173bacbf6c28737266ef93048446902620b49330
braney
  Mon Dec 14 12:33:16 2015 -0800
some tweaks to CRAM support #14717

diff --git src/hg/hgTables/bam.c src/hg/hgTables/bam.c
index 68ed386..4066b77 100644
--- src/hg/hgTables/bam.c
+++ src/hg/hgTables/bam.c
@@ -153,30 +153,32 @@
 struct asObject *as = bamAsObj();
 struct asFilter *filter = NULL;
 
 if (anyFilter())
     {
     filter = asFilterFromCart(cart, db, table, as);
     if (filter)
         {
 	fprintf(f, "# Filtering on %d columns\n", slCount(filter->columnList));
 	}
     }
 
 /* Loop through outputting each region */
 struct region *region, *regionList = getRegions();
 
+struct trackDb *tdb = findTdbForTable(db, curTrack, table, ctLookupName);
+cramInit(tdb);
 int maxOut = bigFileMaxOutput();
 for (region = regionList; region != NULL && (maxOut > 0); region = region->next)
     {
     struct lm *lm = lmInit(0);
     char *fileName = bamFileName(table, conn, region->chrom);
     struct samAlignment *sam, *samList = bamFetchSamAlignment(fileName, region->chrom,
     	region->start, region->end, lm);
     char *row[SAMALIGNMENT_NUM_COLS];
     char numBuf[BAM_NUM_BUF_SIZE];
     for (sam = samList; sam != NULL && (maxOut > 0); sam = sam->next)
         {
 	samAlignmentToRow(sam, numBuf, row);
 	if (asFilterOnRow(filter, row))
 	    {
 	    /* if we're looking for identifiers, check if this matches */