1 files changed, 0 insertions, 125 deletions
diff --git a/benchmarks/CUDA/MUM/genreads.py b/benchmarks/CUDA/MUM/genreads.py
deleted file mode 100644
index 4302470..0000000
--- a/benchmarks/CUDA/MUM/genreads.py
+++ /dev/null
@@ -1,125 +0,0 @@
-#!/usr/bin/env python
-# encoding: utf-8
-"""
-untitled.py
-
-Created by Cole Trapnell on 2007-04-26.
-Copyright (c) 2007 __MyCompanyName__. All rights reserved.
-"""
-
-import sys
-import getopt
-import random
-
-
-help_message = """
-genreads outputs a multi-FASTA file containing a random sampling of 
-read-sized subsequences of the provided reference sequence.  
-
-Usage:
-	genreads [options] <reference file> <length of reads> <# of reads>	
-	
-Options:
-	-m < % mismatch>   --mismatches=  the % of bases in each read that
-	                                  don't match the reference
-	-s <integer value> --seed=        the seed for the random number 
-	                                  generator
-"""
-
-
-class Usage(Exception):
-	def __init__(self, msg):
-		self.msg = msg
-
-
-def main(argv=None):
-
-	if argv is None:
-		argv = sys.argv
-	try:
-		try:
-			opts, args = getopt.getopt(argv[1:], "hSd:m:s:v", ["help","distribution=", "mismatches=", "seed=", "sort"])
-		except getopt.error, msg:
-			raise Usage(msg)
-	
-		mismatch = 0.0
-	
-		seed_val = 0
-		sorted = False
-		# option processing
-		for option, value in opts:
-			if option == "-v":
-				verbose = True
-			if option in ("-h", "--help"):
-				raise Usage(help_message)
-			if option in ("-d", "--distribution"):
-				dist = value
-			if option in ("-m", "--mismatches"):
-				mismatch = float(value)
-			if option in ("-s", "--seed"):
-				seed_val = long(value)
-			if option in ("-S", "--sort"):
-				sorted = True
-			
-		random.seed(seed_val)
-		
-		if len(args) != 3:
-			raise Usage(help_message)
-	
-		fasta_input = args[0]
-		read_length = int(args[1])
-		num_reads = int(args[2])
-	
-		#fasta_input = "NC_003997.fna"
-		#read_length = 47
-		#num_reads = 10000
-		
-		f = open(fasta_input, "r")
-		lines = f.readlines()
-		
-		if lines[0].find(">") == -1:
-			raise Usage("File is not FASTA format")
-	
-	
-		seq = "".join([line.strip() for line in lines[1:]])
-		
-#		for line in lines[1:]:
-#			line = line.strip()
-#			if line.find(">") != -1:
-#				raise("Multi-FASTA format not supported")
-#			seq += line
-
-
-
-		#print seq
-		L = len(seq)
-	
-		#allowable = range(0, L - read_length)
-		
-		rid = 0
-		
-		base_mismatcher = {
-			"A" : "C",
-			"C"	: "G",
-			"G" : "T",
-			"T" : "A"
-		}
-
-		reads = []
-		
-		for i in range(0, num_reads):
-			start = random.randint(0, L - read_length)
-			#assert start <= L - read_length
-			end = start + read_length
-
-			rid +=1
-			print ">" + "rid" + str(rid)
-			print seq[start:end]
-			
-	except Usage, err:
-		print >> sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
-		return 2
-
-
-if __name__ == "__main__":
-	sys.exit(main())