src/hg/hgTracks/bamTrack.c 1.4

Index: src/hg/hgTracks/bamTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/bamTrack.c,v
retrieving revision 1.3
retrieving revision 1.4
diff -b -B -U 4 -r1.3 -r1.4
--- src/hg/hgTracks/bamTrack.c	27 Jul 2009 19:31:48 -0000	1.3
+++ src/hg/hgTracks/bamTrack.c	27 Jul 2009 21:52:09 -0000	1.4
@@ -9,12 +9,9 @@
 #include "linefile.h"
 #include "jksql.h"
 #include "hdb.h"
 #include "hgTracks.h"
-// bam.h is incomplete without _IOLIB set to 1, 2 or 3.  2 is used by Makefile.generic:
-#define _IOLIB 2
-#include "bam.h"
-#include "sam.h"
+#include "bamFile.h"
 
 static char const rcsid[] = "$Id$";
 
 #define BAM_MAX_ZOOM 200000
@@ -190,9 +187,9 @@
 return 0;
 }
 
 #define MAX_ITEMS_FOR_MAPBOX 1500
-void dontMapItem(struct track *tg, struct hvGfx *hvg, void *item,
+static void dontMapItem(struct track *tg, struct hvGfx *hvg, void *item,
 		    char *itemName, char *mapItemName, int start, int end,
 		    int x, int y, int width, int height)
 /* When there are many many items, drawing hgc links can really slow us down. */
 {
@@ -203,33 +200,18 @@
  * that the data would just end up in dense mode and be super-slow. */
 {
 if (winEnd-winStart > BAM_MAX_ZOOM)
     return;
-struct sqlConnection *conn = hAllocConn(database);
-char *bamFileName = bbiNameFromTable(conn, tg->mapName);
-hFreeConn(&conn);
-
-// TODO: if bamFile is URL, convert URL to path a la UDC, but under udcFuse mountpoint.
-// new hg.conf setting for udcFuse mountpoint/support.
-
-bam_index_t *idx = bam_index_load(bamFileName);
-samfile_t *fh = samopen(bamFileName, "rb", NULL);
-int chromId, s, e;
-
-// TODO: watch out for presence/absence of initial "chr" in bam -- need trackDb setting
-char *posToParse = position;
-if (startsWith("chr", position))
-    posToParse += 3;
+char *seqNameForBam = chromName;
+char *stripPrefix = trackDbSetting(tg->tdb, "stripPrefix");
+if (stripPrefix && startsWith(stripPrefix, chromName))
+    seqNameForBam = chromName + strlen(stripPrefix);
+char posForBam[512];
+safef(posForBam, sizeof(posForBam), "%s:%d-%d", seqNameForBam, winStart, winEnd);
 
-bam_parse_region(fh->header, posToParse, &chromId, &s, &e);
 struct hash *pairHash = isPaired ? hashNew(18) : NULL;
 struct bamTrackData btd = {tg, pairHash};
-int ret = bam_fetch(fh->x.bam, idx, chromId, winStart, winEnd, &btd,
-		    isPaired ? addBamPaired : addBam);
-if (ret != 0)
-    errAbort("bam_fetch(%s, %s=%d:%d-%d failed (%d)", bamFileName, chromName,
-	     chromId, winStart+1, winEnd, ret);
-samclose(fh);
+bamFetch(database, tg->mapName, posForBam, (isPaired ? addBamPaired : addBam), &btd);
 if (isPaired)
     {
     struct hashEl *hel;
     struct hashCookie cookie = hashFirst(pairHash);