da33d70c10ddaae6c3290cb900d7d0cc2b6ee01b
hiram
  Tue Mar 17 13:57:24 2026 -0700
allow calculation of GC percent on the fly with code help from claude refs #35958

diff --git src/hg/hgc/togaClick.c src/hg/hgc/togaClick.c
index de092e4773d..dadc3da2016 100644
--- src/hg/hgc/togaClick.c
+++ src/hg/hgc/togaClick.c
@@ -1,722 +1,725 @@
 /* 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 togaDataBB *togaDataBBLoad(char **row, bits16 fieldCount)
 /* Load a togaData from row fetched with select * from togaData
  * from database.  Dispose of this with togaDataFree(). */
 {
     struct togaDataBB *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]);
     ret->ref_link = cloneString(row[20]);
     ret->inact_mut_html_table = cloneString(row[21]);
     ret->exon_ali_html = cloneString(row[22]);
 
     /* read two optional new items, CDSseq and frame-corrected protein */
     ret->CDSseq = NULL;
     if (fieldCount >= 35)   /* 0-11 are bed core fields. This fct gets a pointer starting with element 12. 12+23 = 35 */
        ret->CDSseq = cloneString(row[23]);
     ret->protseqFrameCorrected = NULL;
     if (fieldCount >= 36)   /* 12+24 = 36 */
        ret->protseqFrameCorrected = cloneString(row[24]);
     /* number and percent of mutated exons (additional data now shown for the gene loss status) */
     ret->numExonsMutated = NULL;
     ret->percentExonsMutated = NULL;
     if (fieldCount >= 37)   /* 12+25 = 37 */
        ret->numExonsMutated = cloneString(row[25]);
     if (fieldCount >= 38)   /* 12+26 = 38 */
        ret->percentExonsMutated = cloneString(row[26]);
     return ret;
 }
 
 
 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 togaDataBBFree(struct togaDataBB **pEl)
 /* Free a single dynamically allocated togaDatasuch as created
  * with togaDataLoad(). */
 {
     struct togaDataBB *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);
     freeMem(el->ref_link);
     freeMem(el->inact_mut_html_table);
     freeMem(el->exon_ali_html);
     freez(pEl);
 }
 
 
 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 HLprintQueryProtSeqForAli(char *proteinAlignment) {
     // take protein sequence alignment
     // print only the query sequence
     char *str = proteinAlignment;
     int printed_char_num = 0;
     while ((str = strstr(str, "que:")) != NULL)
     {
         str += 10;
         char ch;
         while ((ch = *str++) != '<') {
             if (ch != '-') {
                 putchar(ch);
                 ++printed_char_num;
             }
             if (printed_char_num == 80) {
                 printed_char_num = 0;
                 printf("<BR>");
             }
         }
     }
 }
 
 void print_with_newlines(const char *str) {
     int line_length = 80; // Number of characters per line
     int length = strlen(str);
     int i = 0;
 
     while (i < length) {
         /* Print up to 80 characters or the remainder of the string */
         int chars_to_print = (length - i < line_length) ? (length - i) : line_length;
         printf("%.*s<BR>", chars_to_print, &str[i]);
         i += chars_to_print;
     }
 }
 
 static void panelPrompt(char *target, char *prompt)
-/* output span element for an expandable text element */
+/* output span element for an expandable text element
+ *  this opens a <div> element, you need to close it </div> after your text in
+ *  this section has been output.
+ */
 {
 printf("<span class='hideToggle' dataTarget='%s' style='cursor: pointer; color: blue;'><img height='18' width='18' src='../images/add_sm.gif'>&nbsp;%s:</span>\n", target, prompt);
 printf("<div id='%s' style='display: none;'>\n", target);
 }
 
