04cec773db5f693feee13b50f64c2f58579400cc
gperez2
  Thu Jul 17 14:33:36 2025 -0700
Updating the mouseOver and the hgc fields for bedMethyl, refs #33504

diff --git src/hg/lib/bedMethyl.c src/hg/lib/bedMethyl.c
index 4c60d013a1f..543f1a03289 100644
--- src/hg/lib/bedMethyl.c
+++ src/hg/lib/bedMethyl.c
@@ -1,305 +1,305 @@
 /* bedMethyl.c was originally generated by the autoSql program, which also 
  * generated bedMethyl.h and bedMethyl.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "bedMethyl.h"
 
 
 
 char *bedMethylCommaSepFieldNames = "chrom,chromStart,chromEnd,name,score,strand,thickStart,thickEnd,reserved,nValidCov,percMod,nMod,nCanon,nOther,nDelete,nFail,nDiff,nNoCall";
 
 void bedMethylStaticLoad(char **row, struct bedMethyl *ret)
 /* Load a row from bedMethyl table into ret.  The contents of ret will
  * be replaced at the next call to this function. */
 {
 
 ret->chrom = row[0];
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = row[3];
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 //ret->reserved = sqlUnsigned(row[8]);
 ret->nValidCov = row[9];
 ret->percMod = row[10];
 ret->nMod = row[11];
 ret->nCanon = row[12];
 ret->nOther = row[13];
 ret->nDelete = row[14];
 ret->nFail = row[15];
 ret->nDiff = row[16];
 ret->nNoCall = row[17];
 }
 
 struct bedMethyl *bedMethylLoadByQuery(struct sqlConnection *conn, char *query)
 /* Load all bedMethyl from table that satisfy the query given.  
  * Where query is of the form 'select * from example where something=something'
  * or 'select example.* from example, anotherTable where example.something = 
  * anotherTable.something'.
  * Dispose of this with bedMethylFreeList(). */
 {
 struct bedMethyl *list = NULL, *el;
 struct sqlResult *sr;
 char **row;
 
 sr = sqlGetResult(conn, query);
 while ((row = sqlNextRow(sr)) != NULL)
     {
     el = bedMethylLoad(&row[1]);
     slAddHead(&list, el);
     }
 slReverse(&list);
 sqlFreeResult(&sr);
 return list;
 }
 
 void bedMethylSaveToDb(struct sqlConnection *conn, struct bedMethyl *el, char *tableName, int updateSize)
 /* Save bedMethyl as a row to the table specified by tableName. 
  * As blob fields may be arbitrary size updateSize specifies the approx size
  * of a string that would contain the entire query. Arrays of native types are
  * converted to comma separated strings and loaded as such, User defined types are
  * inserted as NULL. This function automatically escapes quoted strings for mysql. */
 {
 struct dyString *update = dyStringNew(updateSize);
 sqlDyStringPrintf(update, "insert into %s values ( '%s',%u,%u,'%s',%u,'%s',%u,%u,%u,'%s','%s','%s','%s','%s','%s','%s','%s','%s')", 
 	tableName,  el->chrom,  el->chromStart,  el->chromEnd,  el->name,  el->score,  el->strand,  el->thickStart,  el->thickEnd,  el->reserved,  el->nValidCov,  el->percMod,  el->nMod,  el->nCanon,  el->nOther,  el->nDelete,  el->nFail,  el->nDiff,  el->nNoCall);
 sqlUpdate(conn, update->string);
 dyStringFree(&update);
 }
 
 struct bedMethyl *bedMethylLoad(char **row)
 /* Load a bedMethyl from row fetched with select * from bedMethyl
  * from database.  Dispose of this with bedMethylFree(). */
 {
 struct bedMethyl *ret;
 
 AllocVar(ret);
 ret->chrom = cloneString(row[0]);
 ret->chromStart = sqlUnsigned(row[1]);
 ret->chromEnd = sqlUnsigned(row[2]);
 ret->name = cloneString(row[3]);
 ret->score = sqlUnsigned(row[4]);
 safecpy(ret->strand, sizeof(ret->strand), row[5]);
 ret->thickStart = sqlUnsigned(row[6]);
 ret->thickEnd = sqlUnsigned(row[7]);
 //ret->reserved = sqlUnsigned(row[8]);
 ret->nValidCov = cloneString(row[9]);
 ret->percMod = cloneString(row[10]);
 ret->nMod = cloneString(row[11]);
 ret->nCanon = cloneString(row[12]);
 ret->nOther = cloneString(row[13]);
 ret->nDelete = cloneString(row[14]);
 ret->nFail = cloneString(row[15]);
 ret->nDiff = cloneString(row[16]);
 ret->nNoCall = cloneString(row[17]);
 return ret;
 }
 
