# Path: lib/gsample.py
# def log(msg):
# def index(reference, fastindex_path = "tools/fastindex"):
# def index_legacy(reference):
# def downsample(index, contig_filename, downsampled_filename, region_count, target_len, single_contig=False,
# 			   region_list=False, spacer_len=200):
# def csample(infile, region_size, sample_fraction, spacer_len=200, fastindex_path=""):
# def ctranslate(reference_file, sampled_index_file, sam_file, target_file, fastindex_path=""):
# 
# Path: tools/fastq2sam.py
# def encode_qname(qname, retain_petag=True):
# 	def __init__(self):
# 	def __init__(self, filename, pe):
# 	def readline(self):
# 	def next_read(self):
# 	def __init__(self):
# 	def align(read):
# 	def align(self, read, paired=False, is_read1=True):
# 	def align_pair(self, read1, read2):
# 	def align(self, read, paired=False, is_read1=True):
# 	def align_pair(self, read1, read2):
# 	def __init__(self, aligner, outfile):
# 	def write(self, what):
# 	def write_sam_header(self, reads):
# 	def write_single(self, read, to):
# 	def align_se(self, infile):
# 	def align_pe(self, infile_1, infile_2):
# class Object:
# class FASTQ:
# class Aligner:
# class DummyAligner(Aligner):
# class dwgsim(Aligner):
# class Converter:
# 
# Path: lib/sam.py
# class SAMRow:
# class SAMFile:
# class Object:
# class FASTQ:
# 	def __init__(self):
# 	def getTag(self,tag_name):
# 	def __init__(self, filename):
# 	def close(self):
# 	def hasLast(self):
# 	def getLast(self):
# 	def getCurr(self):
# 	def getHeader(self):
# 	def isSorted(self):
# 	def next(self):
# 	def __init__(self):
# 	def __init__(self, filename, write=False):
# 	def readline(self):
# 	def next_read(self):
# 	def write_read(self,read):
# 	def close(self):


import os
import shutil
import time
import yaml
import util
import simulator
	import main
from lib import gsample
from tools import fastq2sam
from lib import sam

	def cp(self, a, b):
		self.log("copy %s -> %s" % (a, b))
		shutil.copy(a, b)

	def main(self):
		self.mate.pushLogPrefix("Teaser")
		self.log("Init. Creating %d test datasets." % len(self.tests))

		try:
			self.preprocessTests()
		except RuntimeError as e:
			self.mate.error("Teaser: " + str(e))
			raise SystemExit

		force_recreate = self.mate.force_gen

		for name in sorted(self.tests, key=lambda k: self.tests[k]["order"]):
			if self.mate.run_only != False:
				if name not in self.mate.run_only:
					self.created_count += 1
					self.log("Data set %s is excluded, not creating." % name)
					continue

			if self.existsTest(self.tests[name]) and not force_recreate:
				self.mate.getReport().generateProgress()
				self.created_count += 1
				self.log("Data set %s already exists, not creating." % name)
				continue


# Path: lib/gsample.py
# def log(msg):
# def index(reference, fastindex_path = "tools/fastindex"):
# def index_legacy(reference):
# def downsample(index, contig_filename, downsampled_filename, region_count, target_len, single_contig=False,
# 			   region_list=False, spacer_len=200):
# def csample(infile, region_size, sample_fraction, spacer_len=200, fastindex_path=""):
# def ctranslate(reference_file, sampled_index_file, sam_file, target_file, fastindex_path=""):
# 
# Path: tools/fastq2sam.py
# def encode_qname(qname, retain_petag=True):
# 	def __init__(self):
# 	def __init__(self, filename, pe):
# 	def readline(self):
# 	def next_read(self):
# 	def __init__(self):
# 	def align(read):
# 	def align(self, read, paired=False, is_read1=True):
# 	def align_pair(self, read1, read2):
# 	def align(self, read, paired=False, is_read1=True):
# 	def align_pair(self, read1, read2):
# 	def __init__(self, aligner, outfile):
# 	def write(self, what):
# 	def write_sam_header(self, reads):
# 	def write_single(self, read, to):
# 	def align_se(self, infile):
# 	def align_pe(self, infile_1, infile_2):
# class Object:
# class FASTQ:
# class Aligner:
# class DummyAligner(Aligner):
# class dwgsim(Aligner):
# class Converter:
# 
# Path: lib/sam.py
# class SAMRow:
# class SAMFile:
# class Object:
# class FASTQ:
# 	def __init__(self):
# 	def getTag(self,tag_name):
# 	def __init__(self, filename):
# 	def close(self):
# 	def hasLast(self):
# 	def getLast(self):
# 	def getCurr(self):
# 	def getHeader(self):
# 	def isSorted(self):
# 	def next(self):
# 	def __init__(self):
# 	def __init__(self, filename, write=False):
# 	def readline(self):
# 	def next_read(self):
# 	def write_read(self,read):
# 	def close(self):


# Path: lib/teaser.py
import os
import shutil
import time
import yaml
import util
import simulator
	import main
from lib import gsample
from tools import fastq2sam
from lib import sam


	def cp(self, a, b):
		self.log("copy %s -> %s" % (a, b))
		shutil.copy(a, b)

	def main(self):
		self.mate.pushLogPrefix("Teaser")
		self.log("Init. Creating %d test datasets." % len(self.tests))

		try:
			self.preprocessTests()
		except RuntimeError as e:
			self.mate.error("Teaser: " + str(e))
			raise SystemExit

		force_recreate = self.mate.force_gen

		for name in sorted(self.tests, key=lambda k: self.tests[k]["order"]):
			if self.mate.run_only != False:
				if name not in self.mate.run_only:
					self.created_count += 1
					self.log("Data set %s is excluded, not creating." % name)
					continue

			if self.existsTest(self.tests[name]) and not force_recreate:
				self.mate.getReport().generateProgress()
				self.created_count += 1
				self.log("Data set %s already exists, not creating." % name)
				continue


			try: