def test_partition_nodedup_minabund(capsys):
infile = kevlar.tests.data_file('dupl-part-2reads.augfastq.gz')
readstream = kevlar.parse_augmented_fastx(kevlar.open(infile, 'r'))
partitioner = partition(readstream, minabund=5, dedup=False)
partitions = list(partitioner)
assert len(partitions) == 0
def test_pico_ccs():
infile = kevlar.tests.data_file('pico-filtered.fq.gz')
readstream = kevlar.parse_augmented_fastx(kevlar.open(infile, 'r'))
partitions = [p for p in partition(readstream, minabund=6)]
assert len(partitions) == 10
ksize=ksize,
casemin=casemin,
ctrlmax=ctrlmax,
updateint=100000,
logstream=logstream)
filterer = kfilter(discoverer,
mask=mask,
casemin=casemin,
ctrlmax=ctrlmax,
ksize=ksize,
memory=filtermem,
maxfpr=filterfpr,
logstream=logstream)
partitioner = partition(filterer,
dedup=dedup,
minabund=partminabund,
maxabund=partmaxabund,
logstream=logstream)
caller = alac(partitioner,
refrfile,
threads=threads,
ksize=ksize,
delta=delta,
seedsize=seedsize,
match=match,
mismatch=mismatch,
gapopen=gapopen,
gapextend=gapextend,
logstream=logstream)