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
@@ -1,570 +1,570 @@
 /* togaClick - click handling for TOGA tracks */
 #include "common.h"
 #include "hgc.h"
 #include "togaClick.h"
 #include "string.h"
 #include "htmshell.h"
 #include "chromAlias.h"
 
 
 struct togaData *togaDataLoad(char **row)
 /* Load a togaData from row fetched with select * from togaData
  * from database.  Dispose of this with togaDataFree(). */
 {
     struct togaData *ret;
     AllocVar(ret);
     ret->projection = cloneString(row[0]);
     ret->ref_trans_id = cloneString(row[1]);
     ret->ref_region = cloneString(row[2]);
     ret->query_region = cloneString(row[3]);
     ret->chain_score = cloneString(row[4]);
 
     ret->chain_synteny = cloneString(row[5]);
     ret->chain_flank = cloneString(row[6]);
     ret->chain_gl_cds_fract = cloneString(row[7]);
     ret->chain_loc_cds_fract = cloneString(row[8]);
     ret->chain_exon_cov = cloneString(row[9]);
 
     ret->chain_intron_cov = cloneString(row[10]);
     ret->status = cloneString(row[11]);
     ret->perc_intact_ign_M = cloneString(row[12]);
     ret->perc_intact_int_M = cloneString(row[13]);
     ret->intact_codon_prop = cloneString(row[14]);
 
     ret->ouf_prop = cloneString(row[15]);
     ret->mid_intact = cloneString(row[16]);
     ret->mid_pres = cloneString(row[17]);
     ret->prot_alignment = cloneString(row[18]);
     ret->svg_line = cloneString(row[19]);
     return ret;
 }
 
 
 void togaDataFree(struct togaData **pEl)
 /* Free a single dynamically allocated togaDatasuch as created
  * with togaDataLoad(). */
 {
     struct togaData *el;
 
     if ((el = *pEl) == NULL) return;
     freeMem(el->projection);
     freeMem(el->ref_trans_id);
     freeMem(el->ref_region);
     freeMem(el->query_region);
     freeMem(el->chain_score);
 
     freeMem(el->chain_synteny);
     freeMem(el->chain_flank);
     freeMem(el->chain_gl_cds_fract);
     freeMem(el->chain_loc_cds_fract);
     freeMem(el->chain_exon_cov);
 
     freeMem(el->chain_intron_cov);
     freeMem(el->status);
     freeMem(el->perc_intact_ign_M);
     freeMem(el->perc_intact_int_M);
     freeMem(el->intact_codon_prop);
 
     freeMem(el->ouf_prop);
     freeMem(el->mid_intact);
     freeMem(el->mid_pres);
     freeMem(el->prot_alignment);
     freeMem(el->svg_line);
     freez(pEl);
 }
 
 struct togaNucl *togaNuclLoad(char **row)
 /* Load a togaNucl from row fetched with select * from togaNucl
  * from database.  Dispose of this with togaNuclFree(). */
 {
     struct togaNucl *ret;
     AllocVar(ret);
     ret->transcript = cloneString(row[0]);
     ret->exon_num = cloneString(row[1]);
     ret->exon_region = cloneString(row[2]);
     ret->pid = cloneString(row[3]);
     ret->blosum = cloneString(row[4]);
 
     ret->gaps = cloneString(row[5]);
     ret->ali_class = cloneString(row[6]);
     ret->exp_region = cloneString(row[7]);
     ret->in_exp_region = cloneString(row[8]);
     ret->alignment = cloneString(row[9]);
     return ret;
 }
 
 
 void togaNuclFree(struct togaNucl **pEl)
 /* Free a single dynamically allocated togaNucl such as created
  * with togaNuclLoad(). */
 {
     struct togaNucl *el;
 
     if ((el = *pEl) == NULL) return;
     freeMem(el->transcript);
     freeMem(el->exon_num);
     freeMem(el->exon_region);
     freeMem(el->pid);
     freeMem(el->blosum);
 