 void doHillerLabTOGAGeneBig(char *database, struct trackDb *tdb, char *item, char *table_name)
 /* Put up TOGA Gene track info. */
 // To think about -> put into a single bigBed
 // string: HTML formatted inact mut
 // string: HTML formatted exon ali section
 {
 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), 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 v2 %s</h3>\n", item);
 struct togaDataBB *info = togaDataBBLoad(&fields[11], bbi->fieldCount);  // Bogdan: why 11? 0-11 are bed-like fields likely
 
 printf("<B>Reference transcript: </B>%s<BR>", info->ref_link);
 printf("<B>Genomic locus in reference: </B>%s<BR>\n", info->ref_region);
 printf("<B>Genomic locus in query: </B>%s<BR>\n", info->query_region);
 
 printf("<B>Projection classification: </B>%s<BR>\n", info->status);
 printf("<B>Probability that query locus is orthologous: </B>%s<BR>\n", info->chain_score);
 // list of chain features (for orthology classification)
 panelPrompt("collapseChain", "Show features used for ortholog probability");
 printf("<p><ul>\n");
 printf("<li>Synteny (log10 value): %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></p>\n");
 
 printf("<p>\n<b>Feature description:</b>\n");
 printf("For each projection (one reference transcript and one overlapping chain),\n");
 printf("TOGA computes the following features by intersecting the reference coordinates of aligning\n");
 printf("blocks in the chain with different gene parts (coding exons, UTR (untranslated region) exons, introns)\n");
 printf("and the respective intergenic regions.\n</p>\n");
 
 printf("<p>We define the following variables:\n<ul>\n");
 printf("<li>c: number of reference bases in the intersection between chain blocks and coding exons of the gene under consideration.</li>\n");
 printf("<li>C: number of reference bases in the intersection between chain blocks and coding exons of all genes. </li>\n");
 printf("<li>a: number of reference bases in the intersection between chain blocks and coding exons and introns of the gene under consideration. </li>\n");
 printf("<li>A: number of reference bases in the intersection between chain blocks and coding exons and introns of all genes and the intersection\n");
 printf("between chain blocks and intergenic regions (excludes UTRs). </li>\n");
 printf("<li>f: number of reference bases in chain blocks overlapping the 10 kb flanks of the gene under consideration.\n");
 printf("Alignment blocks overlapping exons of another gene that is located in these 10 kb flanks are ignored. </li>\n");
 printf("<li>i: number of reference bases in the intersection between chain blocks and introns of the gene under consideration. </li>\n");
 printf("<li>CDS (coding sequence): length of the coding region of the gene under consideration. </li>\n");
 printf("<li>I: sum of all intron lengths of the gene under consideration. </li>\n");
 printf("</ul></p>\n");
 printf("<p>Using these variables, TOGA computes the following features:\n");
 printf("<ul>\n");
 printf("<li>&quot;global CDS fraction&quot; as C / A. Chains with a high value have alignments that largely overlap coding exons,");
 printf("which is a hallmark of paralogous or processed pseudogene chains. In contrast, chains with a low value also align many ");
 printf("intronic and intergenic regions, which is a hallmark of orthologous chains. </li>\n");
 printf("<li>&quot;local CDS fraction&quot; as c / a. Orthologous chains tend to have a lower value, as intronic ");
 printf("regions partially align. This feature is not computed for single-exon genes. </li>\n");
 printf("<li>&quot;local intron fraction&quot; as i / I. Orthologous chains tend to have a higher value.");
 printf("This feature is not computed for single-exon genes. </li>\n");
 printf("<li>&quot;flank fraction&quot; as f / 20,000. Orthologous chains tend to have higher values,");
 printf("as flanking intergenic regions partially align. This feature is important to detect orthologous loci of single-exon genes. </li>\n");
 printf("<li>&quot;synteny&quot; as log10 of the number of genes, whose coding exons overlap by at least one base aligning");
 printf("blocks of this chain. Orthologous chains tend to cover several genes located in a conserved order, resulting in higher synteny values. </li>\n");
 printf("<li>&quot;local CDS coverage&quot; as c / CDS, which is only used for single-exon genes. </li>\n");
 printf("</ul></p>\n");
 
 
 printf("</div>\n");
 printf("<hr style='margin-bottom:-0.5em;color:black;'>\n");
 
