14dbb674fd1cc2300b157847a50dae414aa44e40
jcasper
  Mon May 6 10:08:20 2019 -0700
Moved chromAlias.h from hg/inc to hg/lib, apparently git missed the memo, no ticket

diff --git src/hg/inc/chromAlias.h src/hg/inc/chromAlias.h
new file mode 100644
index 0000000..3542623
--- /dev/null
+++ src/hg/inc/chromAlias.h
@@ -0,0 +1,72 @@
+/* chromAlias.h was originally generated by the autoSql program, which also 
+ * generated chromAlias.c and chromAlias.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef CHROMALIAS_H
+#define CHROMALIAS_H
+
+#define CHROMALIAS_NUM_COLS 3
+
+extern char *chromAliasCommaSepFieldNames;
+
+struct chromAlias
+/* correspondence of UCSC chromosome names to refseq, genbank, and ensembl names */
+    {
+    struct chromAlias *next;  /* Next in singly linked list. */
+    char *alias;	/* external name */
+    char *chrom;	/* UCSC genome browser chromosome name */
+    char *source;	/* comma separated list, when available: refseq,genbank,ensembl */
+    };
+
+void chromAliasStaticLoad(char **row, struct chromAlias *ret);
+/* Load a row from chromAlias table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct chromAlias *chromAliasLoad(char **row);
+/* Load a chromAlias from row fetched with select * from chromAlias
+ * from database.  Dispose of this with chromAliasFree(). */
+
+struct chromAlias *chromAliasLoadAll(char *fileName);
+/* Load all chromAlias from whitespace-separated file.
+ * Dispose of this with chromAliasFreeList(). */
+
+struct chromAlias *chromAliasLoadAllByChar(char *fileName, char chopper);
+/* Load all chromAlias from chopper separated file.
+ * Dispose of this with chromAliasFreeList(). */
+
+#define chromAliasLoadAllByTab(a) chromAliasLoadAllByChar(a, '\t');
+/* Load all chromAlias from tab separated file.
+ * Dispose of this with chromAliasFreeList(). */
+
+struct chromAlias *chromAliasCommaIn(char **pS, struct chromAlias *ret);
+/* Create a chromAlias out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new chromAlias */
+
+void chromAliasFree(struct chromAlias **pEl);
+/* Free a single dynamically allocated chromAlias such as created
+ * with chromAliasLoad(). */
+
+void chromAliasFreeList(struct chromAlias **pList);
+/* Free a list of dynamically allocated chromAlias's */
+
+void chromAliasOutput(struct chromAlias *el, FILE *f, char sep, char lastSep);
+/* Print out chromAlias.  Separate fields with sep. Follow last field with lastSep. */
+
+#define chromAliasTabOut(el,f) chromAliasOutput(el,f,'\t','\n');
+/* Print out chromAlias as a line in a tab-separated file. */
+
+#define chromAliasCommaOut(el,f) chromAliasOutput(el,f,',',',');
+/* Print out chromAlias as a comma separated list including final comma. */
+
+void chromAliasJsonOutput(struct chromAlias *el, FILE *f);
+/* Print out chromAlias in JSON format. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+struct hash *chromAliasMakeLookupTable(char *database);
+/* Given a database name and a connection to that database, construct a lookup table
+ * that takes chromosome alias names to a matching struct chromAlias.  Returns NULL
+ * if the given database does not have a chromAlias table. */
+
+#endif /* CHROMALIAS_H */