# 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: lib/stats.py
# class ReferenceMappingStatistics:
# class MappingRow:
# 	def __init__(self):
# 	def to_string(self):
# 	def to_csv(self):
# 	def computeMeasures(self):
# 	def diff(self, other):
# 	def __init__(self, alignment=None):


import os
import csv
from lib import util
from lib import stats


percent = util.percent

def calc_stats(self):
	self.dbg("Compute mapping statistics (%s, threshold %d)... " % (self._("evaluation:class"),self._("evaluation:pos_threshold")) )
	self.enterWorkingDirectory()

	actual_comparison_path = self._("input:mapping_comparison")
	if os.path.exists(self._("input:sorted_mapping_comparison")):
		actual_comparison_path = self._("input:sorted_mapping_comparison")


# 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: lib/stats.py
# class ReferenceMappingStatistics:
# class MappingRow:
# 	def __init__(self):
# 	def to_string(self):
# 	def to_csv(self):
# 	def computeMeasures(self):
# 	def diff(self, other):
# 	def __init__(self, alignment=None):


# Path: tests_base/base_mapping_real/calc_stats.py
import os
import csv
from lib import util
from lib import stats



percent = util.percent

def calc_stats(self):
	self.dbg("Compute mapping statistics (%s, threshold %d)... " % (self._("evaluation:class"),self._("evaluation:pos_threshold")) )
	self.enterWorkingDirectory()

	actual_comparison_path = self._("input:mapping_comparison")
	if os.path.exists(self._("input:sorted_mapping_comparison")):
		actual_comparison_path = self._("input:sorted_mapping_comparison")


	eval_class = util.locate(self._("evaluation:class"))