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

diff --git src/hg/hgBlat/hgBlat.c src/hg/hgBlat/hgBlat.c
index 7dafa61..4c0c80a 100644
--- src/hg/hgBlat/hgBlat.c
+++ src/hg/hgBlat/hgBlat.c
@@ -21,30 +21,31 @@
 #include "dbDb.h"
 #include "blatServers.h"
 #include "web.h"
 #include "hash.h"
 #include "botDelay.h"
 #include "trashDir.h"
 #include "trackHub.h"
 #include "hgConfig.h"
 #include "errCatch.h"
 #include "portable.h"
 #include "portable.h"
 #include "dystring.h"
 #include "chromInfo.h"
 #include "net.h"
 #include "fuzzyFind.h"
+#include "chromAlias.h"
 
 struct cart *cart;	/* The user's ui state. */
 struct hash *oldVars = NULL;
 boolean orgChange = FALSE;
 boolean dbChange = FALSE;
 boolean allGenomes = FALSE;
 boolean allResults = FALSE;
 static long enteredMainTime = 0;
 
 /* for earlyBotCheck() function at the beginning of main() */
 #define delayFraction   0.5    /* standard penalty is 1.0 for most CGIs */
                                 /* this one is 0.5 */
 static boolean issueBotWarning = FALSE;
 
 struct gfResult
@@ -706,32 +707,33 @@
             printf("<A TITLE='%s' TARGET=_BLANK HREF=\"%s?position=%s:%d-%d&db=%s&ss=%s+%s&%s\">new tab%s</A>&nbsp;",
                 helpText, browserUrl, psl->tName, psl->tStart + 1, psl->tEnd, database, 
                 pslName, faName, unhideTrack, icon);
             }
 	printf("<A title='Show query sequence, genome hit and sequence alignment' "
                 "HREF=\"%s?o=%d&g=htcUserAli&i=%s+%s+%s&c=%s&l=%d&r=%d&db=%s&%s\">", 
 	    hgcUrl, psl->tStart, pslName, cgiEncode(faName), psl->qName,  psl->tName,
 	    psl->tStart, psl->tEnd, database, uiState);
 	printf("details</A> ");
 
 	printf("%s",psl->qName);
 	spaceOut(stdout, maxQChromNameSize - strlen(psl->qName));
 	printf(" %5d %5d %5d %5d   %5.1f%%  ",
 	    pslScore(psl), psl->qStart+1, psl->qEnd, psl->qSize,
 	    100.0 - pslCalcMilliBad(psl, TRUE) * 0.1);
-	printf("%s",psl->tName);
-	spaceOut(stdout, maxTChromNameSize - strlen(psl->tName));
+        char *displayChromName = chromAliasGetDisplayChrom(database, cart, psl->tName);
+	printf("%s",displayChromName);
+	spaceOut(stdout, maxTChromNameSize - strlen(displayChromName));
 	printf("  %-2s  %9d %9d %6d",
 	    psl->strand, psl->tStart+1, psl->tEnd,
 	    psl->tEnd - psl->tStart);
 
         // if you modify this, also modify hgPcr.c:doQuery, which implements a similar feature
         char *seq = psl->tName;
         if (endsWith(seq, "_fix"))
             printf("   <A target=_blank HREF=\"../FAQ/FAQdownloads.html#downloadFix\">What is chrom_fix?</A>");
         else if (endsWith(seq, "_alt"))
             printf("   <A target=_blank HREF=\"../FAQ/FAQdownloads.html#downloadAlt\">What is chrom_alt?</A>");
         else if (endsWith(seq, "_random"))
             printf("   <A target=_blank HREF=\"../FAQ/FAQdownloads.html#download10\">What is chrom_random?</A>");
         else if (startsWith(seq, "chrUn"))
             printf("   <A target=_blank HREF=\"../FAQ/FAQdownloads.html#download11\">What is a chrUn sequence?</A>");
         printf("\n");
@@ -2145,30 +2147,31 @@
 /* Write header and body of html page. */
 {
 char *userSeq;
 char *db, *organism;
 
 boolean clearUserSeq = cgiBoolean("Clear");
 allGenomes = cgiVarExists("allGenomes");
 
 cart = theCart;
 dnaUtilOpen();
 
 orgChange = sameOk(cgiOptionalString("changeInfo"),"orgChange");
 if (orgChange)
     cgiVarSet("db", hDefaultDbForGenome(cgiOptionalString("org"))); 
 getDbAndGenome(cart, &db, &organism, oldVars);
+chromAliasSetup(db);
 char *oldDb = cloneString(db);
 
 // n.b. this changes to default db if db doesn't have BLAT
 findClosestServer(&db, &organism);
 
 allResults = cartUsualBoolean(cart, "allResults", allResults);
 
 /* Get sequence - from userSeq variable, or if 
  * that is empty from a file. */
 if (clearUserSeq)
     {
     cartSetString(cart, "userSeq", "");
     cartSetString(cart, "seqFile", "");
     }
 userSeq = cartUsualString(cart, "userSeq", "");