4ac9486a77f0ed4e87de2e946f29e203b354398b
markd
  Thu Jun 13 13:56:46 2024 -0700
added chainToBigChain command

diff --git src/hg/inc/bigLink.h src/hg/inc/bigLink.h
new file mode 100644
index 0000000..6ca1964
--- /dev/null
+++ src/hg/inc/bigLink.h
@@ -0,0 +1,70 @@
+/* bigLink.h was originally generated by the autoSql program, which also 
+ * generated bigLink.c and bigLink.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef BIGLINK_H
+#define BIGLINK_H
+
+#define BIGLINK_NUM_COLS 5
+
+extern char *bigLinkCommaSepFieldNames;
+
+struct bigLink
+/* bigLink pairwise alignment */
+    {
+    struct bigLink *next;  /* Next in singly linked list. */
+    char *chrom;	/* Reference sequence chromosome or scaffold */
+    unsigned chromStart;	/* Start position in chromosome */
+    unsigned chromEnd;	/* End position in chromosome */
+    char *name;	/* Name or ID of item, ideally both human readable and unique */
+    unsigned qStart;	/* start of alignment on query sequence */
+    };
+
+void bigLinkStaticLoad(char **row, struct bigLink *ret);
+/* Load a row from bigLink table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct bigLink *bigLinkLoad(char **row);
+/* Load a bigLink from row fetched with select * from bigLink
+ * from database.  Dispose of this with bigLinkFree(). */
+
+struct bigLink *bigLinkLoadAll(char *fileName);
+/* Load all bigLink from whitespace-separated file.
+ * Dispose of this with bigLinkFreeList(). */
+
+struct bigLink *bigLinkLoadAllByChar(char *fileName, char chopper);
+/* Load all bigLink from chopper separated file.
+ * Dispose of this with bigLinkFreeList(). */
+
+#define bigLinkLoadAllByTab(a) bigLinkLoadAllByChar(a, '\t');
+/* Load all bigLink from tab separated file.
+ * Dispose of this with bigLinkFreeList(). */
+
+struct bigLink *bigLinkCommaIn(char **pS, struct bigLink *ret);
+/* Create a bigLink out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new bigLink */
+
+void bigLinkFree(struct bigLink **pEl);
+/* Free a single dynamically allocated bigLink such as created
+ * with bigLinkLoad(). */
+
+void bigLinkFreeList(struct bigLink **pList);
+/* Free a list of dynamically allocated bigLink's */
+
+void bigLinkOutput(struct bigLink *el, FILE *f, char sep, char lastSep);
+/* Print out bigLink.  Separate fields with sep. Follow last field with lastSep. */
+
+#define bigLinkTabOut(el,f) bigLinkOutput(el,f,'\t','\n');
+/* Print out bigLink as a line in a tab-separated file. */
+
+#define bigLinkCommaOut(el,f) bigLinkOutput(el,f,',',',');
+/* Print out bigLink as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+int bigLinkCmpTarget(const void *va, const void *vb);
+/* Compare to sort based on target position. */
+
+#endif /* BIGLINK_H */
+