0564395ec363631f2ff8d295da6f6b50f873fda4
braney
  Mon Jan 24 17:01:53 2022 -0800
more chromAlias work:  some name changes and support for the new genark
chromAlias format

diff --git src/hg/hgc/hgc.c src/hg/hgc/hgc.c
index 0ca6667..d41af03 100644
--- src/hg/hgc/hgc.c
+++ src/hg/hgc/hgc.c
@@ -3230,31 +3230,31 @@
 printf("<PRE><TT>\n");
 printf("#match\tmisMatches\trepMatches\tnCount\tqNumInsert\tqBaseInsert\ttNumInsert\tBaseInsert\tstrand\tqName\tqSize\tqStart\tqEnd\ttName\ttSize\ttStart\ttEnd\tblockCount\tblockSizes\tqStarts\ttStarts\n");
 for (psl = pslList; psl != NULL; psl = psl->next)
     {
     pslTabOut(psl, stdout);
     }
 printf("</TT></PRE>\n");
 }
 
 void genericBigPslClick(struct sqlConnection *conn, struct trackDb *tdb,
                      char *item, int start, int end)
 /* Handle click in big psl track. */
 {
 struct psl* pslList = NULL;
 char *fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table);
-struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasGetHash(database));
+struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasChromToAliasHash(database));
 struct lm *lm = lmInit(0);
 int ivStart = start, ivEnd = end;
 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++;
     }  
 
 boolean showEvery = sameString(item, "PrintAllSequences");
 boolean showAll = trackDbSettingOn(tdb, "showAll");
 unsigned seqTypeField =  bbExtraFieldIndex(bbi, "seqType");
 struct bigBedInterval *bb, *bbList = NULL;
 
 // If showAll is on, show all alignments with this qName, not just the
@@ -7640,31 +7640,31 @@
 if (!trackHubDatabase(database))
     conn = hAllocConnTrack(database, tdb);
 
 char title[1024];
 safef(title, sizeof title, "%s vs Genomic [%s]", acc, aliTable);
 htmlFramesetStart(title);
 
 /* 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, conn, tdb->table);
-struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasGetHash(database));
+struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasChromToAliasHash(database));
 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->start == start) && (bb->end == end))
 	{
 	bb->next = NULL;
 	break;
 	}
     }
 if (bb == NULL)
     errAbort("item %s not found in range %s:%d-%d in bigBed %s (%s)",
@@ -7704,31 +7704,31 @@
     }
 else
     tdb = hashFindVal(trackHash, aliTable);
 char title[1024];
 safef(title, sizeof title, "%s vs Genomic [%s]", acc, aliTable);
 htmlFramesetStart(title);
 
 /* 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 =  bigBedFileOpenAlias(fileName, chromAliasGetHash(database));
+struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasChromToAliasHash(database));
 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;
 	}
     }
 unsigned seqTypeField =  bbExtraFieldIndex(bbi, "seqType");
 wholePsl = pslFromBigPsl(seqName, bb, seqTypeField, &seq, &cdsString);
@@ -8793,31 +8793,31 @@
 while ((row = sqlNextRow(sr)) != NULL)
     {
     gp = genePredLoad(row+rowOffset);
     slAddHead(&gpList, gp);
     }
 
 sqlFreeResult(&sr);
 hFreeConn(&conn);
 return gpList;
 }
 
 struct genePred *getGenePredForPositionBigGene(struct trackDb *tdb,  char *geneName)
 /* Find the genePred to the current gene using a bigGenePred. */
 {
 char *fileName = hReplaceGbdb(trackDbSetting(tdb, "bigDataUrl"));
-struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasGetHash(database));
+struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasChromToAliasHash(database));
 struct lm *lm = lmInit(0);
 struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, seqName, winStart, winEnd, 0, lm);
 struct genePred *gpList = NULL;
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     struct genePred *gp = (struct genePred *)genePredFromBigGenePred(seqName, bb); 
     if (sameString(gp->name, geneName))
 	slAddHead(&gpList, gp);
     }
 lmCleanup(&lm);
 
 return gpList;
 }
 
 static struct trackDb *getCustomTrackTdb(char *table)
@@ -8894,31 +8894,31 @@
 int start = cartInt(cart, "l");
 int end = cartInt(cart, "r");
 char *table = cartString(cart, "table");
 
 struct trackDb *tdb ;
 if (isCustomTrack(table))
     {
     struct customTrack *ct = lookupCt(table);
     tdb = ct->tdb;
     }
 else if (isHubTrack(table))
     tdb = hubConnectAddHubForTrackAndFindTdb( database, table, NULL, trackHash);
 else
     tdb = hashFindVal(trackHash, table);
 char *fileName = bbiNameFromSettingOrTable(tdb, conn, tdb->table);
-struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasGetHash(database));
+struct bbiFile *bbi =  bigBedFileOpenAlias(fileName, chromAliasChromToAliasHash(database));
 struct lm *lm = lmInit(0);
 int ivStart = start, ivEnd = end;
 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++;
     }  
 
 unsigned seqTypeField =  bbExtraFieldIndex(bbi, "seqType");
 struct bigBedInterval *bb, *bbList = NULL;
 
 bbList = bigBedIntervalQuery(bbi, seqName, ivStart, ivEnd, 0, lm);
 
 char *bedRow[32];
@@ -9268,31 +9268,31 @@
 	{
 	s -= startOffset;
 	if (s < 0 ||  s + size > seq->size)
 	    errAbort("Out of range! %d-%d not in %d-%d", s, s+size, 0, size);
 	toUpperN(seq->dna + s, size);
 	}
     }
 }
 
 
 static struct bed *getBedsFromBigBedRange(struct trackDb *tdb, char *geneName)
 /* get a list of beds from a bigBed in the current range */
 {
 struct bbiFile *bbi;
 char *fileName = hReplaceGbdb(trackDbSetting(tdb, "bigDataUrl"));
-bbi =  bigBedFileOpenAlias(fileName, chromAliasGetHash(database));
+bbi =  bigBedFileOpenAlias(fileName, chromAliasChromToAliasHash(database));
 struct lm *lm = lmInit(0);
 struct bigBedInterval *bb, *bbList = bigBedIntervalQuery(bbi, seqName, winStart, winEnd, 0, lm);
 struct bed *bedList = NULL;
 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, geneName))
 	slAddHead(&bedList, bed);
     }
 lmCleanup(&lm);
 
 return bedList;