 // show inact mut plot
 printf("<h4>Visualization of inactivating mutations on exon-intron structure</h4>\n");
 printf("%s\n", info->svg_line);
 printf("<BR>Exons shown in grey are missing (often overlap assembly gaps).\nExons shown in");
 printf(" red or blue are deleted or do not align at all.\nRed indicates that the exon deletion ");
 printf("shifts the reading frame, while blue indicates that exon deletion(s) are framepreserving.<br>\n");
 
 // GLP features
 panelPrompt("collapseGLP", "Show features used for transcript classification");
 printf("<p><ul>\n");
 printf("<li>Percent intact, ignoring missing sequence: %s</li>\n", info->perc_intact_ign_M);
 printf("<li>Percent intact, treating missing as intact sequence: %s</li>\n", info->perc_intact_int_M);
 printf("<li>Proportion of intact codons: %s</li>\n", info->intact_codon_prop);
 printf("<li>Percent of CDS not covered by this chain (0 unless the chain covers only a part of the gene): %s</li>\n", info->ouf_prop);
 if (sameWord(info->mid_intact, ONE_))
 {
     printf("<li>Middle 80 percent of CDS intact: %s</li>\n", YES_);
 } else {
     printf("<li>Middle 80 percent of CDS intact: %s</li>\n", NO_);
 }
 if (sameWord(info->mid_pres, ONE_))
 {
     printf("<li>Middle 80 percent of CDS present: %s</li>\n", YES_);
 } else {
     printf("<li>Middle 80 percent of CDS present: %s</li>\n", NO_);
 }
 if (info->numExonsMutated != NULL && info->percentExonsMutated != NULL) {
     printf("<li>Number of exons with inactivating mutations: %s (%s%% of the present exons; threshold is 20%%)</li>\n", info->numExonsMutated, info->percentExonsMutated);
 }
 printf("</ul></p>\n</div>\n");
 
 
 printf("<hr style='margin-bottom:-0.5em;color:black;'>\n");
 printf("<h4>Predicted protein sequence</h4>\n");
 
 panelPrompt("collapseProt", "Show protein sequence of query");
 printf("<p><TT>");
 HLprintQueryProtSeqForAli(info->prot_alignment);
 printf("\n</TT></p>\n</div><BR>\n");
 
 if (info->protseqFrameCorrected != NULL) {
   panelPrompt("collapseProtFrameCorrected", "Show frame-corrected protein sequence of query (potential frameshifts are masked)");
   printf("<p><TT>");
   print_with_newlines(info->protseqFrameCorrected);
   printf("\n</TT></p>\n</div>\n");
 }
 
 if (info->CDSseq != NULL) {
   printf("<hr style='margin-bottom:-0.5em;color:black;'>\n");
   printf("<h4>Predicted coding (DNA) sequence</h4>\n");
   panelPrompt("collapseCDS", "Show coding sequence of query");
   printf("<p><TT>");
   print_with_newlines(info->CDSseq);
   printf("\n</TT></p>\n</div>\n");
 }
 
 // and show protein sequence
 printf("<hr style='margin-bottom:-0.5em;color:black;'>\n");
 printf("<h4>Protein sequence alignment</h4>\n");
 panelPrompt("collapseProtAli", "Show alignment between reference and query");
 printf("<p><TT>%s</TT>\n", info->prot_alignment);
 printf("</p></div>\n");
 
 // show inactivating mutations if required
 printf("<hr style='margin-bottom:-0.5em;color:black;'>\n");
 printf("<h4>List of inactivating mutations</h4>\n");
 panelPrompt("collapseMuts", "Show inactivating mutations");
 printf("<p><table border = \"1\" width = \"640\">\n");  // init table
 printf("<tr><th>Exon number</th><th>Codon number</th><th>Mutation class</th><th>Mutation</th><th>Treated as inactivating</th><th>Mutation ID</th>\n");
 printf("</tr>\n");
 printf("%s\n", info->inact_mut_html_table);
 printf("</table></p>\n");
 printf("</div>\n\n");
 
