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

diff --git src/hg/hgTables/bam.c src/hg/hgTables/bam.c
index 341c781..68ed386 100644
--- src/hg/hgTables/bam.c
+++ src/hg/hgTables/bam.c
@@ -302,31 +302,36 @@
     }
 slReverse(&bedList);
 return bedList;
 }
 
 struct slName *randomBamIds(char *table, struct sqlConnection *conn, int count)
 /* Return some semi-random qName based IDs from a BAM file. */
 {
 /* Read 10000 items from bam file,  or if they ask for a big list, then 4x what they ask for. */
 char *fileName = bamFileName(table, conn, NULL);
 samfile_t *fh = bamOpen(fileName, NULL);
 struct lm *lm = lmInit(0);
 int orderedCount = count * 4;
 if (orderedCount < 10000)
     orderedCount = 10000;
+#ifdef USE_HTS
+bam_hdr_t *header = sam_hdr_read(fh);
+struct samAlignment *sam, *samList = bamReadNextSamAlignments(fh, header, orderedCount, lm);
+#else
 struct samAlignment *sam, *samList = bamReadNextSamAlignments(fh, orderedCount, lm);
+#endif
 
 /* Shuffle list and extract qNames from first count of them. */
 shuffleList(&samList);
 struct slName *randomIdList = NULL;
 int i;
 for (i=0, sam = samList; i<count && sam != NULL; ++i, sam = sam->next)
      slNameAddHead(&randomIdList, sam->qName);
 
 /* Clean up and go home. */
 lmCleanup(&lm);
 bamClose(&fh);
 freez(&fileName);
 return randomIdList;
 }
 
@@ -367,31 +372,36 @@
 hTableStart();
 
 /* Print field names as column headers for example */
 hPrintf("<TR>");
 int colIx = 0;
 for (col = as->columnList; col != NULL; col = col->next)
     {
     hPrintf("<TH>%s</TH>", col->name);
     ++colIx;
     }
 hPrintf("</TR>\n");
 
 /* Fetch sample rows. */
 samfile_t *fh = bamOpen(fileName, NULL);
 struct lm *lm = lmInit(0);
+#ifdef USE_HTS
+bam_hdr_t *header = sam_hdr_read(fh);
+struct samAlignment *sam, *samList = bamReadNextSamAlignments(fh, header, 10, lm);
+#else
 struct samAlignment *sam, *samList = bamReadNextSamAlignments(fh, 10, lm);
+#endif
 
 /* Print sample lines. */
 char *row[SAMALIGNMENT_NUM_COLS];
 char numBuf[BAM_NUM_BUF_SIZE];
 for (sam=samList; sam != NULL; sam = sam->next)
     {
     samAlignmentToRow(sam, numBuf, row);
     hPrintf("<TR>");
     for (colIx=0; colIx<colCount; ++colIx)
         {
         hPrintf("<TD>");
         xmlEscapeStringToFile(row[colIx], stdout);
         hPrintf("</TD>");
 	}
     hPrintf("</TR>\n");