Version 2.12.3

RELEASE_HISTORY

+Version 2.13.3 (30-Sept-2011)
+Bug Fixes
+============
+1. intersectBed detected, but did not report overlaps when using BAM input and -bed.
+
+Other
+=====
+1. Warning that -sorted trusts, but does not enforce that data is actually sorted.
+
+
 Version 2.13.2 (23-Sept-2011)
 
 New algorithm

src/intersectBed/intersectMain.cpp

@@ -285,8 +285,8 @@ void ShowHelp(void) {
 
     cerr << "\t-split\t"        << "Treat \"split\" BAM or BED12 entries as distinct BED intervals." << endl << endl;
 
-    cerr << "\t-sorted\t"        << "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input" << endl << endl;
-
+    cerr << "\t-sorted\t"        << "Use the \"chromsweep\" algorithm for sorted (-k1,1 -k2,2n) input" << endl;
+    cerr                        << "\t\tNOTE: this will trust, but not enforce that data is sorted. Caveat emptor." << endl << endl;
 
     // end the program here
     exit(1);

src/utils/version/version.h

@@ -3,6 +3,6 @@
 
 // define the version.  All tools in the
 // suite carry the same version number.
-#define VERSION "2.13.2"
+#define VERSION "2.13.3"
 
 #endif /* VERSION_H */