Version 2.3. Just before paper submission.

RELEASE_HISTORY

+Version 2.3.0 (11/18/2009)
+1. Added four new tools:
+	- shuffleBed. 			Randomly permutes the locations of a BED file among a genome.  Useful for testing for significant overlap enrichments.
+	- slopBed.    			Adds a requested number of base pairs to each end of a BED feature.  Constrained by the size of each chromosome.
+	- maskFastaFromBed. 	Masks a FASTA file based on BED coordinates.  Useful making custom genome files from targeted capture experiment, etc.
+	- pairToPair.			Returns overlaps between two paired-end BED files.  This is great for finding structural variants that are 
+							private or shared among samples.
+							
+2. Increased the speed of intersectBed by nearly 50%.
+3. Improved /corrected some of the help messages.
+4. Improved sanity checking for BED entries.
+
+
 Version 2.2.4 (10/27/2009)
 1. Updated the mergeBed documentation to describe the -names option which allows one to report the names of the
 features that were merged (separated by semicolons).

USAGE_EXAMPLES

 ==============================
-=== BEDTools Version 2.1.2 ===
+===       BEDTools         ===
 ==============================
 
 Created by Aaron Quinlan Spring 2009.
 Copyright 2009 Aaron Quinlan. All rights reserved.
-http://people.virginia.edu/~arq5x/bedtools.html
-
-Free for non-profit or academic use. Please contact me for commercial use.
-
+http://code.google.com/p/bedtools
 
 ===Example Usage===  
 

scripts/gffToBed.py

@@ -15,9 +15,9 @@ import re
 
 help_message = '''
 
-gffToBed -g <gff>
-	
-OPTIONS:
+gffToBed.py -g <gff>
+
+ABSTRACT: Converts genome annotations in GFF format to BED format.	
 '''
 
 """

scripts/samToBed.py

@@ -16,15 +16,30 @@ import re
 
 help_message = '''
 
-samToBed -s <sam> -t <alignment type>
+samToBed.py -s <sam> -t <alignment type>
+
+ABSTRACT: Converts aligned reads in SAM format to BED format.
 	
 OPTIONS:
-	-s	The SAM file to be converted to BED
+	-s	The SAM file to be converted to BED (use "stdin" for piped input)
 	-t	What types of alignments should be reported?
 			"all"	all aligned reads will be reported (Default)
 			"con"	only concordant pairs will be reported
 			"dis"	only discordant pairs will be reported
 
+EXAMPLE:
+	Can be used with samtools to extract alignments and compare them to BED
+	annotations.
+	
+	(1) Land a BED file first.
+	$ samtools view reads.sorted.bam > read.sorted.sam
+	$ samToBed.py -s reads.sorted.sam -t all > reads.sorted.bed
+	$ intersectBed -a reads.sorted.bed -b refseq.bed > reads.intersect.refseq.bed
+
+	(2) "One-liner.
+	$ samtools view reads.sorted.bam | samToBed.py -s stdin -t all | \ 
+	  intersectBed -a stdin -b refseq.bed > reads.intersect.refseq.bed
+
 '''
 
 
@@ -35,15 +50,17 @@ class Usage(Exception):
 
 def processSAM(file, alignType):
 	"""
-		Load a SAM file and convert each line to BED format.
-		
-		We avoid readlines() in this case, as SAM files can 
-		be HUGE, and thus loading it into memory could be painful.
-	"""		
-	for line in open(file,'r'):
-		samLine = splitLine(line.strip())
-		makeBED(samLine, alignType)
-	f.close()	
+		Read a SAM file (or stdin) and convert each line to BED format.
+	"""	
+	if (file != "stdin"):	
+		for line in open(file,'r'):
+			samLine = splitLine(line.strip())
+			makeBED(samLine, alignType)
+		f.close()
+	else:
+		for line in sys.stdin:
+			samLine = splitLine(line.strip())
+			makeBED(samLine, alignType)		
 	
 					
 def makeBED(samFields, aType):
@@ -116,17 +133,18 @@ def main(argv=None):
 				samFile = value
 			if option in ("-t", "--type"):
 				aType = value
-				
-		try:
-		   f = open(samFile, 'r')
-		except IOError, msg:
-			raise Usage(help_message)
-				
+	
+		if (samFile != "stdin"):
+			try:
+			   f = open(samFile, 'r')
+			except IOError, msg:
+				raise Usage(help_message)
+					
 	except Usage, err:
-		print >> sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
+		print >> sys.stderr, str(err.msg)
 		return 2	
 
-	# make a BED file of the SAM file.
+
 	processSAM(samFile, aType)
 
 if __name__ == "__main__":

src/utils/version/version.h

@@ -3,6 +3,6 @@
 
 // define the version.  All tools in the 
 // suite carry the same version number.
-#define VERSION "2.2.4"
+#define VERSION "2.3.0"
 
 #endif /* VERSION_H */