     freeMem(el->gaps);
     freeMem(el->ali_class);
     freeMem(el->exp_region);
     freeMem(el->in_exp_region);
     freeMem(el->alignment);
     freez(pEl);
 }
 
 
 struct togaInactMut *togaInactMutLoad(char **row)
 /* Load a togaInactMut from row fetched with select * from togaInactMut
  * from database.  Dispose of this with togaInactMutFree(). */
 {
     struct togaInactMut *ret;
     AllocVar(ret);
     ret->transcript = cloneString(row[0]);
     ret->exon_num = cloneString(row[1]);
     ret->position = cloneString(row[2]);
     ret->mut_class = cloneString(row[3]);
     ret->mutation = cloneString(row[4]);
 
     ret->is_inact = cloneString(row[5]);
     ret->mut_id = cloneString(row[6]);
     return ret;
 }
 
 
 void togaInactMutFree(struct togaInactMut **pEl)
 /* Free a single dynamically allocated togaInactMut such as created
  * with togaInactMutLoad(). */
 {
     struct togaInactMut *el;
     if ((el = *pEl) == NULL) return;
     freeMem(el->transcript);
     freeMem(el->exon_num);
     freeMem(el->position);
     freeMem(el->mut_class);
     freeMem(el->mutation);
 
     freeMem(el->is_inact);
     freeMem(el->mut_id);
     freez(pEl);
 }
 
 
 void extractHLTOGAsuffix(char *suffix)
 /* Extract suffix from TOGA table name.
 Prefix must be HLTOGAannot */
 {
     int suff_len = strlen(suffix);
     if (suff_len <= HLTOGA_BED_PREFIX_LEN)
     // we cannot chop first PREFIX_LEN characters
     {
         // TODO: NOT SURE IF IT WORKS; but this must not happen
         char empty[5] = { '\0' };
         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;
 
     char startBuf[16], endBuf[16];
     bigBedIntervalToRow(bb, chrom, startBuf, endBuf, fields, bbi->fieldCount);
     break;
     }
 
 printf("<h3>Projection %s</h3><BR>\n", item);
 struct togaData       *info = togaDataLoad(&fields[11]);  
 // fill HTML template:
 printf("<B>Projected via: </B><A HREF=\"http://www.ensembl.org/Homo_sapiens/transview?transcript=%s\" target=_blank>%s</A><BR>",
        info->ref_trans_id, info->ref_trans_id);
 printf("<B>Region in reference: </B>%s<BR>\n", info->ref_region);
 printf("<B>Region in query: </B>%s<BR>\n", info->query_region);
 
 printf("<B>Projection class: </B>%s<BR>\n", info->status);
 printf("<B>Chain score: </B>%s<BR>\n", info->chain_score);
 // list of chain features (for orthology classification)
 printf("<a data-toggle=\"collapse\" href=\"#collapseChain\">Show chain features for classification</a>\n");
 printf("<div id=\"collapseChain\" class=\"panel-collapse collapse\">\n");
 printf("<ul>\n");
 printf("<li>Synteny: %s</li>\n", info->chain_synteny);
 printf("<li>Global CDS fraction: %s</li>\n", info->chain_gl_cds_fract);
 printf("<li>Local CDS fraction: %s</li>\n", info->chain_loc_cds_fract);
 printf("<li>Local intron fraction: %s</li>\n", info->chain_intron_cov);
 printf("<li>Local CDS coverage: %s</li>\n", info->chain_exon_cov);
 printf("<li>Flank fraction: %s</li>\n", info->chain_flank);
 printf("</ul>\n</div>\n<BR>\n");
 htmlHorizontalLine();
 
 // show inact mut plot
 printf("<h4>Inactivating mutations plot</h4>\n");
 printf("%s<BR>\n", info->svg_line);
 
