42ccdd815277a3dc7d78b48fa0ac36d469ab628a
markd
  Mon Feb 28 19:07:04 2022 -0800
added bigRmsk autoSql files from Robert Hubley

diff --git src/hg/inc/bigRmskBed.h src/hg/inc/bigRmskBed.h
new file mode 100644
index 0000000..2d5db08
--- /dev/null
+++ src/hg/inc/bigRmskBed.h
@@ -0,0 +1,76 @@
+/* bigRmskBed.h was originally generated by the autoSql program, which also 
+ * generated bigRmskBed.c and bigRmskBed.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef BIGRMSKBED_H
+#define BIGRMSKBED_H
+
+#define BIGRMSKBED_NUM_COLS 14
+
+extern char *bigRmskBedCommaSepFieldNames;
+
+struct bigRmskBed
+/* Repetitive Element Annotation */
+    {
+    struct bigRmskBed *next;  /* Next in singly linked list. */
+    char *chrom;	/* Reference sequence chromosome or scaffold */
+    unsigned chromStart;	/* Start position of visualization on chromosome */
+    unsigned chromEnd;	/* End position of visualation on chromosome */
+    char *name;	/* Name repeat, including the type/subtype suffix */
+    unsigned score;	/* Divergence score */
+    char strand[2];	/* + or - for strand */
+    unsigned thickStart;	/* Start position of aligned sequence on chromosome */
+    unsigned thickEnd;	/* End position of aligned sequence on chromosome */
+    unsigned reserved;	/* Reserved */
+    unsigned blockCount;	/* Count of sequence blocks */
+    char *blockSizes;	/* A comma-separated list of the block sizes(+/-) */
+    char *blockStarts;	/* A comma-separated list of the block starts(+/-) */
+    unsigned id;	/* A unique identifier for the joined annotations in this record */
+    char *description;	/* A comma separated list of technical annotation descriptions */
+    };
+
+void bigRmskBedStaticLoad(char **row, struct bigRmskBed *ret);
+/* Load a row from bigRmskBed table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct bigRmskBed *bigRmskBedLoad(char **row);
+/* Load a bigRmskBed from row fetched with select * from bigRmskBed
+ * from database.  Dispose of this with bigRmskBedFree(). */
+
+struct bigRmskBed *bigRmskBedLoadAll(char *fileName);
+/* Load all bigRmskBed from whitespace-separated file.
+ * Dispose of this with bigRmskBedFreeList(). */
+
+struct bigRmskBed *bigRmskBedLoadAllByChar(char *fileName, char chopper);
+/* Load all bigRmskBed from chopper separated file.
+ * Dispose of this with bigRmskBedFreeList(). */
+
+#define bigRmskBedLoadAllByTab(a) bigRmskBedLoadAllByChar(a, '\t');
+/* Load all bigRmskBed from tab separated file.
+ * Dispose of this with bigRmskBedFreeList(). */
+
+struct bigRmskBed *bigRmskBedCommaIn(char **pS, struct bigRmskBed *ret);
+/* Create a bigRmskBed out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bigRmskBed */
+
+void bigRmskBedFree(struct bigRmskBed **pEl);
+/* Free a single dynamically allocated bigRmskBed such as created
+ * with bigRmskBedLoad(). */
+
+void bigRmskBedFreeList(struct bigRmskBed **pList);
+/* Free a list of dynamically allocated bigRmskBed's */
+
+void bigRmskBedOutput(struct bigRmskBed *el, FILE *f, char sep, char lastSep);
+/* Print out bigRmskBed.  Separate fields with sep. Follow last field with lastSep. */
+
+#define bigRmskBedTabOut(el,f) bigRmskBedOutput(el,f,'\t','\n');
+/* Print out bigRmskBed as a line in a tab-separated file. */
+
+#define bigRmskBedCommaOut(el,f) bigRmskBedOutput(el,f,',',',');
+/* Print out bigRmskBed as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* BIGRMSKBED_H */
+