src/hg/hgTracks/bamTrack.c 1.9

1.9 2009/09/14 23:44:25 angie
Added bamFileNameFromTable to bamFile.h and changed bamFetch to take a filename, not db+table, so it can be used for CT files someday. bamFileNameFromTable supports an optional seqName column in the db table, for per-chrom BAM files (as we get from 1000Genomes).

Index: src/hg/hgTracks/bamTrack.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgTracks/bamTrack.c,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 4 -r1.8 -r1.9
--- src/hg/hgTracks/bamTrack.c	8 Sep 2009 21:39:38 -0000	1.8
+++ src/hg/hgTracks/bamTrack.c	14 Sep 2009 23:44:25 -0000	1.9
@@ -221,9 +221,10 @@
 char cartVarName[512];
 safef(cartVarName, sizeof(cartVarName), "%s_minAliQual", tg->tdb->tableName);
 int minAliQual = cartUsualInt(cart, cartVarName, 0);
 struct bamTrackData btd = {tg, pairHash, minAliQual};
-bamFetch(database, tg->mapName, posForBam, (isPaired ? addBamPaired : addBam), &btd);
+char *fileName = bamFileNameFromTable(database, tg->mapName, seqNameForBam);
+bamFetch(fileName, posForBam, (isPaired ? addBamPaired : addBam), &btd);
 if (isPaired)
     {
     struct hashEl *hel;
     struct hashCookie cookie = hashFirst(pairHash);