def __init__(self, normal_bam_filename, tumor_bam_filename, reference_genome_filename, input_filename_base, segments_bed, min_depth=20, min_bqual=10, min_mqual=10, process_num=1): self.normal_bam_filename = normal_bam_filename self.tumor_bam_filename = tumor_bam_filename self.reference_genome_filename = reference_genome_filename self.input_filename_base = input_filename_base self.segments_bed = segments_bed self.min_depth = min_depth self.min_bqual = min_bqual self.min_mqual = min_mqual self.process_num = process_num self.data = Data()
def __init__(self, normal_bam_filename, tumor_bam_filename, reference_genome_filename, input_filename_base, segments_bed, BICseq_bed_fileName_corrected, pkl_path="", max_copynumber=6, subclone_num=1, baseline_thred_LOH=0.3, baseline_thred_APM=0.01, min_depth=20, min_bqual=10, min_mqual=10, process_num=1): self.normal_bam_filename = normal_bam_filename self.tumor_bam_filename = tumor_bam_filename self.reference_genome_filename = reference_genome_filename self.input_filename_base = input_filename_base self.segments_bed = segments_bed self.BICseq_bed_fileName_corrected = BICseq_bed_fileName_corrected self.pkl_path = pkl_path self.max_copynumber = max_copynumber self.subclone_num = subclone_num self.baseline_thred_LOH = baseline_thred_LOH self.baseline_thred_APM = baseline_thred_APM self.min_depth = min_depth self.min_bqual = min_bqual self.min_mqual = min_mqual print "process_num = {}".format(process_num) self.process_num = process_num self.data = Data()