 // GLP features
 printf("<a data-toggle=\"collapse\" href=\"#collapseGLP\">Show GLP features</a>\n");
 printf("<div id=\"collapseGLP\" class=\"panel-collapse collapse\">\n");
 printf("<ul>\n");
 printf("<li>Percent intact ignoring missing seq: %s</li>\n", info->perc_intact_ign_M);
 printf("<li>Percent intact (miss == intact): %s</li>\n", info->perc_intact_int_M);
 printf("<li>Intact codon proportion %s</li>\n", info->intact_codon_prop);
 printf("<li>Out of chain proportion: %s</li>\n", info->ouf_prop);
 if (sameWord(info->mid_intact, ONE_))
 {
     printf("<li>Middle 80 percent intact: %s</li>\n", YES_);
 } else {
     printf("<li>Middle 80 percent intact: %s</li>\n", NO_);
 }
 if (sameWord(info->mid_pres, ONE_))
 {
     printf("<li>Middle 80 percent present: %s</li>\n", YES_);
 } else {
     printf("<li>Middle 80 percent present: %s</li>\n", NO_);
 }
 printf("</ul>\n</div>\n<BR>\n");
 
 // and show protein sequence
 htmlHorizontalLine();
 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);
         struct togaInactMut *info = NULL;
         info = togaInactMutLoad(&fields[3]);
         printf("<tr>\n");
         printf("<td>%s</td>\n", info->exon_num);
         printf("<td>%s</td>\n", info->position);
         printf("<td>%s</td>\n", info->mut_class);
         printf("<td>%s</td>\n", info->mutation);
         if (sameWord(info->is_inact, ONE_)){
             printf("<td>%s</td>\n", YES_);
         } else {
             printf("<td>%s</td>\n", NO_);
         }
         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);
     struct togaNucl *info = NULL;
     info = togaNuclLoad(&fields[3]);
     printf("<h5>Exon number: %s</h5><BR>\n", info->exon_num);
     printf("<B>Exon region:</B> %s<BR>\n", info->exon_region);
     printf("<B>Nucleotide percent identity:</B> %s | <B>BLOSUM:</B> %s <BR>\n", info->pid, info->blosum);
     if (sameWord(info->gaps, ONE_)){
         printf("<B>Intersects assembly gaps:</B> %s<BR>\n", YES_);
     } else {
         printf("<B>Intersects assembly gaps:</B> %s<BR>\n", NO_);
     }
     printf("<B>Exon alignment class:</B> %s<BR>\n", info->ali_class);
     if (sameWord(info->in_exp_region, ONE_)){
         printf("<B>Detected within expected region:</B> %s<BR>\n", YES_);
     } else {
         printf("<B>Detected within expected region:</B> %s<BR>\n", NO_);
     }
     printf("<B>Expected region:</B> %s<BR>\n", info->exp_region);
     printf("<BR>\n");
     printf("<B>Sequence alignment:</B><BR>\n");
     printf("%s<BR>\n", info->alignment);
     togaNuclFree(&info);
     }
 
     //sqlFreeResult(&sr);
     printf("</div>\n<BR><BR>\n");
 
 htmlHorizontalLine();
 
 // TODO: check whether I need this
 printf("%s", hgTracksPathAndSettings());
 hPrintf("<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.4.1/css/bootstrap.min.css\">");
 hPrintf("<script src=\"https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js\"></script>");
 hPrintf("<script src=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.4.1/js/bootstrap.min.js\"></script>");
 
 
 printTrackHtml(tdb);  // and do I need this?
 }
 
 void doHillerLabTOGAGene(char *database, struct trackDb *tdb, char *item, char *table_name)
 /* Put up TOGA Gene track info. */
 {
     //int start = cartInt(cart, "o");
     char headerTitle[512];
     char suffix[512];
     strcpy(suffix, table_name);
     extractHLTOGAsuffix(suffix);
     safef(headerTitle, sizeof(headerTitle), "%s", item);
     genericHeader(tdb, headerTitle);
     printf("<h2>TOGA gene annotation</h2>\n");
     // htmlHorizontalLine();
     if (startsWith("bigBed", tdb->type))
         {
         doHillerLabTOGAGeneBig(database, tdb, item, table_name);
         return;
         }
 
     struct sqlConnection *conn = hAllocConn(database);
     
