src/hg/hgc/bamClick.c 1.8
1.8 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/hgc/bamClick.c
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/hgc/bamClick.c,v
retrieving revision 1.7
retrieving revision 1.8
diff -b -B -U 4 -r1.7 -r1.8
--- src/hg/hgc/bamClick.c 24 Aug 2009 23:47:56 -0000 1.7
+++ src/hg/hgc/bamClick.c 14 Sep 2009 23:44:25 -0000 1.8
@@ -135,9 +135,10 @@
bamIgnoreStrand();
struct hash *pairHash = isPaired ? hashNew(0) : NULL;
struct bamTrackData btd = {start, item, pairHash};
-bamFetch(database, tdb->tableName, posForBam, oneBam, &btd);
+char *fileName = bamFileNameFromTable(database, tdb->tableName, seqNameForBam);
+bamFetch(fileName, posForBam, oneBam, &btd);
if (isPaired && hashNumEntries(pairHash) > 0)
{
char *setting = trackDbSettingOrDefault(tdb, "pairSearchRange", "1000");
int pairSearchRange = atoi(setting);
@@ -149,9 +150,9 @@
btd.itemName = hel->name;
btd.pairHash = newPairHash;
safef(posForBam, sizeof(posForBam), "%s:%d-%d", seqNameForBam,
winStart-pairSearchRange, winEnd+pairSearchRange);
- bamFetch(database, tdb->tableName, posForBam, oneBam, &btd);
+ bamFetch(fileName, posForBam, oneBam, &btd);
if (hashNumEntries(newPairHash) > 0)
{
struct hashCookie cookie2 = hashFirst(pairHash);
while ((hel = hashNext(&cookie2)) != NULL)