13b584581e6d7b1860e0cab97adc3594b1899308
braney
  Mon Aug 7 12:05:10 2023 -0700
add instaPort to bigBed support

diff --git src/hg/hgc/bigBedClick.c src/hg/hgc/bigBedClick.c
index 20bdd03..0140cb5 100644
--- src/hg/hgc/bigBedClick.c
+++ src/hg/hgc/bigBedClick.c
@@ -2,30 +2,31 @@
 
 /* Copyright (C) 2013 The Regents of the University of California 
  * See kent/LICENSE or http://genome.ucsc.edu/license/ for licensing information. */
 
 #include "common.h"
 #include "wiggle.h"
 #include "cart.h"
 #include "hgc.h"
 #include "hCommon.h"
 #include "hgColors.h"
 #include "bigBed.h"
 #include "hui.h"
 #include "subText.h"
 #include "web.h"
 #include "chromAlias.h"
+#include "instaPort.h"
 
 static void bigGenePredLinks(char *track, char *item)
 /* output links to genePred driven sequence dumps */
 {
 printf("<H3>Links to sequence:</H3>\n");
 printf("<UL>\n");
 puts("<LI>\n");
 hgcAnchorSomewhere("htcTranslatedPredMRna", item, "translate", seqName);
 printf("Translated Protein</A> from genomic DNA\n");
 puts("</LI>\n");
 
 puts("<LI>\n");
 hgcAnchorSomewhere("htcGeneMrna", item, track, seqName);
 printf("Predicted mRNA</A> \n");
 puts("</LI>\n");
@@ -360,51 +361,55 @@
 /* Handle click in generic bigBed track. */
 {
 char *chrom = cartString(cart, "c");
 
 /* Open BigWig file and get interval list. */
 struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasFindAliases);
 struct lm *lm = lmInit(0);
 int ivStart = start, ivEnd = end;
 char *itemForUrl = item;
 if (start == end)
     {
     // item is an insertion; expand the search range from 0 bases to 2 so we catch it:
     ivStart = max(0, start-1);
     ivEnd++;
     }
-struct bigBedInterval *bbList = bigBedIntervalQuery(bbi, chrom, ivStart, ivEnd, 0, lm);
+char *instaFile = cloneString(trackDbSetting(tdb, "instaPortUrl"));
+struct hash *chainHash = NULL;
+struct bigBedInterval *bbList = NULL;
+if (instaFile)
+    bbList = instaIntervals(instaFile, bbi, chrom, ivStart, ivEnd, &chainHash);
+else
+    bbList = bigBedIntervalQuery(bbi, chrom, ivStart, ivEnd, 0, lm);
 
 /* Get bedSize if it's not already defined. */
 if (bedSize == 0)
     {
     bedSize = bbi->definedFieldCount;
     }
 
 char *scoreFilter = cartOrTdbString(cart, tdb, "scoreFilter", NULL);
 int minScore = 0;
 if (scoreFilter)
     minScore = atoi(scoreFilter);
 
 /* Find particular item in list - matching start, and item if possible. */
 boolean found = FALSE;
 boolean firstTime = TRUE;
 struct bigBedInterval *bb;
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
-    if (!(bb->start == start && bb->end == end))
-	continue;
     if (bedSize > 3)
 	{
 	char *name = cloneFirstWordByDelimiterNoSkip(bb->rest, '\t');
 	boolean match = (isEmpty(name) && isEmpty(item)) || sameOk(name, item);
 	freez(&name);
 	if (!match)
 	    continue;
 	}
 
     found = TRUE;
     if (firstTime)
 	printf("<BR>\n");
     int seq1Seq2Fields = 0;
     // check for seq1 and seq2 in columns 7+8 (eg, pairedTagAlign)
     boolean seq1Seq2 = sameOk(trackDbSetting(tdb, BASE_COLOR_USE_SEQUENCE), "seq1Seq2");
@@ -425,32 +430,43 @@
         restBedFields = bedSize - 3;
         if (restCount > restBedFields)
             {
             extraFields = (restFields + restBedFields);
             extraFieldCount = restCount - restBedFields;
             extraFieldPairs = getExtraFields(tdb, extraFields, extraFieldCount);
             }
         }
     int bbFieldCount = bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields,
                                            bedSize+seq1Seq2Fields);
     if (bbFieldCount != bedSize+seq1Seq2Fields)
         {
         errAbort("Disagreement between trackDb field count (%d) and %s fieldCount (%d)",
 		bedSize, fileName, bbFieldCount);
 	}
-    struct bed *bed = bedLoadN(fields, bedSize);
-    if (bedSize >= 6 && scoreFilter && bed->score < minScore)
+    struct bed *bed = NULL;
+    if (instaFile)
+        {
+        if ((bed = instaBed(bbi, chainHash, bb)) == NULL)
+            errAbort("can't port %s",fields[3]);
+        }
+    else
+        {
+        bed = bedLoadN(fields, bedSize);
+        }
+    if ((bed == NULL) || (bedSize >= 6 && scoreFilter && bed->score < minScore))
+        continue;
+    if (!(bed->chromStart == start && bed->chromEnd == end))
 	continue;
 
     // if there are extra fields, load them up because we may want to use them in URL:
     itemForUrl = getIdInUrl(tdb, item);
     printCustomUrlWithFields(tdb, bed->name, bed->name, item == itemForUrl, extraFieldPairs);
     if (itemForUrl)
         printIframe(tdb, itemForUrl);
 
     bedPrintPos(bed, bedSize, tdb);
 
     // display seq1 and seq2
     if (seq1Seq2 && bedSize+seq1Seq2Fields == 8)
         printf("<table><tr><th>Sequence 1</th><th>Sequence 2</th></tr>"
             "<tr><td> %s </td><td> %s </td></tr></table>", fields[6], fields[7]);
     else if (restCount > 0)