Strandedness. reportBed in bedFile. peIntersect

	1. Added strandedness to relevant programs (e.g. intersectBed, mergeBed, etc.)
	2. Moved reportBed and reportBedRange to bedFile.cpp to clean up code
	3. Sped up file parsing.  Added lineFileUtilities.cpp
	4. Added peIntersectBed

Makefile

@@ -19,7 +19,7 @@ export CXX ?= g++
 #include includes/$(BLD_PLATFORM).inc
 
 # define our source subdirectories
-SUBDIRS = $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/sortBed $(SRC_DIR)/windowBed $(SRC_DIR)/subtractBed $(SRC_DIR)/linksBed
+SUBDIRS = $(SRC_DIR)/closestBed $(SRC_DIR)/complementBed $(SRC_DIR)/coverageBed $(SRC_DIR)/intersectBed $(SRC_DIR)/mergeBed $(SRC_DIR)/genomeCoverageBed $(SRC_DIR)/fastaFromBed $(SRC_DIR)/sortBed $(SRC_DIR)/windowBed $(SRC_DIR)/subtractBed $(SRC_DIR)/linksBed $(SRC_DIR)/peIntersectBed
 
 UTIL_SUBDIRS = $(SRC_DIR)/utils/bedFile $(SRC_DIR)/utils/sequenceUtilities
 all:

RELEASE_HISTORY

+VERSION 2.0
+1.  Sped up the file parsing.  ~10-20% increase in speed.
+2.  Created reportBed() as a common method in the bedFile class.  Cleans up the code quite nicely.
+3.  Added the ability to compare BED files accounting for strandedness.
+4.  Paired-end intersect.
+5.  Fixed bug that prevented overlaps from being reported when the overlap fraction requested is 1.0
+
+
+VERSION 1.2, 04/27/2009. (1eb06115bdf3c49e75793f764a70c3501bb53f33)
+1.  Added subtractBed.
+	A. Fixed bug that prevented "split" overlaps from being reported.
+	B. Prevented A from being reported if >=1 feature in B completely spans it.
+2.  Added linksBed.
+3.  Added the ability to define separate windows for upstream and downstream to windowBed.
+
+
+VERSION 1.1, 04/23/2009. (b74eb1afddca9b70bfa90ba763d4f2981a56f432)
+Initial release.
\ No newline at end of file