b622d147b7dbac52dbf3ba26928cd18e02d42bd8
braney
  Sat Feb 26 12:34:37 2022 -0800
add support for using a bigBed as the chromAlias file

diff --git src/hg/hgc/togaClick.c src/hg/hgc/togaClick.c
index db78aa9..62b7627 100644
--- src/hg/hgc/togaClick.c
+++ src/hg/hgc/togaClick.c
@@ -165,31 +165,31 @@
         strcpy(suffix, empty);
     } else {
         // just start the string 11 characters upstream
         memmove(suffix, suffix + HLTOGA_BED_PREFIX_LEN, suff_len - HLTOGA_BED_PREFIX_LEN + 1);
     }
 }
 
 
 void doHillerLabTOGAGeneBig(char *database, struct trackDb *tdb, char *item, char *table_name)
 /* Put up TOGA Gene track info. */
 {
 int start = cartInt(cart, "o");
 int end = cartInt(cart, "t");
 char *chrom = cartString(cart, "c");
 char *fileName = bbiNameFromSettingOrTable(tdb, NULL, tdb->table);
-struct bbiFile *bbi =  bigBedFileOpenAlias(hReplaceGbdb(fileName), chromAliasChromToAliasHash(database));
+struct bbiFile *bbi =  bigBedFileOpenAlias(hReplaceGbdb(fileName), chromAliasFindAliases);
 struct lm *lm = lmInit(0);
 struct bigBedInterval *bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm);
 struct bigBedInterval *bb;
 char *fields[bbi->fieldCount];
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     if (!(bb->start == start && bb->end == end))
 	continue;
 
     // our names are unique
     char *name = cloneFirstWordByDelimiterNoSkip(bb->rest, '\t');
     boolean match = (isEmpty(name) && isEmpty(item)) || sameOk(name, item);
     if (!match)
         continue;
 
@@ -252,31 +252,31 @@
 printf("<h4>Protein sequence</h4><BR>\n");
 printf("<a data-toggle=\"collapse\" href=\"#collapseProt\">Show protein alignment</a>\n");
 printf("<div id=\"collapseProt\" class=\"panel-collapse collapse\">\n");
 printf("<TT>%s</TT><BR>\n", info->prot_alignment);
 printf("</div>\n<BR><BR>\n");
 
 // show inactivating mutations if required
 printf("<h4>Inactivating mutations</h4><BR>\n");
 
 printf("<a data-toggle=\"collapse\" href=\"#collapseMuts\">Show inactivating mutations</a>\n");
 printf("<div id=\"collapseMuts\" class=\"panel-collapse collapse\">\n");
 printf("<table border = \"1\" width = \"640\">\n");  // init table
 printf("<tr><th>exon</th><th>pos</th><th>m_class</th><th>mut</th><th>is_inact</th><th>mut_id</th>\n");
 printf("</tr>\n");
 fileName = trackDbSetting(tdb, "inactMutUrl");
-bbi =  bigBedFileOpenAlias(hReplaceGbdb(fileName), chromAliasChromToAliasHash(database));
+bbi =  bigBedFileOpenAlias(hReplaceGbdb(fileName), chromAliasFindAliases);
 //struct lm *lm = lmInit(0);
 bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm);
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     if (!(bb->start == start && bb->end == end))
 	continue;
 
     // our names are unique
     char *name = cloneFirstWordByDelimiterNoSkip(bb->rest, '\t');
     boolean match = (isEmpty(name) && isEmpty(item)) || sameOk(name, item);
     if (!match)
         continue;
 
     char startBuf[16], endBuf[16];
     bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields, bbi->fieldCount);
@@ -295,31 +295,31 @@
         printf("<td>%s</td>\n", info->mut_id);
         printf("</tr>\n");
         togaInactMutFree(&info);
     }
     //sqlFreeResult(&sr);
     printf("</table>\n");
     printf("</div>\n<BR>\n");
 
 // show exons data
 htmlHorizontalLine();
 printf("<h4>Exons data</h4><BR>\n");
 
 printf("<a data-toggle=\"collapse\" href=\"#collapseExons\">Show exon sequences and features</a>\n");
 printf("<div id=\"collapseExons\" class=\"panel-collapse collapse\">\n");
 fileName = trackDbSetting(tdb, "nuclUrl");
-bbi =  bigBedFileOpenAlias(hReplaceGbdb(fileName), chromAliasChromToAliasHash(database));
+bbi =  bigBedFileOpenAlias(hReplaceGbdb(fileName), chromAliasFindAliases);
 //struct lm *lm = lmInit(0);
 bbList = bigBedIntervalQuery(bbi, chrom, start, end, 0, lm);
 for (bb = bbList; bb != NULL; bb = bb->next)
     {
     if (!(bb->start == start && bb->end == end))
 	continue;
 
     // our names are unique
     char *name = cloneFirstWordByDelimiterNoSkip(bb->rest, '\t');
     boolean match = (isEmpty(name) && isEmpty(item)) || sameOk(name, item);
     if (!match)
         continue;
 
     char startBuf[16], endBuf[16];
     bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields, bbi->fieldCount);