4418dae2476e397d9c03c1301e573e2c45b1a58e
hiram
  Fri Feb 10 12:16:43 2023 -0800
adding asmEquivalent functions to this library no redmine

diff --git src/hg/inc/asmEquivalent.h src/hg/inc/asmEquivalent.h
new file mode 100644
index 0000000..8463390
--- /dev/null
+++ src/hg/inc/asmEquivalent.h
@@ -0,0 +1,103 @@
+/* asmEquivalent.h was originally generated by the autoSql program, which also 
+ * generated asmEquivalent.c and asmEquivalent.sql.  This header links the database and
+ * the RAM representation of objects. */
+
+#ifndef ASMEQUIVALENT_H
+#define ASMEQUIVALENT_H
+
+#include "jksql.h"
+#define ASMEQUIVALENT_NUM_COLS 7
+
+extern char *asmEquivalentCommaSepFieldNames;
+
+enum asmEquivalentAuthority
+    {
+    asmEquivalentEnsembl = 0,
+    asmEquivalentUcsc = 1,
+    asmEquivalentGenbank = 2,
+    asmEquivalentRefseq = 3,
+    };
+struct asmEquivalent
+/* Equivalence relationship of assembly versions, Ensembl: UCSC, NCBI genbank/refseq */
+    {
+    struct asmEquivalent *next;  /* Next in singly linked list. */
+    char *source;	/* assembly name */
+    char *destination;	/* equivalent assembly name */
+    enum asmEquivalentAuthority sourceAuthority;	/* origin of source assembly */
+    enum asmEquivalentAuthority destinationAuthority;	/* origin of equivalent assembly */
+    long long matchCount;	/* number of exactly matching sequences */
+    long long sourceCount;	/* number of sequences in source assembly */
+    long long destinationCount;	/* number of sequences in equivalent assembly */
+    };
+
+void asmEquivalentStaticLoad(char **row, struct asmEquivalent *ret);
+/* Load a row from asmEquivalent table into ret.  The contents of ret will
+ * be replaced at the next call to this function. */
+
+struct asmEquivalent *asmEquivalentLoadByQuery(struct sqlConnection *conn, char *query);
+/* Load all asmEquivalent 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 asmEquivalentFreeList(). */
+
+void asmEquivalentSaveToDb(struct sqlConnection *conn, struct asmEquivalent *el, char *tableName, int updateSize);
+/* Save asmEquivalent 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 asmEquivalent *asmEquivalentLoad(char **row);
+/* Load a asmEquivalent from row fetched with select * from asmEquivalent
+ * from database.  Dispose of this with asmEquivalentFree(). */
+
+struct asmEquivalent *asmEquivalentLoadAll(char *fileName);
+/* Load all asmEquivalent from whitespace-separated file.
+ * Dispose of this with asmEquivalentFreeList(). */
+
+struct asmEquivalent *asmEquivalentLoadAllByChar(char *fileName, char chopper);
+/* Load all asmEquivalent from chopper separated file.
+ * Dispose of this with asmEquivalentFreeList(). */
+
+#define asmEquivalentLoadAllByTab(a) asmEquivalentLoadAllByChar(a, '\t');
+/* Load all asmEquivalent from tab separated file.
+ * Dispose of this with asmEquivalentFreeList(). */
+
+struct asmEquivalent *asmEquivalentCommaIn(char **pS, struct asmEquivalent *ret);
+/* Create a asmEquivalent out of a comma separated string. 
+ * This will fill in ret if non-null, otherwise will
+ * return a new asmEquivalent */
+
+void asmEquivalentFree(struct asmEquivalent **pEl);
+/* Free a single dynamically allocated asmEquivalent such as created
+ * with asmEquivalentLoad(). */
+
+void asmEquivalentFreeList(struct asmEquivalent **pList);
+/* Free a list of dynamically allocated asmEquivalent's */
+
+void asmEquivalentOutput(struct asmEquivalent *el, FILE *f, char sep, char lastSep);
+/* Print out asmEquivalent.  Separate fields with sep. Follow last field with lastSep. */
+
+#define asmEquivalentTabOut(el,f) asmEquivalentOutput(el,f,'\t','\n');
+/* Print out asmEquivalent as a line in a tab-separated file. */
+
+#define asmEquivalentCommaOut(el,f) asmEquivalentOutput(el,f,',',',');
+/* Print out asmEquivalent as a comma separated list including final comma. */
+
+void asmEquivalentJsonOutput(struct asmEquivalent *el, FILE *f);
+/* Print out asmEquivalent in JSON format. */
+
+/* -------------------------------- End autoSql Generated Code -------------------------------- */
+
+char *asmEquivalentUcscToNCBI(char *ucscName);
+/* check if there is a RefSeq/GenBank equivalent to this UCSC assembly name.
+ *    If RefSeq exists, return that first, else if GenBank than return that.
+ * No checking of sequence match counts in this first implementation,
+ *    therefore, could be a fuzzy match, and since it is returning only the
+ *    first one, it might not be the best match.  Could add more specifics
+ *    later to get better match.
+ */
+
+#endif /* ASMEQUIVALENT_H */
+