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()
