d2482e22232f8a2296fcc6706b2630f5499f7a83
braney
  Wed Jul 17 13:45:02 2024 -0700
change chroms to chromAuthority names in hgBlat and hgPcr

diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 9e1ea2f..71c1f64 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -6515,34 +6515,35 @@
 for (isClicked = 1; isClicked >= 0; isClicked -= 1)
     {
     for (psl = pslList; psl != NULL; psl = psl->next)
 	{
 	if (isPslToPrintByClick(psl, startFirst, isClicked))
 	    {
             char otherString[512];
             char *qName = itemIn;
             if (sameString(itemIn, "PrintAllSequences"))
                 qName = psl->qName;
 	    safef(otherString, sizeof(otherString), "%d&aliTable=%s", psl->tStart, tableName);
             printf("<A HREF=\"%s&db=%s&position=%s%%3A%d-%d\">browser</A> | ",
                    hgTracksPathAndSettings(), database, psl->tName, psl->tStart+1, psl->tEnd);
 	    if (psl->qSize <= MAX_DISPLAY_QUERY_SEQ_SIZE) // Only anchor if small enough 
 		hgcAnchorWindow(hgcCommand, qName, psl->tStart, psl->tEnd, otherString, psl->tName);
+            char *displayChromName = chromAliasGetDisplayChrom(database, cart, psl->tName);
 	    printf("%5d  %5.1f%%  %9s     %s %9d %9d  %20s %5d %5d %5d",
 		   psl->match + psl->misMatch + psl->repMatch,
 		   100.0 - pslCalcMilliBad(psl, TRUE) * 0.1,
-		   skipChr(psl->tName), psl->strand, psl->tStart + 1, psl->tEnd,
+		   skipChr(displayChromName), psl->strand, psl->tStart + 1, psl->tEnd,
 		   psl->qName, psl->qStart+1, psl->qEnd, psl->qSize);
 	    if (psl->qSize <= MAX_DISPLAY_QUERY_SEQ_SIZE)
 	        printf("</A>");
 	    printf("\n");
 	    }
 	}
     }
 printf("</TT></PRE>");
 }
 
 void printAlignmentsExtra(struct psl *pslList, int startFirst, char *hgcCommand, char *hgcCommandInWindow,
 		     char *tableName, char *itemIn)
 /* Print list of mRNA alignments with special "in window" alignment function. */
 {
 if (pslList == NULL || tableName == NULL)
@@ -7793,38 +7794,39 @@
 
 int rnaStart = 0;
 int rnaEnd = rnaSize;
 
 if (restrictToWindow)
     {
     /* Find start/end in ffAli, which is clipped to target from PSL and maybe RC'd */
     ffStartEndQ(rna, ffAli, &rnaStart, &rnaEnd);
 
     /* Add 100 bases either side if possible */
     if (rnaStart >= 100) rnaStart -= 100;
     if (rnaEnd + 100 <= rnaSize) rnaEnd += 100;
     }
 
 /* Write body heading info. */
+char *displayChromName = chromAliasGetDisplayChrom(database, cart, psl->tName);
 fprintf(body, "<H2>Alignment of %s and %s:%d-%d</H2>\n",
-	psl->qName, psl->tName, partTStart+1, partTEnd);
+	psl->qName, displayChromName, partTStart+1, partTEnd);
 fprintf(body, "Click on links in the frame to the left to navigate through "
 	"the alignment.\n");
 
 blockCount = ffShAliPart(body, ffAli, wholePsl->qName,
                          rna + rnaStart, rnaEnd - rnaStart, rnaStart,
-			 dnaSeq->name, dnaSeq->dna, dnaSeq->size,
+			 displayChromName, dnaSeq->dna, dnaSeq->size,
 			 wholeTStart, 8, FALSE, isRc,
 			 FALSE, TRUE, TRUE, TRUE, TRUE,
                          cdsS, cdsE, partTStart, partTEnd);
 return blockCount;
 }
 
 void showSomeAlignment(struct psl *psl, bioSeq *oSeq,
                        enum gfType qType, int qStart, int qEnd,
                        char *qName, int cdsS, int cdsE)
 /* Display protein or DNA alignment in a frame. */
 {
 int blockCount, i;
 struct tempName indexTn, bodyTn;
 FILE *index, *body;
 
@@ -7837,31 +7839,32 @@
 if (qType == gftRna || qType == gftDna)
     blockCount = showPartialDnaAlignment(psl, oSeq, body, cdsS, cdsE, FALSE);
 else
     blockCount = showGfAlignment(psl, oSeq, body, qType, qStart, qEnd, qName);
 htmEnd(body);
 fclose(body);
 chmod(bodyTn.forCgi, 0666);
 
 /* Write index. */
 index = mustOpen(indexTn.forCgi, "w");
 if (qName == NULL)
     qName = psl->qName;
 htmStartDirDepth(index, qName, 2);
 fprintf(index, "<H3>Alignment of %s</H3>", qName);
 fprintf(index, "<A HREF=\"../%s#cDNA\" TARGET=\"body\">%s</A><BR>\n", bodyTn.forCgi, qName);
-fprintf(index, "<A HREF=\"../%s#genomic\" TARGET=\"body\">%s.%s</A><BR>\n", bodyTn.forCgi, hOrganism(database), psl->tName);
+char *displayChromName = chromAliasGetDisplayChrom(database, cart, psl->tName);
+fprintf(index, "<A HREF=\"../%s#genomic\" TARGET=\"body\">%s.%s</A><BR>\n", bodyTn.forCgi, hOrganism(database), displayChromName);
 for (i=1; i<=blockCount; ++i)
     {
     fprintf(index, "<A HREF=\"../%s#%d\" TARGET=\"body\">block%d</A><BR>\n",
 	    bodyTn.forCgi, i, i);
     }
 fprintf(index, "<A HREF=\"../%s#ali\" TARGET=\"body\">together</A><BR>\n", bodyTn.forCgi);
 htmEnd(index);
 fclose(index);
 chmod(indexTn.forCgi, 0666);
 
 /* Write (to stdout) the main html page containing just the frame info. */
 puts("<FRAMESET COLS = \"13%,87% \" >");
 printf("  <FRAME SRC=\"%s\" NAME=\"index\">\n", indexTn.forCgi);
 printf("  <FRAME SRC=\"%s\" NAME=\"body\">\n", bodyTn.forCgi);
 puts("<NOFRAMES><BODY></BODY></NOFRAMES>");