# only_chunks is used when we fragment the mapping into small aliquots
# to use the short_queue on the cluster (it's a hack). [0] means all
# chunks, automatically detected by the presence of the input files;
# [None] means normal mapping, [1, 2, ..] means to map only those chunks.
if only_chunks == [0]:
only_chunks_sample = range(1, get_number_chunks(pname, samplename, fragment, VERBOSE=VERBOSE) + 1)
else:
only_chunks_sample = only_chunks
for only_chunk in only_chunks_sample:
# If the input file if missing, skip
input_filename = get_input_filename(sample.seqrun_folder,
sample.adapter,
sample.convert_region(fragment),
type='bam',
only_chunk=only_chunk,
filtered=filtered)
if not os.path.isfile(input_filename):
if VERBOSE:
print 'WARNING: input file not found'
continue
if submit:
fork_self(samplename, fragment,
VERBOSE=VERBOSE, threads=threads,
n_pairs=n_pairs,
summary=summary,
only_chunks=[only_chunk],
filtered=filtered)
