98874f1656202cd5781466a5d9b25f47da1f104d
hiram
  Mon Feb 13 16:03:53 2023 -0800
a bit closer to correct NCBI links, not perfect, but better than it was no redmine

diff --git src/hg/inc/asmEquivalent.h src/hg/inc/asmEquivalent.h
index 8463390..42c1388 100644
--- src/hg/inc/asmEquivalent.h
+++ src/hg/inc/asmEquivalent.h
@@ -1,103 +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.
+char *asmEquivalentUcscToNCBI(char *ucscName, char *authority);
+/* check if there is an "authority" equivalent to this UCSC assembly name.
+ *    where 'authority' in this case is either 'refseq' or 'genbank'
  * 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 */