parser.add_argument('-B','--bams',default=[],action="append" ,help="File containing breaks")
parser.add_argument('-i','--infile',default=False ,help="Input layout in p: lines format.")
parser.add_argument('-j','--nprocesses',default=16,type=int ,help="Number of subprocesses to use when making PDF reports.")
parser.add_argument('-H','--head',default=False,type=int ,help="Maximum number of breaks to make visualizations for.")
parser.add_argument('-o','--outfile',default=False,help="Filename for output.")
parser.add_argument('-R','--report',default=False ,metavar="FILE", help="Generate a PDF report with visualizations of the breaks made.")
parser.add_argument('-t','--threshold',default=5.0,type=float,help="Minimum acceptable LLR support.")
parser.add_argument('-T','--contig_break_threshold',type=float,help="Minimum acceptable LLR support within contig sequence.")
parser.add_argument('-q','--mapq',default=10.0,type=float,help="Mapping quality score cutoff.")
parser.add_argument('--mask',default=False,help="File with segments to mask for dot-plot visualization.")
args = parser.parse_args()
if args.contig_break_threshold==None: args.contig_break_threshold = args.threshold
asf = HiriseAssembly()
asf.load_playout(args.infile)
breaks=[]
scores={}
stype={}
for l in open(args.breaks):
if l[0]=="#": continue
fields = l.strip().split()
scaffold,a,b,c,score,slen = fields[:6]
lowest_raw_score=args.threshold+5
clipped=False
if "clippedLLR" in fields:
clipped=True
if not fields[6]=="False":
lowest_raw_score = float(fields[6])
#
from __future__ import division
from __future__ import print_function
from builtins import range
from past.utils import old_div
from hirise_assembly import HiriseAssembly
if __name__=="__main__":
import sys
import argparse
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-d','--debug',default=False ,action="store_true",help="Turn on debugging ouput")
parser.add_argument('-L','--layout',default=False ,help="A file containing a layout of contigs.")
parser.add_argument('-i','--infile',default=False ,help="Filename for serialised assembly input file.")
parser.add_argument('-o','--outfile',default=False,help="Filename for writing a list of segments on the raw contigs to mask for being promiscuous in linking.")
args = parser.parse_args()
if args.infile:
asf = HiriseAssembly()
asf.load_assembly(args.infile)
if args.layout:
asf.load_playout(args.layout)
if args.outfile:
asf.save_assembly( args.outfile )
