3afb1ad18d251832c36c02910ba194a3996ab47a
braney
  Mon May 9 14:56:22 2016 -0700
some changes to bigPsl format

diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 53cde9a..8204cad 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -2929,31 +2929,31 @@
 
 struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, seqName, ivStart, ivEnd, 0, lm);
 
 char *bedRow[32];
 char startBuf[16], endBuf[16];
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     bigBedIntervalToRow(bb, seqName, startBuf, endBuf, bedRow, 4);
     struct bed *bed = bedLoadN(bedRow, 4);
     if (sameString(bed->name, item))
 	{
 	bb->next = NULL;
 	break;
 	}
     }
-pslList = pslFromBigPsl(seqName, bb,  hChromSize(database, seqName), NULL, NULL);
+pslList = pslFromBigPsl(seqName, bb, NULL, NULL);
 
 printf("<H3>%s/Genomic Alignments</H3>", item);
 printAlignments(pslList, start, "htcBigPslAli", tdb->table, item);
 pslFreeList(&pslList);
 printItemDetailsHtml(tdb, item);
 }
 
 void genericPslClick(struct sqlConnection *conn, struct trackDb *tdb,
                      char *item, int start, char *subType)
 /* Handle click in generic psl track. */
 {
 struct psl* pslList = getAlignments(conn, tdb->table, item);
 
 /* check if there is an alignment available for this sequence.  This checks
  * both genbank sequences and other sequences in the seq table.  If so,
@@ -7076,31 +7076,31 @@
 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];
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     bigBedIntervalToRow(bb, seqName, startBuf, endBuf, bedRow, ArraySize(bedRow));
     struct bed *bed = bedLoadN(bedRow, 12);
     if (sameString(bed->name, acc))
 	{
 	bb->next = NULL;
 	break;
 	}
     }
-psl = pslFromBigPsl(seqName, bb,  hChromSize(database, seqName), &seq, &cdsString);
+psl = pslFromBigPsl(seqName, bb, &seq, &cdsString);
 genbankParseCds(cdsString,  &cdsStart, &cdsEnd);
 
 
 struct dnaSeq *rnaSeq = newDnaSeq(seq, strlen(seq), acc);
 showSomeAlignment(psl, rnaSeq, gftRna, 0, rnaSeq->size, NULL, cdsStart, cdsEnd);
 }
 
 static struct dnaSeq *getBaseColorSequence(char *itemName, char *table)
 /* Grab sequence using the sequence and extFile table names out of BASE_COLOR_USE_SEQUENCE. */
 {
 struct trackDb *tdb = hashMustFindVal(trackHash, table);
 char *spec = trackDbRequiredSetting(tdb, BASE_COLOR_USE_SEQUENCE);
 char *specCopy = cloneString(spec);
 
 // value is: extFile seqTbl extFileTbl