 struct bedMethyl *bedMethylLoadAll(char *fileName) 
 /* Load all bedMethyl from a whitespace-separated file.
  * Dispose of this with bedMethylFreeList(). */
 {
 struct bedMethyl *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileRow(lf, row))
     {
     el = bedMethylLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct bedMethyl *bedMethylLoadAllByChar(char *fileName, char chopper) 
 /* Load all bedMethyl from a chopper separated file.
  * Dispose of this with bedMethylFreeList(). */
 {
 struct bedMethyl *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[18];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = bedMethylLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct bedMethyl *bedMethylCommaIn(char **pS, struct bedMethyl *ret)
 /* Create a bedMethyl out of a comma separated string. 
  * This will fill in ret if non-null, otherwise will
  * return a new bedMethyl */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->chrom = sqlStringComma(&s);
 ret->chromStart = sqlUnsignedComma(&s);
 ret->chromEnd = sqlUnsignedComma(&s);
 ret->name = sqlStringComma(&s);
 ret->score = sqlUnsignedComma(&s);
 sqlFixedStringComma(&s, ret->strand, sizeof(ret->strand));
 ret->thickStart = sqlUnsignedComma(&s);
 ret->thickEnd = sqlUnsignedComma(&s);
 ret->reserved = sqlUnsignedComma(&s);
 ret->nValidCov = sqlStringComma(&s);
 ret->percMod = sqlStringComma(&s);
 ret->nMod = sqlStringComma(&s);
 ret->nCanon = sqlStringComma(&s);
 ret->nOther = sqlStringComma(&s);
 ret->nDelete = sqlStringComma(&s);
 ret->nFail = sqlStringComma(&s);
 ret->nDiff = sqlStringComma(&s);
 ret->nNoCall = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void bedMethylFree(struct bedMethyl **pEl)
 /* Free a single dynamically allocated bedMethyl such as created
  * with bedMethylLoad(). */
 {
 struct bedMethyl *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->chrom);
 freeMem(el->name);
 freeMem(el->nValidCov);
 freeMem(el->percMod);
 freeMem(el->nMod);
 freeMem(el->nCanon);
 freeMem(el->nOther);
 freeMem(el->nDelete);
 freeMem(el->nFail);
 freeMem(el->nDiff);
 freeMem(el->nNoCall);
 freez(pEl);
 }
 
 void bedMethylFreeList(struct bedMethyl **pList)
 /* Free a list of dynamically allocated bedMethyl's */
 {
 struct bedMethyl *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     bedMethylFree(&el);
     }
 *pList = NULL;
 }
 
 void bedMethylOutput(struct bedMethyl *el, FILE *f, char sep, char lastSep) 
 /* Print out bedMethyl.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->chromStart);
 fputc(sep,f);
 fprintf(f, "%u", el->chromEnd);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->name);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->score);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->strand);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 fprintf(f, "%u", el->thickStart);
 fputc(sep,f);
 fprintf(f, "%u", el->thickEnd);
 fputc(sep,f);
 fprintf(f, "%u", el->reserved);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->nValidCov);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->percMod);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->nMod);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->nCanon);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->nOther);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->nDelete);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->nFail);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->nDiff);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->nNoCall);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 /* -------------------------------- End autoSql Generated Code -------------------------------- */
 
 static char *bedMethylAutoSqlString =
 {
 "table bedMethyl\n"
 "\"Browser extensible data for bedmethyl files (bed9+9)\"\n"
 "    (\n"
 "    string chrom;      \"Chromosome (or contig, scaffold, etc.)\"\n"
 "    uint   chromStart; \"Start position in chromosome\"\n"
 "    uint   chromEnd;   \"End position in chromosome\"\n"
 "    string name;       \"Name of item\"\n"
 "    uint   score;      \"Score from 0-1000\"\n"
 "    char[1] strand;    \"+ or -\"\n"
 "    uint thickStart;   \"Start of where display should be thick (start codon)\"\n"
 "    uint thickEnd;     \"End of where display should be thick (stop codon)\"\n"
 "    uint reserved;     \"Used as itemRgb as of 2004-11-22\"\n"
-"    string nValidCov;       \"Valid Coverage|N_mod + N_otherMod + N_canonical\"\n"
-"    string percMod;       \"Percent Modified\"\n"
-"    string nMod;       \"N_mod|Number of calls with a modified base\"\n"
-"    string nCanon;       \"N_canonical|Number of calls with a canonical base\"\n"
-"    string nOther;       \"N_otherMod|Number of calls with a modified base, other modification\"\n"
-"    string nDelete;       \"N_delete|Number of reads with a deletion at this reference position\"\n"
-"    string nFail;       \"N_fail|Number of calls where the probability of the call was below the threshold. \"\n"
-"    string nDiff;       \"N_diff|Number of reads with a base other than the canonical base for this modification. \"\n"
-"    string nNoCall;       \"N_nocall|Number of reads aligned to this reference position, with the correct canonical base, but without a base modification call.\"\n"
+"    string nValidCov;       \"Valid coverage|Reads with valid modification calls\"\n"
+"    string percMod;       \"Percent modified|Percent of valid calls that are modified\"\n"
+"    string nMod;       \"Modified calls|Number of calls with a modified base\"\n"
+"    string nCanon;       \"Canonical calls|Number of calls with a canonical base\"\n"
+"    string nOther;       \"Other modification calls|Number of calls with a modified base, other modification\"\n"
+"    string nDelete;       \"Reads with a deletion|Number of reads with a deletion at this reference position\"\n"
+"    string nFail;       \"Low-confidence calls|Number of calls where the probability of the call was below the threshold\"\n"
+"    string nDiff;       \"Reads with a base mismatch|Number of reads with a base other than the canonical base for this modification\"\n"
+"    string nNoCall;       \"Reads with no modification call|Number of reads aligned to this reference position, with the correct canonical base, but without a base modification call\"\n"
 "    )\n"
 "\n"
 };
 
 #include "asParse.h"
 
 struct asObject *bedMethylAsObj()
 /* Return asObject describing fields of bedMethyl object */
 {   
 return asParseText(bedMethylAutoSqlString);
 }