# 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):


from lib import util
	import json
	import json
	import json
	import json
    import json
    import math
	import json
	import json
	import json
	import json
			not_mapped=float(100 * (test.getRunResults().not_mapped + test.getRunResults().not_found))/total
		else:
			correct=0
			wrong=0
			not_mapped=0

		maptime=test.getRunResults().maptime
		if maptime != 0:
			throughput=total/float(test.getRunResults().maptime)		
		else:
			throughput=-1

		if errors == 0:
			html += "<td>%.3f%%</td>" % correct
			html += "<td>%.3f%%</td>" % wrong
			html += "<td>%.3f%%</td>" % not_mapped
			html += "<td>%d</td>" % throughput
			csv+="%s,%s,%.4f,%.4f,%.4f,%d\n" % (test.getMapper().getTitle(),test.getMapper().param_string,correct,wrong,not_mapped,throughput)
		else:
			html += "<td></td>"
			html += "<td></td>"
			html += "<td></td>"
			html += "<td></td>"
			csv+="%s,%s,-,-,-,-\n" % (test.getMapper().getTitle(),test.getMapper().param_string)

		html += "</tr>"

	csv_filename = self.writeCSV("overview",csv)

	html += "</table>"

# 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/report_overview.py
from lib import util
	import json
	import json
	import json
	import json
    import json
    import math
	import json
	import json
	import json
	import json

			not_mapped=float(100 * (test.getRunResults().not_mapped + test.getRunResults().not_found))/total
		else:
			correct=0
			wrong=0
			not_mapped=0

		maptime=test.getRunResults().maptime
		if maptime != 0:
			throughput=total/float(test.getRunResults().maptime)		
		else:
			throughput=-1

		if errors == 0:
			html += "<td>%.3f%%</td>" % correct
			html += "<td>%.3f%%</td>" % wrong
			html += "<td>%.3f%%</td>" % not_mapped
			html += "<td>%d</td>" % throughput
			csv+="%s,%s,%.4f,%.4f,%.4f,%d\n" % (test.getMapper().getTitle(),test.getMapper().param_string,correct,wrong,not_mapped,throughput)
		else:
			html += "<td></td>"
			html += "<td></td>"
			html += "<td></td>"
			html += "<td></td>"
			csv+="%s,%s,-,-,-,-\n" % (test.getMapper().getTitle(),test.getMapper().param_string)

		html += "</tr>"

	csv_filename = self.writeCSV("overview",csv)

	html += "</table>"

	html += util.makeExportDropdown("",csv_filename) 