src/hg/hgTracks/bamTrack.c 1.23
1.23 2010/01/05 05:36:26 angie
Oops, don't use global var position -- when we zoom, that is not updated and still has the old pos. Use chromName:winStart-winEnd instead (samtools uses 0-based offsets).
Index: src/hg/hgTracks/bamTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/bamTrack.c,v
retrieving revision 1.22
retrieving revision 1.23
diff -b -B -U 4 -r1.22 -r1.23
--- src/hg/hgTracks/bamTrack.c 5 Jan 2010 00:34:49 -0000 1.22
+++ src/hg/hgTracks/bamTrack.c 5 Jan 2010 05:36:26 -0000 1.23
@@ -351,14 +351,15 @@
errAbort("bamLoadItemsCore: can't find bigDataUrl for custom track %s", tg->mapName);
}
else
fileName = bamFileNameFromTable(database, tg->mapName, chromName);
+
+char posForBam[512];
+safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName, winStart, winEnd);
if (!isPaired)
- bamFetch(fileName, position, addBam, &btd);
+ bamFetch(fileName, posForBam, addBam, &btd);
else
{
- char posForBam[512];
- safecpy(posForBam, sizeof(posForBam), position);
char *setting = trackDbSettingClosestToHomeOrDefault(tg->tdb, "pairSearchRange", "20000");
int pairSearchRange = atoi(setting);
if (pairSearchRange > 0)
safef(posForBam, sizeof(posForBam), "%s:%d-%d", chromName,