diff --git a/scripts/gffToBed.py b/scripts/gffToBed.py
new file mode 100755
index 0000000000000000000000000000000000000000..5200e0903acc87310ca30200c2bf50f3cdd140e9
--- /dev/null
+++ b/scripts/gffToBed.py
@@ -0,0 +1,130 @@
+#!/usr/bin/env python
+# encoding: utf-8
+"""
+gffToBed.py
+
+Created by Aaron Quinlan on 2009-08-27.
+
+PURPOSE:
+ Convert GFF files to BED format.
+"""
+
+import sys
+import getopt
+import re
+
+help_message = '''
+
+gffToBed -g <gff>
+
+OPTIONS:
+'''
+
+"""
+GFF Definition:
+
+## Header lines
+
+0. (used) seqname - The name of the sequence. Must be a chromosome or scaffold.
+1. (ignd) source - The program that generated this feature.
+2. (used) feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
+3. (used) start - The starting position of the feature in the sequence. The first base is numbered 1.
+4. (used) end - The ending position of the feature (inclusive).
+5. (used) score - A score between 0 and 1000.
+6. (used) strand - Valid entries include '+', '-', or '.' (for don't know/don't care).
+7. (ignd) frame - If the feature is a coding exon,
+8. (ignd) group - All lines with the same group are linked together into a single item.
+"""
+
+class Usage(Exception):
+ def __init__(self, msg):
+ self.msg = msg
+
+
+def processGFF(file):
+ """
+ Load a GFF file and convert each line to BED format.
+ """
+ for line in open(file,'r'):
+ gffLine = splitLine(line.strip())
+
+ if (gffLine[:2] != "##"):
+ makeBED(gffLine)
+ f.close()
+
+
+def makeBED(gffFields):
+ """
+ Convert a single GFF line to BED.
+ """
+
+ chrom = gffFields[0]
+ start = str(int(gffFields[3])-1)
+ end = str(int(gffFields[4]))
+ name = str(gffFields[2])
+ score = str(getScore(gffFields[5])) # Default to 0 if "."
+ strand = str(getStrand(gffFields[6])) # Default to + if "."
+
+ # Write the BED line per user's request.
+ printBED(chrom, start, end, name, score, strand)
+
+
+def splitLine(line, delim="\t"):
+ splitline = line.split(delim)
+ return splitline
+
+
+def getScore(gffScore):
+ if (gffScore == "."):
+ return 0
+ else:
+ return gffScore
+
+
+def getStrand(gffStrand):
+ if (gffStrand == "."):
+ return "+"
+ else:
+ return gffStrand
+
+
+def printBED(chrom, start, end, name, score, strand):
+ try:
+ print chrom + "\t" + start + "\t" + end + "\t" + name + "\t" + score + "\t" + strand
+ except IOError, e:
+ sys.exit()
+ except KeyboardInterrupt, e:
+ sys.exit()
+
+
+def main(argv=None):
+ if argv is None:
+ argv = sys.argv
+ try:
+ try:
+ opts, args = getopt.getopt(argv[1:], "hg:", ["help", "gff"])
+ except getopt.error, msg:
+ raise Usage(help_message)
+
+ # option processing
+ gffFile = ""
+ for option, value in opts:
+ if option in ("-h", "--help"):
+ raise Usage(help_message)
+ if option in ("-g", "--gff"):
+ gffFile = value
+
+ try:
+ f = open(gffFile, 'r')
+ except IOError, msg:
+ raise Usage(help_message)
+
+ except Usage, err:
+ print >> sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
+ return 2
+
+ # make a BED file of the GFF file.
+ processGFF(gffFile)
+
+if __name__ == "__main__":
+ sys.exit(main())
diff --git a/scripts/samToBed.py b/scripts/samToBed.py
new file mode 100755
index 0000000000000000000000000000000000000000..f3da61f0dba2b22a0db002c15ed061940124dbc9
--- /dev/null
+++ b/scripts/samToBed.py
@@ -0,0 +1,133 @@
+#!/usr/bin/env python
+# encoding: utf-8
+"""
+samToBed.py
+
+Created by Aaron Quinlan on 2009-08-27.
+
+PURPOSE:
+ Convert SAM format alignment files to BED format, where each alignment
+ will conrrespond to a distnct BED line.
+"""
+
+import sys
+import getopt
+import re
+
+help_message = '''
+
+samToBed -s <sam> -t <alignment type>
+
+OPTIONS:
+ -s The SAM file to be converted to BED
+ -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
+
+'''
+
+
+class Usage(Exception):
+ def __init__(self, msg):
+ self.msg = msg
+
+
+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()
+
+
+def makeBED(samFields, aType):
+
+ samFlag = int(samFields[1])
+
+ # Only create a BED entry if the read was aligned
+ if (not (samFlag & 0x0004)):
+
+ chrom = samFields[2]
+ start = str(int(samFields[3])-1)
+ end = str(int(samFields[3]) + len(samFields[9]) - 1)
+ name = samFields[0]
+ score = samFields[1] # we'll use the SAM flag as a score.
+ strand = getStrand(samFlag)
+
+
+ # Write the BED line per user's request.
+ printBED(aType, properPairing(samFlag),
+ chrom, start, end, name, score, strand)
+
+
+def splitLine(line, delim="\t"):
+ splitline = line.split(delim)
+ return splitline
+
+
+def properPairing(samFlag):
+ return samFlag & (0x0002)
+
+
+def getStrand(samFlag):
+ strand = "+"
+ if (samFlag & (0x0010)): # minus strand if true.
+ strand = "-"
+ return strand
+
+
+def printBED(aType, concordant, chrom, start, end, name, score, strand):
+ try:
+ if (aType == "all"):
+ print chrom + "\t" + start + "\t" + end + "\t" + name + "\t" + score + "\t" + strand
+ else:
+ if (aType == "con") and concordant:
+ print chrom + "\t" + start + "\t" + end + "\t" + name + "\t" + score + "\t" + strand
+ elif (aType == "dis") and not concordant:
+ print chrom + "\t" + start + "\t" + end + "\t" + name + "\t" + score + "\t" + strand
+ except IOError, e:
+ sys.exit()
+ except KeyboardInterrupt, e:
+ sys.exit()
+
+
+def main(argv=None):
+ if argv is None:
+ argv = sys.argv
+ try:
+ try:
+ opts, args = getopt.getopt(argv[1:], "hs:t:", ["help", "sam", "type"])
+ except getopt.error, msg:
+ raise Usage(help_message)
+
+ # option processing
+ samFile = ""
+ aType = "all"
+ for option, value in opts:
+ if option in ("-h", "--help"):
+ raise Usage(help_message)
+ if option in ("-s", "--sam"):
+ samFile = value
+ if option in ("-t", "--type"):
+ aType = value
+
+ 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)
+ return 2
+
+ # make a BED file of the SAM file.
+ processSAM(samFile, aType)
+
+if __name__ == "__main__":
+ sys.exit(main())