src/hg/hgc/hgc.c 699bed02317b5aa434c08fd446099623c4f7f54a

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("<HTML>");
 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("<HEAD>\n<TITLE>%s vs Genomic [%s]</TITLE>\n</HEAD>\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("<H2>%s</H2>\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)