# TODO: Do we really need to track replicate numbers?
import os, sys
from src.galaxyAnalysis import GalaxyAnalysis
from src.steps.mergeBamStep import MergeBamStep
###############
testOnly = False
###############
if sys.argv[1] == '--version':
settingsFile = os.path.split(os.path.abspath(
sys.argv[0]))[0] + '/' + "settingsE3.txt"
if os.path.isfile(
settingsFile): # Unfortunately can't get xml arg for settings
ana = GalaxyAnalysis(settingsFile, 'versions', 'hg19')
MergeBamStep(ana).writeVersions(allLevels=True) # Prints to stdout
else:
print "Can't locate " + settingsFile
exit(0)
galaxyInputBamA = sys.argv[1]
repA = sys.argv[2]
galaxyInputBamB = sys.argv[3]
repB = sys.argv[4]
galaxyOutMergedBam = sys.argv[5]
genome = sys.argv[6]
expType = sys.argv[7]
anaId = sys.argv[8]
# No longer command line parameters:
