7e5840e03baf4a7b7c198016c393d0b86f7b72b6
braney
  Tue Nov 16 15:25:19 2021 -0800
allow hgc pages on chains to provide a link to the "other" browser if
the other assembly is an unattached genark assembly hub

diff --git src/hg/inc/genark.h src/hg/inc/genark.h
new file mode 100644
index 0000000..9bb2151
--- /dev/null
+++ src/hg/inc/genark.h
@@ -0,0 +1,101 @@
+/* genark.h was originally generated by the autoSql program, which also 
+ * generated genark.c and genark.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef GENARK_H
+#define GENARK_H
+
+#include "jksql.h"
+#define GENARK_NUM_COLS 6
+
+#define defaultGenarkTableName "genark"
+/* Name of table that maintains the names of hubs we'll automatically attach if referenced. */
+
+#define genarkTableConfVariable    "hub.genArkTableName"
+/* the name of the hg.conf variable to use something other than the default */
+
+
+extern char *genarkCommaSepFieldNames;
+
+struct genark
+/* index to UCSC assembly hubs */
+    {
+    struct genark *next;  /* Next in singly linked list. */
+    char *gcAccession;	/* GC[AF] accssion identifier, e.g.: GCF_000001405.39 */
+    char *hubUrl;	/* path name to hub.txt: GCF/000/001/405/GCF_000001405.39/hub.txt */
+    char *asmName;	/* assembly name: GRCh38.p13 */
+    char *scientificName;	/* scientific name: Homo sapiens */
+    char *commonName;	/* common name: human */
+    int taxId;	/* taxon id: 9606 */
+    };
+
+void genarkStaticLoad(char **row, struct genark *ret);
+/* Load a row from genark table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct genark *genarkLoadByQuery(struct sqlConnection *conn, char *query);
+/* Load all genark from table that satisfy the query given.  
+ * Where query is of the form 'select * from example where something=something'
+ * or 'select example.* from example, anotherTable where example.something = 
+ * anotherTable.something'.
+ * Dispose of this with genarkFreeList(). */
+
+void genarkSaveToDb(struct sqlConnection *conn, struct genark *el, char *tableName, int updateSize);
+/* Save genark as a row to the table specified by tableName. 
+ * As blob fields may be arbitrary size updateSize specifies the approx size
+ * of a string that would contain the entire query. Arrays of native types are
+ * converted to comma separated strings and loaded as such, User defined types are
+ * inserted as NULL. This function automatically escapes quoted strings for mysql. */
+
+struct genark *genarkLoad(char **row);
+/* Load a genark from row fetched with select * from genark
+ * from database.  Dispose of this with genarkFree(). */
+
+struct genark *genarkLoadAll(char *fileName);
+/* Load all genark from whitespace-separated file.
+ * Dispose of this with genarkFreeList(). */
+
+struct genark *genarkLoadAllByChar(char *fileName, char chopper);
+/* Load all genark from chopper separated file.
+ * Dispose of this with genarkFreeList(). */
+
+#define genarkLoadAllByTab(a) genarkLoadAllByChar(a, '\t');
+/* Load all genark from tab separated file.
+ * Dispose of this with genarkFreeList(). */
+
+struct genark *genarkCommaIn(char **pS, struct genark *ret);
+/* Create a genark out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new genark */
+
+void genarkFree(struct genark **pEl);
+/* Free a single dynamically allocated genark such as created
+ * with genarkLoad(). */
+
+void genarkFreeList(struct genark **pList);
+/* Free a list of dynamically allocated genark's */
+
+void genarkOutput(struct genark *el, FILE *f, char sep, char lastSep);
+/* Print out genark.  Separate fields with sep. Follow last field with lastSep. */
+
+#define genarkTabOut(el,f) genarkOutput(el,f,'\t','\n');
+/* Print out genark as a line in a tab-separated file. */
+
+#define genarkCommaOut(el,f) genarkOutput(el,f,',',',');
+/* Print out genark as a comma separated list including final comma. */
+
+void genarkJsonOutput(struct genark *el, FILE *f);
+/* Print out genark in JSON format. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+char *genarkUrl(char *accession);
+/* Return the URL to the genark assembly with this accession if present,
+ * otherwise return NULL
+ * */
+
+char *genarkTableName();
+/* return the genark table name from the environment, 
+ * or hg.conf, or use the default.  Cache the result */
+#endif /* GENARK_H */
+