68684c7c01875a771889d1fd03354f58bae34427
braney
  Tue Oct 31 15:01:59 2023 -0700
rename bedCollect to chainArrangeCollect in response to code review

diff --git src/hg/lib/chainArrange.h src/hg/lib/chainArrange.h
new file mode 100644
index 0000000..e53b9ce
--- /dev/null
+++ src/hg/lib/chainArrange.h
@@ -0,0 +1,74 @@
+/* chainArrange.h was originally generated by the autoSql program, which also 
+ * generated chainArrange.c and chainArrange.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef CHAINARRANGE_H
+#define CHAINARRANGE_H
+
+#define CHAINARRANGE_NUM_COLS 12
+
+extern char *chainArrangeCommaSepFieldNames;
+
+struct chainArrange
+/* A list of assembly rearrangements */
+    {
+    struct chainArrange *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 itemRgb;	/* Color */
+    char *source;	/* List of assemblies where break occures */
+    unsigned querySize;	/* size of item on query side */
+    char *label;	/* label for item */
+    };
+
+void chainArrangeStaticLoad(char **row, struct chainArrange *ret);
+/* Load a row from chainArrange table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct chainArrange *chainArrangeLoad(char **row);
+/* Load a chainArrange from row fetched with select * from chainArrange
+ * from database.  Dispose of this with chainArrangeFree(). */
+
+struct chainArrange *chainArrangeLoadAll(char *fileName);
+/* Load all chainArrange from whitespace-separated file.
+ * Dispose of this with chainArrangeFreeList(). */
+
+struct chainArrange *chainArrangeLoadAllByChar(char *fileName, char chopper);
+/* Load all chainArrange from chopper separated file.
+ * Dispose of this with chainArrangeFreeList(). */
+
+#define chainArrangeLoadAllByTab(a) chainArrangeLoadAllByChar(a, '\t');
+/* Load all chainArrange from tab separated file.
+ * Dispose of this with chainArrangeFreeList(). */
+
+struct chainArrange *chainArrangeCommaIn(char **pS, struct chainArrange *ret);
+/* Create a chainArrange out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new chainArrange */
+
+void chainArrangeFree(struct chainArrange **pEl);
+/* Free a single dynamically allocated chainArrange such as created
+ * with chainArrangeLoad(). */
+
+void chainArrangeFreeList(struct chainArrange **pList);
+/* Free a list of dynamically allocated chainArrange's */
+
+void chainArrangeOutput(struct chainArrange *el, FILE *f, char sep, char lastSep);
+/* Print out chainArrange.  Separate fields with sep. Follow last field with lastSep. */
+
+#define chainArrangeTabOut(el,f) chainArrangeOutput(el,f,'\t','\n');
+/* Print out chainArrange as a line in a tab-separated file. */
+
+#define chainArrangeCommaOut(el,f) chainArrangeOutput(el,f,',',',');
+/* Print out chainArrange as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* CHAINARRANGE_H */
+