602fa08316183790dd1e1d633c6d7510ae45d8cb
braney
  Fri Feb 11 15:32:03 2011 -0800
add intersections, identifier filtering, and file length limits to BAM output
diff --git src/hg/hgTables/intersect.c src/hg/hgTables/intersect.c
index 866885d..4726b4a 100644
--- src/hg/hgTables/intersect.c
+++ src/hg/hgTables/intersect.c
@@ -31,30 +31,32 @@
 static char *nextVars[] = {hgtaNextIntersectGroup, hgtaNextIntersectTrack,
 	hgtaNextIntersectTable,
 	hgtaNextIntersectOp, hgtaNextMoreThreshold, hgtaNextLessThreshold,
 	hgtaNextInvertTable, hgtaNextInvertTable2,
 	};
 
 /* This is already duplicated in correlate.c and is handy -- should be
  * libified, probably in cart.h. */
 void removeCartVars(struct cart *cart, char **vars, int varCount);
 
 static boolean canIntersect(char *db, char *table)
 /* Return true if table exists and is positional. */
 {
 if (isCustomTrack(table) && ctLookupName(table) != NULL)
     return TRUE;
+if (isBamTable(table))
+    return TRUE;
 if (isHubTrack(table))
     return TRUE;
 if (sameWord(table, WIKI_TRACK_TABLE))
     return TRUE;
 if (hTableOrSplitExists(db, table))
     return isPositional(db, table);
 return FALSE;
 }
 
 boolean anyIntersection()
 /* Return TRUE if there's an intersection to do. */
 {
 boolean specd = (cartVarExists(cart, hgtaIntersectTrack) &&
 		 cartVarExists(cart, hgtaIntersectTable));
 if (specd && canIntersect(database, curTable))