 // show exons data
 printf("<hr style='margin-bottom:-0.5em;color:black;'>\n");
 printf("<h4>Exon alignments</h4>\n");
 
 panelPrompt("collapseExons", "Show exon sequences and features");
 printf("<p>%s</p>\n", info->exon_ali_html);
 
 printf("<hr style='margin-bottom:-0.5em;color:black;'>\n");
 printf("</div>\n<BR><BR>\n");
 
 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>Reference transcript: </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>Genomic locus in reference: </B>%s<BR>\n", info->ref_region);
             printf("<B>Genomic locus in query: </B>%s<BR>\n", info->query_region);
 
             printf("<B>Projection classification: </B>%s<BR>\n", info->status);
             printf("<B>Probability that query locus is orthologous: </B>%s<BR>\n", info->chain_score);
             // list of chain features (for orthology classification)
             panelPrompt("collapseChain", "Show features used for ortholog probability");
             printf("<p><ul>\n");
             printf("<li>Synteny (log10 value): %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></p>\n");
 
             printf("<br>\n<b>Feature description:</b>\n");
             printf("For each projection (one reference transcript and one overlapping chain),\n");
             printf("TOGA computes the following features by intersecting the reference coordinates of aligning\n");
             printf("blocks in the chain with different gene parts (coding exons, UTR (untranslated region) exons, introns)\n");
             printf("and the respective intergenic regions.\n<br>\n");
 
             printf("We define the following variables:\n<ul>\n");
             printf("<li>c: number of reference bases in the intersection between chain blocks and coding exons of the gene under consideration.</li>\n");
             printf("<li>C: number of reference bases in the intersection between chain blocks and coding exons of all genes. </li>\n");
             printf("<li>a: number of reference bases in the intersection between chain blocks and coding exons and introns of the gene under consideration. </li>\n");
             printf("<li>A: number of reference bases in the intersection between chain blocks and coding exons and introns of all genes and the intersection\n");
             printf("between chain blocks and intergenic regions (excludes UTRs). </li>\n");
             printf("<li>f: number of reference bases in chain blocks overlapping the 10 kb flanks of the gene under consideration.\n");
             printf("Alignment blocks overlapping exons of another gene that is located in these 10 kb flanks are ignored. </li>\n");
             printf("<li>i: number of reference bases in the intersection between chain blocks and introns of the gene under consideration. </li>\n");
             printf("<li>CDS (coding sequence): length of the coding region of the gene under consideration. </li>\n");
             printf("<li>I: sum of all intron lengths of the gene under consideration. </li>\n");
             printf("</ul>\n");
             printf("Using these variables, TOGA computes the following features:\n");
             printf("<ul>\n");
             printf("<li>&quot;global CDS fraction&quot; as C / A. Chains with a high value have alignments that largely overlap coding exons,");
             printf("which is a hallmark of paralogous or processed pseudogene chains. In contrast, chains with a low value also align many ");
             printf("intronic and intergenic regions, which is a hallmark of orthologous chains. </li>\n");
             printf("<li>&quot;local CDS fraction&quot; as c / a. Orthologous chains tend to have a lower value, as intronic ");
             printf("regions partially align. This feature is not computed for single-exon genes. </li>\n");
             printf("<li>&quot;local intron fraction&quot; as i / I. Orthologous chains tend to have a higher value.");
             printf("This feature is not computed for single-exon genes. </li>\n");
             printf("<li>&quot;flank fraction&quot; as f / 20,000. Orthologous chains tend to have higher values,");
             printf("as flanking intergenic regions partially align. This feature is important to detect orthologous loci of single-exon genes. </li>\n");
             printf("<li>&quot;synteny&quot; as log10 of the number of genes, whose coding exons overlap by at least one base aligning");
             printf("blocks of this chain. Orthologous chains tend to cover several genes located in a conserved order, resulting in higher synteny values. </li>\n");
             printf("<li>&quot;local CDS coverage&quot; as c / CDS, which is only used for single-exon genes. </li>\n");
             printf("</ul>\n");
 
 
             printf("</ul>\n</div>\n<BR>\n");
             htmlHorizontalLine();
 
