# 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: