a7cdd40a9c37d4d90c7aa9766c5248c0cb3f259a
braney
  Wed May 21 17:22:17 2025 -0700
add bedMethyl type for custom and native tracks

diff --git src/hg/lib/bedMethyl.c src/hg/lib/bedMethyl.c
new file mode 100644
index 00000000000..4c60d013a1f
--- /dev/null
+++ src/hg/lib/bedMethyl.c
@@ -0,0 +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"
+"    )\n"
+"\n"
+};
+
+#include "asParse.h"
+
+struct asObject *bedMethylAsObj()
+/* Return asObject describing fields of bedMethyl object */
+{   
+return asParseText(bedMethylAutoSqlString);
+}