     // define TOGA table names: initate with pre-defined prefixes
     char togaDataTableName[256];
     char togaNuclTableName[256];
     char togaInactMutTableName[256];
     strcpy(togaDataTableName, HLTOGA_DATA_PREFIX);
     strcpy(togaNuclTableName, HLTOGA_NUCL_PREFIX);
     strcpy(togaInactMutTableName, HLTOGA_INACT_PREFIX);
     // add suffix
     strcat(togaDataTableName, suffix);
     strcat(togaNuclTableName, suffix);
     strcat(togaInactMutTableName, suffix);
 
 
     if (hTableExists(database, togaDataTableName)) 
     {
         printf("<h3>Projection %s</h3><BR>\n", item);
         char query[256];
         struct sqlResult *sr = NULL;
         char **row;
         struct togaData *info = NULL;
 
         sqlSafef(query, sizeof(query), "select * from %s where transcript='%s'", togaDataTableName, item);
         sr = sqlGetResult(conn, query);
 
         if ((row = sqlNextRow(sr)) != NULL) {
             info = togaDataLoad(row);  // parse sql output
             // fill HTML template:
             printf("<B>Projected via: </B><A HREF=\"http://www.ensembl.org/Homo_sapiens/transview?transcript=%s\" target=_blank>%s</A><BR>",
                    info->ref_trans_id, info->ref_trans_id);
             printf("<B>Region in reference: </B>%s<BR>\n", info->ref_region);
             printf("<B>Region in query: </B>%s<BR>\n", info->query_region);
 
             printf("<B>Projection class: </B>%s<BR>\n", info->status);
             printf("<B>Chain score: </B>%s<BR>\n", info->chain_score);
             // list of chain features (for orthology classification)
             printf("<a data-toggle=\"collapse\" href=\"#collapseChain\">Show chain features for classification</a>\n");
             printf("<div id=\"collapseChain\" class=\"panel-collapse collapse\">\n");
             printf("<ul>\n");
             printf("<li>Synteny: %s</li>\n", info->chain_synteny);
             printf("<li>Global CDS fraction: %s</li>\n", info->chain_gl_cds_fract);
             printf("<li>Local CDS fraction: %s</li>\n", info->chain_loc_cds_fract);
             printf("<li>Local intron fraction: %s</li>\n", info->chain_intron_cov);
             printf("<li>Local CDS coverage: %s</li>\n", info->chain_exon_cov);
             printf("<li>Flank fraction: %s</li>\n", info->chain_flank);
             printf("</ul>\n</div>\n<BR>\n");
             htmlHorizontalLine();
 
             // show inact mut plot
             printf("<h4>Inactivating mutations plot</h4>\n");
             printf("%s<BR>\n", info->svg_line);
 
             // GLP features
             printf("<a data-toggle=\"collapse\" href=\"#collapseGLP\">Show GLP features</a>\n");
             printf("<div id=\"collapseGLP\" class=\"panel-collapse collapse\">\n");
             printf("<ul>\n");
             printf("<li>Percent intact ignoring missing seq: %s</li>\n", info->perc_intact_ign_M);
             printf("<li>Percent intact (miss == intact): %s</li>\n", info->perc_intact_int_M);
             printf("<li>Intact codon proportion %s</li>\n", info->intact_codon_prop);
             printf("<li>Out of chain proportion: %s</li>\n", info->ouf_prop);
             if (sameWord(info->mid_intact, ONE_))
             {
                 printf("<li>Middle 80 percent intact: %s</li>\n", YES_);
             } else {
                 printf("<li>Middle 80 percent intact: %s</li>\n", NO_);
             }
             if (sameWord(info->mid_pres, ONE_))
             {
                 printf("<li>Middle 80 percent present: %s</li>\n", YES_);
             } else {
                 printf("<li>Middle 80 percent present: %s</li>\n", NO_);
             }
             printf("</ul>\n</div>\n<BR>\n");
 
             // and show protein sequence
             htmlHorizontalLine();
             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");
 
             // do not forget to free toga data struct
             togaDataFree(&info);
         } else {
             // no data found, need to report this
             printf("Not found data for %s\n", item);
         }
         sqlFreeResult(&sr);
     }
 
