699bed02317b5aa434c08fd446099623c4f7f54a
braney
Thu May 5 14:51:21 2016 -0700
working on bigMaf doc
diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 6efff4b..772fa1e 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -7041,30 +7041,40 @@
}
void htcBigPslAli(char *acc)
/* Show alignment for accession in bigPsl file. */
{
struct psl *psl;
char *aliTable;
int start;
unsigned int cdsStart = 0, cdsEnd = 0;
/* Print start of HTML. */
writeFramesetType();
puts("");
aliTable = cartString(cart, "aliTable");
+if (isCustomTrack(aliTable))
+ {
+ struct customTrack *ctList = getCtList();
+ struct customTrack *ct = NULL;
+ for (ct = ctList; ct != NULL; ct = ct->next)
+ if (sameString(aliTable, ct->tdb->track))
+ break;
+ tdb = ct->tdb;
+ }
+else
tdb = hashFindVal(trackHash, aliTable);
printf("\n%s vs Genomic [%s]\n\n\n", acc, aliTable);
/* Get some environment vars. */
start = cartInt(cart, "l");
int end = cartInt(cart, "r");
char *chrom = cartString(cart, "c");
char *seq, *cdsString = NULL;
struct lm *lm = lmInit(0);
char *fileName = bbiNameFromSettingOrTable(tdb, NULL, tdb->table);
struct bbiFile *bbi = bigBedFileOpen(fileName);
struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm);
char *bedRow[32];
char startBuf[16], endBuf[16];
@@ -20705,47 +20715,51 @@
footPrinterSampleClick(conn, tdb, item, start, num);
}
printTrackHtml(tdb);
freez(&dupe);
hFreeConn(&conn);
}
void hgCustom(char *trackId, char *fileItem)
/* Process click on custom track. */
{
char *fileName, *itemName;
struct customTrack *ctList = getCtList();
struct customTrack *ct;
struct bed *bed = (struct bed *)NULL;
int start = cartInt(cart, "o");
+int end = cartInt(cart, "t");
+char *item = cartString(cart, "i");
char *type;
fileName = nextWord(&fileItem);
for (ct = ctList; ct != NULL; ct = ct->next)
if (sameString(trackId, ct->tdb->track))
break;
if (ct == NULL)
errAbort("Couldn't find '%s' in '%s'", trackId, fileName);
type = ct->tdb->type;
cartWebStart(cart, database, "Custom Track: %s", ct->tdb->shortLabel);
itemName = skipLeadingSpaces(fileItem);
printf("%s
\n", ct->tdb->longLabel);
if (sameWord(type, "array"))
doExpRatio(ct->tdb, fileItem, ct);
else if (sameWord(type, "encodePeak"))
doEncodePeak(ct->tdb, ct, fileName);
else if (sameWord(type, "bigWig"))
bigWigCustomClick(ct->tdb);
+else if (sameWord(type, "bigPsl"))
+ genericBigPslClick(NULL, ct->tdb, item, start, end);
else if (sameWord(type, "bigBed") || sameWord(type, "bigGenePred"))
bigBedCustomClick(ct->tdb);
#ifdef USE_BAM
else if (sameWord(type, "bam"))
doBamDetails(ct->tdb, itemName);
#endif//def USE_BAM
#ifdef USE_TABIX
else if (sameWord(type, "vcfTabix"))
doVcfTabixDetails(ct->tdb, itemName);
#endif//def USE_TABIX
else if (sameWord(type, "vcf"))
doVcfDetails(ct->tdb, itemName);
else if (sameWord(type, "makeItems"))
doMakeItemsDetails(ct, fileName); // fileName is first word, which is, go figure, id
else if (ct->wiggle)