# Path: lib/util.py
# STATUS_NORMAL=1
# STATUS_MAX_MEMORY_EXCEEDED=2
# STATUS_MAX_RUNTIME_EXCEEDED=3
# MAX_LEN_OUT = 10000
# def runAndMeasure(command,detailed=True,maxtime=0,maxmem=0):
# def runSimple(command):
# def runAndMeasureInternal(return_queue,command,maxtime=0,maxmem=0):
# def runInternal(control_queue,command,max_memory):
# def measureProcess(queue, initial_pids, command, measurement_interval=1, max_runtime=0, max_memory=0, debug=False):
# 	def extendTargets(targets, proc):
# 	def killTargets(targets):
# 	def updateTargets(targets, metrics):
# 	def updateMetrics(target, metrics):
# def loadConfig(name, parent_dir="", already_included=[]):
# def setCallDir(d):
# def setRootDir(d):
# def enterCallDir():
# def enterRootDir():
# def getRootDir():
# def nl2br(text):
# def msg(text="", level=1):
# def yes_no(b):
# def md5(text):
# def merge(x, y):
# def formatFilesize(n):
# def percent(val, base, offset=0):
# def abs_path(path):
# def get_sam_header_line_count(filename):
# def is_sam_sorted(filename):
# def sort_sam(filename,threads=1):
# def sort_sam_picard(filename,threads=-1):
# def line_count(filename):
# def sanitize_string(s):
# def makeExportDropdown(plot_id,csv_filename):
# def parseMD(md,seq):


import math
import os
import yaml
from lib import util
		mapper.setInReadFiles(self._("input:reads"))
		mapper.setInPaired(self._("input:reads_paired_end"))
		mapper.setOutMappingFile(self._("output:testee_path"))
		mapper.addParams(self._("params"))

		os.remove(dummy_fastq_name)
		self.restoreWorkingDirectory()

		with open(base_runtime_file, "w") as f:
			init_time={}
			init_time["time"]=result["time"]
			init_time["usrtime"]=result["usrtime"]
			init_time["systime"]=result["systime"]
			init_time["cputime"]=result["usrtime"]+result["systime"]
			f.write(yaml.dump(init_time))

		self.enterWorkingDirectory()
		try:
			os.remove(self._("output:testee_path"))
		except:
			pass

	with open(base_runtime_file, "r") as f:
		self.setc("output:mapper_init_time", yaml.load(f.read()))

	self.enterWorkingDirectory()

	cmd = mapper.getCommandLineMain()
	self.dbg("Command(main): " + cmd)


# Path: lib/util.py
# STATUS_NORMAL=1
# STATUS_MAX_MEMORY_EXCEEDED=2
# STATUS_MAX_RUNTIME_EXCEEDED=3
# MAX_LEN_OUT = 10000
# def runAndMeasure(command,detailed=True,maxtime=0,maxmem=0):
# def runSimple(command):
# def runAndMeasureInternal(return_queue,command,maxtime=0,maxmem=0):
# def runInternal(control_queue,command,max_memory):
# def measureProcess(queue, initial_pids, command, measurement_interval=1, max_runtime=0, max_memory=0, debug=False):
# 	def extendTargets(targets, proc):
# 	def killTargets(targets):
# 	def updateTargets(targets, metrics):
# 	def updateMetrics(target, metrics):
# def loadConfig(name, parent_dir="", already_included=[]):
# def setCallDir(d):
# def setRootDir(d):
# def enterCallDir():
# def enterRootDir():
# def getRootDir():
# def nl2br(text):
# def msg(text="", level=1):
# def yes_no(b):
# def md5(text):
# def merge(x, y):
# def formatFilesize(n):
# def percent(val, base, offset=0):
# def abs_path(path):
# def get_sam_header_line_count(filename):
# def is_sam_sorted(filename):
# def sort_sam(filename,threads=1):
# def sort_sam_picard(filename,threads=-1):
# def line_count(filename):
# def sanitize_string(s):
# def makeExportDropdown(plot_id,csv_filename):
# def parseMD(md,seq):


# Path: tests_base/base_mapping/map.py
import math
import os
import yaml
from lib import util

		mapper.setInReadFiles(self._("input:reads"))
		mapper.setInPaired(self._("input:reads_paired_end"))
		mapper.setOutMappingFile(self._("output:testee_path"))
		mapper.addParams(self._("params"))

		os.remove(dummy_fastq_name)
		self.restoreWorkingDirectory()

		with open(base_runtime_file, "w") as f:
			init_time={}
			init_time["time"]=result["time"]
			init_time["usrtime"]=result["usrtime"]
			init_time["systime"]=result["systime"]
			init_time["cputime"]=result["usrtime"]+result["systime"]
			f.write(yaml.dump(init_time))

		self.enterWorkingDirectory()
		try:
			os.remove(self._("output:testee_path"))
		except:
			pass

	with open(base_runtime_file, "r") as f:
		self.setc("output:mapper_init_time", yaml.load(f.read()))

	self.enterWorkingDirectory()

	cmd = mapper.getCommandLineMain()
	self.dbg("Command(main): " + cmd)


	self.dbg("   Mapping " + util.formatFilesize(reads_size) + " to " + util.formatFilesize(os.path.getsize(