     // show inactivating mutations if required
     printf("<h4>Inactivating mutations</h4><BR>\n");
 
     if (hTableExists(database, togaInactMutTableName))
     {
         char query[256];
         struct sqlResult *sr = NULL;
         char **row;
         sqlSafef(query, sizeof(query), "select * from %s where transcript='%s'", togaInactMutTableName, item);
         sr = sqlGetResult(conn, query);
         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");
         while ((row = sqlNextRow(sr)) != NULL)
         {
             struct togaInactMut *info = NULL;
             info = togaInactMutLoad(row);
             printf("<tr>\n");
             printf("<td>%s</td>\n", info->exon_num);
             printf("<td>%s</td>\n", info->position);
             printf("<td>%s</td>\n", info->mut_class);
             printf("<td>%s</td>\n", info->mutation);
             if (sameWord(info->is_inact, ONE_)){
                 printf("<td>%s</td>\n", YES_);
             } else {
                 printf("<td>%s</td>\n", NO_);
             }
             printf("<td>%s</td>\n", info->mut_id);
             printf("</tr>\n");
             togaInactMutFree(&info);
         }
         sqlFreeResult(&sr);
         printf("</table>\n");
         printf("</div>\n<BR>\n");
     } else {
         printf("<B>Sorry, cannot find TOGAInactMut table.</B><BR>\n");
     }
 
     // show exons data
     htmlHorizontalLine();
     printf("<h4>Exons data</h4><BR>\n");
 
     if (hTableExists(database, togaNuclTableName))
     {
         char query[256];
         struct sqlResult *sr = NULL;
         char **row;
         printf("<a data-toggle=\"collapse\" href=\"#collapseExons\">Show exon sequences and features</a>\n");
         printf("<div id=\"collapseExons\" class=\"panel-collapse collapse\">\n");
         sqlSafef(query, sizeof(query), "select * from %s where transcript='%s'", togaNuclTableName, item);
         sr = sqlGetResult(conn, query);
 
         while ((row = sqlNextRow(sr)) != NULL)
         {
             struct togaNucl *info = NULL;
             info = togaNuclLoad(row);
             printf("<h5>Exon number: %s</h5><BR>\n", info->exon_num);
             printf("<B>Exon region:</B> %s<BR>\n", info->exon_region);
             printf("<B>Nucleotide percent identity:</B> %s | <B>BLOSUM:</B> %s <BR>\n", info->pid, info->blosum);
             if (sameWord(info->gaps, ONE_)){
                 printf("<B>Intersects assembly gaps:</B> %s<BR>\n", YES_);
             } else {
                 printf("<B>Intersects assembly gaps:</B> %s<BR>\n", NO_);
             }
             printf("<B>Exon alignment class:</B> %s<BR>\n", info->ali_class);
             if (sameWord(info->in_exp_region, ONE_)){
                 printf("<B>Detected within expected region:</B> %s<BR>\n", YES_);
             } else {
                 printf("<B>Detected within expected region:</B> %s<BR>\n", NO_);
             }
             printf("<B>Expected region:</B> %s<BR>\n", info->exp_region);
             printf("<BR>\n");
             printf("<B>Sequence alignment:</B><BR>\n");
             printf("%s<BR>\n", info->alignment);
             togaNuclFree(&info);
         }
         sqlFreeResult(&sr);
         printf("</div>\n<BR><BR>\n");
     } else {
         printf("<B>Sorry, cannot find TOGANucl table.</B><BR>\n");
     }
 
     htmlHorizontalLine();
 
     // TODO: check whether I need this
     printf("%s", hgTracksPathAndSettings());
     hPrintf("<link rel=\"stylesheet\" href=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.4.1/css/bootstrap.min.css\">");
     hPrintf("<script src=\"https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js\"></script>");
     hPrintf("<script src=\"https://maxcdn.bootstrapcdn.com/bootstrap/3.4.1/js/bootstrap.min.js\"></script>");
 
 
     printTrackHtml(tdb);  // and do I need this?
     hFreeConn(&conn);
 }