def do_chunk(coords,ecount,args):
bf = BAMFile(args.input,blockStart=coords[0],innerStart=coords[1])
results = []
for i in range(0,ecount):
e = bf.read_entry()
if e.is_aligned():
rng = e.get_target_range()
results.append([rng.get_range_string(),e.get_aligned_bases_count()])
else:
results.append(['',0])
return results
def do_chunk(ilines, infile, args):
ilines = [x.rstrip().split("\t") for x in ilines]
coord = [int(x) for x in ilines[0][2:4]]
bf = BAMFile(infile, blockStart=coord[0], innerStart=coord[1])
results = []
for i in range(0, len(ilines)):
flag = int(ilines[i][5])
e = bf.read_entry()
#if not e: break
#print {'qlen':e.get_original_query_length(),'alen':e.get_aligned_bases_count()}
value = None
if e.is_aligned():
tx = e.get_target_transcript(args.minimum_intron_size)
value = {
'qrng': e.get_actual_original_query_range().get_range_string(),
'tx': tx.get_gpd_line(),
'flag': flag,
'qlen': e.get_original_query_length(),
'aligned_bases': e.get_aligned_bases_count()
}
results.append(
e.value('qname') + "\t" +
base64.b64encode(zlib.compress(pickle.dumps(value))))
#results.append([e.value('qname'),zlib.compress(pickle.dumps(value))])
else:
value = {
'qrng': '',
'tx': '',
'flag': flag,
'qlen': e.get_original_query_length(),
'aligned_bases': 0
}
results.append(
e.value('qname') + "\t" +
base64.b64encode(zlib.compress(pickle.dumps(value))))
#results.append([e.value('qname'),zlib.compress(pickle.dumps(value))])
return results
