b763a93bef738004614cb657ccab6805f94dda8e
braney
  Thu Aug 15 19:06:39 2013 -0700
make HAL linked in by default, fix the problem with mismatched bases nothaving the right chars in them, start adding HAL to the table browser.
refs #10637

diff --git src/hg/hgTables/hgTables.c src/hg/hgTables/hgTables.c
index f842f4d..82ea9ef 100644
--- src/hg/hgTables/hgTables.c
+++ src/hg/hgTables/hgTables.c
@@ -1381,55 +1381,59 @@
     freez(&filter);
     }
 
 /* Do some error diagnostics for user. */
 if (outCount == 0)
     explainWhyNoResults(f);
 hashFree(&idHash);
 }
 
 
 void doTabOutTable( char *db, char *table, FILE *f, struct sqlConnection *conn, char *fields)
 /* Do tab-separated output on fields of a single table. */
 {
 if (isBigBed(database, table, curTrack, ctLookupName))
     bigBedTabOut(db, table, conn, fields, f);
+else if (isHalTable(table))
+    halTabOut(db, table, conn, fields, f);
 else if (isBamTable(table))
     bamTabOut(db, table, conn, fields, f);
 else if (isVcfTable(table))
     vcfTabOut(db, table, conn, fields, f);
 else if (isCustomTrack(table))
     {
     doTabOutCustomTracks(db, table, conn, fields, f);
     }
 else
     doTabOutDb(db, db, table, table, f, conn, fields);
 }
 
 struct slName *fullTableFields(char *db, char *table)
 /* Return list of fields in db.table.field format. */
 {
 char dtBuf[256];
 struct sqlConnection *conn=NULL;
 struct slName *fieldList = NULL, *dtfList = NULL, *field, *dtf;
 if (isBigBed(database, table, curTrack, ctLookupName))
     {
     if (!trackHubDatabase(database))
 	conn = hAllocConn(db);
     fieldList = bigBedGetFields(table, conn);
     hFreeConn(&conn);
     }
+else if (isHalTable(table))
+    fieldList = getBedFields(6);
 else if (isBamTable(table))
     fieldList = bamGetFields(table);
 else if (isVcfTable(table))
     fieldList = vcfGetFields(table);
 else if (isCustomTrack(table))
     {
     struct customTrack *ct = ctLookupName(table);
     char *type = ct->dbTrackType;
     if (type != NULL)
         {
 	conn = hAllocConn(CUSTOM_TRASH);
 	if (startsWithWord("maf", type) || startsWithWord("makeItems", type) || sameWord("bedDetail", type) || sameWord("pgSnp", type))
 	    fieldList = sqlListFields(conn, ct->dbTableName);
 	hFreeConn(&conn);
 	}