nodes = {}
range_cutoff = args.range_cutoff
t1 = args.end_threshold
t2 = args.support_cutoff
# recombinings2.max_n_breaks=args.max_n_breaks
fmodel = open(args.set_insert_size_dist_fit_params)
contents = fmodel.read()
try:
fit_params = eval(contents)
except:
"couldn't deal with option", args.param
fmodel.close
ces.set_exp_insert_size_dist_fit_params(fit_params)
cache_cutoff = 150000
log_score_cache = {}
bamfiles = args.bamfiles.split(",")
contigs = []
chunkf = open(args.chunk, "rt")
while True:
l = chunkf.readline()
if not l: break
contigs.append(l.strip())
chunkf.close()
oname = {}
args = parser.parse_args()
if args.top:
import psutil
hra = HiriseAssembly()
hra.load_assembly(args.infile)
hra.merge_masked_regions(debug=args.debug)
print(len(hra.layout_lines))
if len(hra.layout_lines) == 0:
print("#make trivial layout")
hra.make_trivial_layout_lines(debug=args.debug)
ces.set_exp_insert_size_dist_fit_params(hra.model_params)
model = ces.model
nbams = len(hra.bams)
inq = JoinableQueue(maxsize=0)
readers = []
for i in range(nbams):
reader = Process(target=read_pairs_from_bam,
args=(inq, i, hra.bams[i], hra, args.mapq,
args.slice),
daemon=False)
reader.start()
readers.append(reader)
q = JoinableQueue(maxsize=0)
histogram_queue = JoinableQueue(maxsize=0)
def set_fit_params(fit_params):
ces.set_exp_insert_size_dist_fit_params(fit_params)
args = parser.parse_args()
if args.top:
import psutil
hra = HiriseAssembly()
hra.load_assembly(args.infile)
hra.merge_masked_regions(debug=args.debug)
print(len(hra.layout_lines))
if len(hra.layout_lines)==0:
print("#make trivial layout")
hra.make_trivial_layout_lines(debug=args.debug)
ces.set_exp_insert_size_dist_fit_params(hra.model_params)
model=ces.model
nbams = len(hra.bams)
inq = JoinableQueue(maxsize=0)
readers=[]
for i in range(nbams):
reader = Process(target=read_pairs_from_bam, args=(inq,i,hra.bams[i],hra,args.mapq,args.slice),daemon=False)
reader.start()
readers.append(reader)
q = JoinableQueue(maxsize=0)
histogram_queue = JoinableQueue(maxsize=0)
final_histogram_queue = JoinableQueue(maxsize=0)
outfiles = [ open("{}.part.{}".format(args.outfile,i),"wt") for i in range(args.nthreads) ]
