, "bamFileNameFromTable");
 return NULL;
 }
 
+struct samAlignment *bamFetchSamAlignmentPlus(char *fileOrUrl, char *chrom, int start, int end,
+	struct lm *lm,  char *refUrl, char *cacheDir)
+/* 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, "bamFetchSamAlignmentPlus");
+return NULL;
+}
+
 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;
 }
 
+#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. */
 {
 errAbort(COMPILE_WITH_SAMTOOLS, "bamReadNextSamAlignments");
 return NULL;
 }
 
 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. */
 {
 errAbort(COMPILE_WITH_SAMTOOLS, "bamToFfAli");
 return NULL;
 }