             // show inact mut plot
             printf("<h4>Visualization of inactivating mutations on exon-intron structure</h4>\n");
             printf("%s<BR>\n", info->svg_line);
             printf("<BR>Exons shown in grey are missing (often overlap assembly gaps).\nExons shown in");
             printf(" red or blue are deleted or do not align at all.\nRed indicates that the exon deletion ");
             printf("shifts the reading frame, while blue indicates that exon deletion(s) are framepreserving.<br>\n");
 
             // GLP features
             panelPrompt("collapseGLP", "Show features used for transcript classification");
             printf("<p><ul>\n");
             printf("<li>Percent intact, ignoring missing sequence: %s</li>\n", info->perc_intact_ign_M);
             printf("<li>Percent intact, treating missing as intact sequence: %s</li>\n", info->perc_intact_int_M);
             printf("<li>Proportion of intact codons: %s</li>\n", info->intact_codon_prop);
             printf("<li>Percent of CDS not covered by this chain (0 unless the chain covers only a part of the gene): %s</li>\n", info->ouf_prop);
             if (sameWord(info->mid_intact, ONE_))
             {
                 printf("<li>Middle 80 percent of CDS intact: %s</li>\n", YES_);
             } else {
                 printf("<li>Middle 80 percent of CDS intact: %s</li>\n", NO_);
             }
             if (sameWord(info->mid_pres, ONE_))
             {
                 printf("<li>Middle 80 percent of CDS present: %s</li>\n", YES_);
             } else {
                 printf("<li>Middle 80 percent of CDS present: %s</li>\n", NO_);
             }
             printf("</ul></p>\n</div>\n<BR>\n");
             printf("<HR ALIGN=\"CENTER\"><h4>Query protein sequence</h4><BR>");
 
             panelPrompt("collapseProt", "Show protein sequence of query");
             printf("<p><TT>{protein seq of the query without dashes or other things. Should end with *}\n");
             printf("<BR>\n</TT></p>\n</div>\n");
 
             // and show protein sequence
             htmlHorizontalLine();
             printf("<h4>Protein sequence alignment</h4><BR>\n");
             panelPrompt("collapseProtAli", "Show alignment between reference and query");
             printf("<p><TT>%s</TT></p><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("<h3>No found data for %s</h3>\n", item);
         }
         sqlFreeResult(&sr);
     }
 
     // show inactivating mutations if required
     printf("<h4>List of 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);
         panelPrompt("collapseMuts", "Show inactivating mutations");
         printf("<table border = \"1\" width = \"640\">\n");  // init table
         printf("<tr><th>Exon number</th><th>Codon number</th><th>Mutation class</th><th>Mutation</th><th>Treated as inactivating</th><th>Mutation 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>Exon alignments</h4><BR>\n");
 
     if (hTableExists(database, togaNuclTableName))
     {
         char query[256];
         struct sqlResult *sr = NULL;
         char **row;
         panelPrompt("collapseExons", "Show exon sequences and features");
         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 (%s):</B> %s<BR>\n", info->exp_region, YES_);
             } else {
                 printf("<B>Detected within expected region (%s):</B> %s<BR>\n", info->exp_region, NO_);
             }
             // printf("<B>Expected region:</B> %s<BR>\n", info->exp_region);
             printf("<BR>\n");
             printf("<B>Sequence alignment between reference and query exon:</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());
 
     printTrackHtml(tdb);  // and do I need this?
     hFreeConn(&conn);
 }