95efc27edf24bba8d0c7e53d2ef4aead59982826
braney
  Mon Jun 15 18:29:39 2020 -0700
Merging in our gencode merge code to master branch

diff --git src/hg/inc/gencodeToRefSeq.h src/hg/inc/gencodeToRefSeq.h
new file mode 100644
index 0000000..fed77d5
--- /dev/null
+++ src/hg/inc/gencodeToRefSeq.h
@@ -0,0 +1,65 @@
+/* gencodeToRefSeq.h was originally generated by the autoSql program, which also 
+ * generated gencodeToRefSeq.c and gencodeToRefSeq.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef GENCODETOREFSEQ_H
+#define GENCODETOREFSEQ_H
+
+#define GENCODETOREFSEQ_NUM_COLS 3
+
+extern char *gencodeToRefSeqCommaSepFieldNames;
+
+struct gencodeToRefSeq
+/* GENCODE transcript to RefSeq mRNA or non-coding RNA and peptide accession mapping */
+    {
+    struct gencodeToRefSeq *next;  /* Next in singly linked list. */
+    char *transcriptId;	/* GENCODE transcript identifier */
+    char *rnaAcc;	/* RefSeq mRNA or non-coding RNA accession */
+    char *pepAcc;	/* RefSeq peptide identifier for coding accession */
+    };
+
+void gencodeToRefSeqStaticLoad(char **row, struct gencodeToRefSeq *ret);
+/* Load a row from gencodeToRefSeq table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct gencodeToRefSeq *gencodeToRefSeqLoad(char **row);
+/* Load a gencodeToRefSeq from row fetched with select * from gencodeToRefSeq
+ * from database.  Dispose of this with gencodeToRefSeqFree(). */
+
+struct gencodeToRefSeq *gencodeToRefSeqLoadAll(char *fileName);
+/* Load all gencodeToRefSeq from whitespace-separated file.
+ * Dispose of this with gencodeToRefSeqFreeList(). */
+
+struct gencodeToRefSeq *gencodeToRefSeqLoadAllByChar(char *fileName, char chopper);
+/* Load all gencodeToRefSeq from chopper separated file.
+ * Dispose of this with gencodeToRefSeqFreeList(). */
+
+#define gencodeToRefSeqLoadAllByTab(a) gencodeToRefSeqLoadAllByChar(a, '\t');
+/* Load all gencodeToRefSeq from tab separated file.
+ * Dispose of this with gencodeToRefSeqFreeList(). */
+
+struct gencodeToRefSeq *gencodeToRefSeqCommaIn(char **pS, struct gencodeToRefSeq *ret);
+/* Create a gencodeToRefSeq out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new gencodeToRefSeq */
+
+void gencodeToRefSeqFree(struct gencodeToRefSeq **pEl);
+/* Free a single dynamically allocated gencodeToRefSeq such as created
+ * with gencodeToRefSeqLoad(). */
+
+void gencodeToRefSeqFreeList(struct gencodeToRefSeq **pList);
+/* Free a list of dynamically allocated gencodeToRefSeq's */
+
+void gencodeToRefSeqOutput(struct gencodeToRefSeq *el, FILE *f, char sep, char lastSep);
+/* Print out gencodeToRefSeq.  Separate fields with sep. Follow last field with lastSep. */
+
+#define gencodeToRefSeqTabOut(el,f) gencodeToRefSeqOutput(el,f,'\t','\n');
+/* Print out gencodeToRefSeq as a line in a tab-separated file. */
+
+#define gencodeToRefSeqCommaOut(el,f) gencodeToRefSeqOutput(el,f,',',',');
+/* Print out gencodeToRefSeq as a comma separated list including final comma. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+#endif /* GENCODETOREFSEQ_H */
+