fe43cd3394528a515b867eb2e8f69d152bd4d178
jcasper
  Mon May 6 10:01:16 2019 -0700
A few initial library additions for eventual Hi-C support, refs #18842

diff --git src/hg/lib/chromAlias.c src/hg/lib/chromAlias.c
index d8a466d..f400df2 100644
--- src/hg/lib/chromAlias.c
+++ src/hg/lib/chromAlias.c
@@ -1,25 +1,25 @@
 /* chromAlias.c was originally generated by the autoSql program, which also 
  * generated chromAlias.h and chromAlias.sql.  This module links the database and
  * the RAM representation of objects. */
 
 #include "common.h"
 #include "linefile.h"
 #include "dystring.h"
 #include "jksql.h"
 #include "chromAlias.h"
-
+#include "hdb.h"
 
 
 char *chromAliasCommaSepFieldNames = "alias,chrom,source";
 
 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. */
 {
 
 ret->alias = row[0];
 ret->chrom = row[1];
 ret->source = row[2];
 }
 
 struct chromAlias *chromAliasLoad(char **row)
@@ -150,15 +150,39 @@
 fprintf(f, "%s", el->chrom);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"source");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->source);
 fputc('"',f);
 fputc('}',f);
 }
 
 /* -------------------------------- 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. */
+{
+struct hash *hash = NULL;
+if (!hTableExists(database, "chromAlias"))
+    return NULL;
+
+struct sqlConnection *conn = hAllocConn(database);
+hash = hashNew(0);
+char query[2048];
+sqlSafef(query, sizeof(query), "select * from chromAlias");
+struct sqlResult *sr = sqlGetResult(conn, query);
+char **row;
+while ((row = sqlNextRow(sr)) != NULL)
+    {
+    struct chromAlias *new = chromAliasLoad(row);
+    hashAdd(hash, new->alias, new);
+    }
+sqlFreeResult(&sr);
+hFreeConn(&conn);
+return hash;
+}