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

diff --git src/hg/inc/bigRmskAlignBed.h src/hg/inc/bigRmskAlignBed.h
new file mode 100644
index 0000000..6093d75
--- /dev/null
+++ src/hg/inc/bigRmskAlignBed.h
@@ -0,0 +1,79 @@
+/* bigRmskAlignBed.h was originally generated by the autoSql program, which also 
+ * generated bigRmskAlignBed.c and bigRmskAlignBed.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef BIGRMSKALIGNBED_H
+#define BIGRMSKALIGNBED_H
+
+#define BIGRMSKALIGNBED_NUM_COLS 17
+
+extern char *bigRmskAlignBedCommaSepFieldNames;
+
+struct bigRmskAlignBed
+/* Repetitive Element Alignment Auxilary Data */
+    {
+    struct bigRmskAlignBed *next;  /* Next in singly linked list. */
+    char *chrom;	/* Reference sequence chromosome or scaffold */
+    unsigned chromStart;	/* Start position of alignment on chromosome */
+    unsigned chromEnd;	/* End position of alignment on chromosome */
+    unsigned chromRemain;	/* Remaining bp in the chromosome or scaffold */
+    float score;	/* alignment score (sw, bits or evalue) */
+    float percSubst;	/* Base substitution percentage */
+    float percDel;	/* Base deletion percentage */
+    float percIns;	/* Bases insertion percentage */
+    char strand[2];	/* Strand - either + or - */
+    char *repName;	/* Name of repeat */
+    char *repType;	/* Type of repeat */
+    char *repSubtype;	/* Subtype of repeat */
+    unsigned repStart;	/* Start in repeat sequence */
+    unsigned repEnd;	/* End in repeat sequence */
+    unsigned repRemain;	/* Remaining unaligned bp in the repeat sequence */
+    unsigned id;	/* The ID of the hit. Used to link related fragments */
+    char *calignData;	/* The alignment data stored as a single string */
+    };
+
+void bigRmskAlignBedStaticLoad(char **row, struct bigRmskAlignBed *ret);
+/* Load a row from bigRmskAlignBed table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct bigRmskAlignBed *bigRmskAlignBedLoad(char **row);
+/* Load a bigRmskAlignBed from row fetched with select * from bigRmskAlignBed
+ * from database.  Dispose of this with bigRmskAlignBedFree(). */
+
+struct bigRmskAlignBed *bigRmskAlignBedLoadAll(char *fileName);
+/* Load all bigRmskAlignBed from whitespace-separated file.
+ * Dispose of this with bigRmskAlignBedFreeList(). */
+
+struct bigRmskAlignBed *bigRmskAlignBedLoadAllByChar(char *fileName, char chopper);
+/* Load all bigRmskAlignBed from chopper separated file.
+ * Dispose of this with bigRmskAlignBedFreeList(). */
+
+#define bigRmskAlignBedLoadAllByTab(a) bigRmskAlignBedLoadAllByChar(a, '\t');
+/* Load all bigRmskAlignBed from tab separated file.
+ * Dispose of this with bigRmskAlignBedFreeList(). */
+
+struct bigRmskAlignBed *bigRmskAlignBedCommaIn(char **pS, struct bigRmskAlignBed *ret);
+/* Create a bigRmskAlignBed out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bigRmskAlignBed */
+
+void bigRmskAlignBedFree(struct bigRmskAlignBed **pEl);
+/* Free a single dynamically allocated bigRmskAlignBed such as created
+ * with bigRmskAlignBedLoad(). */
+
+void bigRmskAlignBedFreeList(struct bigRmskAlignBed **pList);
+/* Free a list of dynamically allocated bigRmskAlignBed's */
+
+void bigRmskAlignBedOutput(struct bigRmskAlignBed *el, FILE *f, char sep, char lastSep);
+/* Print out bigRmskAlignBed.  Separate fields with sep. Follow last field with lastSep. */
+
+#define bigRmskAlignBedTabOut(el,f) bigRmskAlignBedOutput(el,f,'\t','\n');
+/* Print out bigRmskAlignBed as a line in a tab-separated file. */
+
+#define bigRmskAlignBedCommaOut(el,f) bigRmskAlignBedOutput(el,f,',',',');
+/* Print out bigRmskAlignBed as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* BIGRMSKALIGNBED_H */
+