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
@@ -1,164 +1,188 @@
 /* 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)
 /* Load a chromAlias from row fetched with select * from chromAlias
  * from database.  Dispose of this with chromAliasFree(). */
 {
 struct chromAlias *ret;
 
 AllocVar(ret);
 ret->alias = cloneString(row[0]);
 ret->chrom = cloneString(row[1]);
 ret->source = cloneString(row[2]);
 return ret;
 }
 
 struct chromAlias *chromAliasLoadAll(char *fileName) 
 /* Load all chromAlias from a whitespace-separated file.
  * Dispose of this with chromAliasFreeList(). */
 {
 struct chromAlias *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileRow(lf, row))
     {
     el = chromAliasLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 struct chromAlias *chromAliasLoadAllByChar(char *fileName, char chopper) 
 /* Load all chromAlias from a chopper separated file.
  * Dispose of this with chromAliasFreeList(). */
 {
 struct chromAlias *list = NULL, *el;
 struct lineFile *lf = lineFileOpen(fileName, TRUE);
 char *row[3];
 
 while (lineFileNextCharRow(lf, chopper, row, ArraySize(row)))
     {
     el = chromAliasLoad(row);
     slAddHead(&list, el);
     }
 lineFileClose(&lf);
 slReverse(&list);
 return list;
 }
 
 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 */
 {
 char *s = *pS;
 
 if (ret == NULL)
     AllocVar(ret);
 ret->alias = sqlStringComma(&s);
 ret->chrom = sqlStringComma(&s);
 ret->source = sqlStringComma(&s);
 *pS = s;
 return ret;
 }
 
 void chromAliasFree(struct chromAlias **pEl)
 /* Free a single dynamically allocated chromAlias such as created
  * with chromAliasLoad(). */
 {
 struct chromAlias *el;
 
 if ((el = *pEl) == NULL) return;
 freeMem(el->alias);
 freeMem(el->chrom);
 freeMem(el->source);
 freez(pEl);
 }
 
 void chromAliasFreeList(struct chromAlias **pList)
 /* Free a list of dynamically allocated chromAlias's */
 {
 struct chromAlias *el, *next;
 
 for (el = *pList; el != NULL; el = next)
     {
     next = el->next;
     chromAliasFree(&el);
     }
 *pList = NULL;
 }
 
 void chromAliasOutput(struct chromAlias *el, FILE *f, char sep, char lastSep) 
 /* Print out chromAlias.  Separate fields with sep. Follow last field with lastSep. */
 {
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->alias);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->chrom);
 if (sep == ',') fputc('"',f);
 fputc(sep,f);
 if (sep == ',') fputc('"',f);
 fprintf(f, "%s", el->source);
 if (sep == ',') fputc('"',f);
 fputc(lastSep,f);
 }
 
 void chromAliasJsonOutput(struct chromAlias *el, FILE *f) 
 /* Print out chromAlias in JSON format. */
 {
 fputc('{',f);
 fputc('"',f);
 fprintf(f,"alias");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 fprintf(f, "%s", el->alias);
 fputc('"',f);
 fputc(',',f);
 fputc('"',f);
 fprintf(f,"chrom");
 fputc('"',f);
 fputc(':',f);
 fputc('"',f);
 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;
+}