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

diff --git src/hg/inc/bedMethyl.h src/hg/inc/bedMethyl.h
new file mode 100644
index 00000000000..146eecb398d
--- /dev/null
+++ src/hg/inc/bedMethyl.h
@@ -0,0 +1,97 @@
+/* bedMethyl.h was originally generated by the autoSql program, which also 
+ * generated bedMethyl.c and bedMethyl.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef BEDMETHYL_H
+#define BEDMETHYL_H
+
+#include "jksql.h"
+#define BEDMETHYL_NUM_COLS 18
+
+extern char *bedMethylCommaSepFieldNames;
+
+struct bedMethyl
+/* Browser extensible data for bedmethyl files (bed9+9) */
+    {
+    struct bedMethyl *next;  /* Next in singly linked list. */
+    char *chrom;	/* Chromosome (or contig, scaffold, etc.) */
+    unsigned chromStart;	/* Start position in chromosome */
+    unsigned chromEnd;	/* End position in chromosome */
+    char *name;	/* Name of item */
+    unsigned score;	/* Score from 0-1000 */
+    char strand[2];	/* + or - */
+    unsigned thickStart;	/* Start of where display should be thick (start codon) */
+    unsigned thickEnd;	/* End of where display should be thick (stop codon) */
+    unsigned reserved;	/* Used as itemRgb as of 2004-11-22 */
+    char *nValidCov;	/* Valid Coverage|N_mod + N_otherMod + N_canonical */
+    char *percMod;	/* Percent Modified */
+    char *nMod;	/* N_mod|Number of calls with a modified base */
+    char *nCanon;	/* N_canonical|Number of calls with a canonical base */
+    char *nOther;	/* N_otherMod|Number of calls with a modified base, other modification */
+    char *nDelete;	/* N_delete|Number of reads with a deletion at this reference position */
+    char *nFail;	/* N_fail|Number of calls where the probability of the call was below the threshold.  */
+    char *nDiff;	/* N_diff|Number of reads with a base other than the canonical base for this modification.  */
+    char *nNoCall;	/* N_nocall|Number of reads aligned to this reference position, with the correct canonical base, but without a base modification call. */
+    };
+
+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. */
+
+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(). */
+
+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 bedMethyl *bedMethylLoad(char **row);
+/* Load a bedMethyl from row fetched with select * from bedMethyl
+ * from database.  Dispose of this with bedMethylFree(). */
+
+struct bedMethyl *bedMethylLoadAll(char *fileName);
+/* Load all bedMethyl from whitespace-separated file.
+ * Dispose of this with bedMethylFreeList(). */
+
+struct bedMethyl *bedMethylLoadAllByChar(char *fileName, char chopper);
+/* Load all bedMethyl from chopper separated file.
+ * Dispose of this with bedMethylFreeList(). */
+
+#define bedMethylLoadAllByTab(a) bedMethylLoadAllByChar(a, '\t');
+/* Load all bedMethyl from tab separated file.
+ * Dispose of this with bedMethylFreeList(). */
+
+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 */
+
+void bedMethylFree(struct bedMethyl **pEl);
+/* Free a single dynamically allocated bedMethyl such as created
+ * with bedMethylLoad(). */
+
+void bedMethylFreeList(struct bedMethyl **pList);
+/* Free a list of dynamically allocated bedMethyl's */
+
+void bedMethylOutput(struct bedMethyl *el, FILE *f, char sep, char lastSep);
+/* Print out bedMethyl.  Separate fields with sep. Follow last field with lastSep. */
+
+#define bedMethylTabOut(el,f) bedMethylOutput(el,f,'\t','\n');
+/* Print out bedMethyl as a line in a tab-separated file. */
+
+#define bedMethylCommaOut(el,f) bedMethylOutput(el,f,',',',');
+/* Print out bedMethyl as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+struct asObject *bedMethylAsObj();
+/* Return asObject describing fields of bedMethyl object */
+#endif /* BEDMETHYL_H */
+