def run_bwa_py_sampe_alloc_only(refseq_fname, read_fname, mate_fname):
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
pairs = [x for x in it.izip(read_flow, mate_flow)]
print_meminfo("AFTER READING PAIRS")
bwsa = bwa.build_bws_array(pairs)
print_meminfo("AFTER BUILDING BWSA")
bwts = bwa.restore_index(refseq_fname)
print_meminfo("AFTER RESTORING INDEX")
bnsp, pacseq = bwa.restore_reference(refseq_fname)
print_meminfo("AFTER RESTORING REFERENCE")
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
ii, last_ii = bwa.isize_info_t(), bwa.isize_info_t()
last_ii.avg = -1.0
l = len(pairs)
print_meminfo("AFTER INIT OPT & II")
# deallocate seq & ref data
for i in 0, 1:
bwa.free_seq(l, bwsa[i])
bwa.bwt_destroy(bwts[i])
bwa.bns_destroy(bnsp)
print_meminfo("AFTER DEALLOC")
del pacseq
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
print_meminfo("AFTER DEL PACSEQ")
del pairs
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
print_meminfo("AFTER DEL PAIRS")
def build_bws_array_with_trim_qual_zero(self):
pairs = self.load_pairs_fixture("pairs.txt")
bws_array = bwa.build_bws_array(pairs, qtype="fastq-illumina", src="qseq", trim_qual=0)
for read in 0,1:
for i in xrange(len(pairs)):
seq = bws_array[read][i]
self.assertEqual(seq.full_len, seq.clip_len, "unexpected sequence trimming")
def process_sequences(bwts, bns, pacseq, seq_reader, N, analyze_seqs=None):
gopt = bwa.gap_init_opt()
popt = bwa.pe_init_opt()
ii = bwa.isize_info_t()
last_ii = bwa.isize_info_t()
last_ii.avg = -1.0
while 1:
pairs = read_seq_pairs(seq_reader, N)
seq_pairs_read = len(pairs)
if seq_pairs_read == 0:
break
bwsa = bwa.build_bws_array(pairs)
bwa.cal_sa_reg_gap(0, bwts, seq_pairs_read, bwsa[0], gopt)
bwa.cal_sa_reg_gap(0, bwts, seq_pairs_read, bwsa[1], gopt)
cnt_chg = bwa.cal_pac_pos_pe(bwts, seq_pairs_read, bwsa,
ii, popt, gopt, last_ii)
sys.stderr.write('ii: %r\n' %[ii.avg, ii.std, ii.low, ii.high])
bwa.paired_sw(bns, pacseq, seq_pairs_read, bwsa, popt, ii)
bwa.refine_gapped(bns, seq_pairs_read, bwsa[0], pacseq)
bwa.refine_gapped(bns, seq_pairs_read, bwsa[1], pacseq)
analyze_seqs(gopt[0], bns, seq_pairs_read, bwsa)
bwa.free_seq(N, bwsa[0])
bwa.free_seq(N, bwsa[1])
def process_sequences(bwts, bns, pacseq, seq_reader, N, analyze_seqs=None):
gopt = bwa.gap_init_opt()
popt = bwa.pe_init_opt()
ii = bwa.isize_info_t()
last_ii = bwa.isize_info_t()
last_ii.avg = -1.0
while 1:
pairs = read_seq_pairs(seq_reader, N)
seq_pairs_read = len(pairs)
if seq_pairs_read == 0:
break
bwsa = bwa.build_bws_array(pairs)
bwa.cal_sa_reg_gap(0, bwts, seq_pairs_read, bwsa[0], gopt)
bwa.cal_sa_reg_gap(0, bwts, seq_pairs_read, bwsa[1], gopt)
cnt_chg = bwa.cal_pac_pos_pe(bwts, seq_pairs_read, bwsa, ii, popt,
gopt, last_ii)
sys.stderr.write('ii: %r\n' % [ii.avg, ii.std, ii.low, ii.high])
bwa.paired_sw(bns, pacseq, seq_pairs_read, bwsa, popt, ii)
bwa.refine_gapped(bns, seq_pairs_read, bwsa[0], pacseq)
bwa.refine_gapped(bns, seq_pairs_read, bwsa[1], pacseq)
analyze_seqs(gopt[0], bns, seq_pairs_read, bwsa)
bwa.free_seq(N, bwsa[0])
bwa.free_seq(N, bwsa[1])
def build_bws_array_with_trim_qual(self):
pairs = self.load_pairs_fixture("pairs.txt")
bws_array = bwa.build_bws_array(pairs,
qtype="fastq-illumina",
src="qseq",
trim_qual=15)
sequences = [bws_array[read][i] for i in xrange(5) for read in 0, 1]
clipped = map(lambda seq: seq.full_len > seq.clip_len, sequences)
self.assertTrue(any(clipped))
def build_bws_array_with_trim_qual_zero(self):
pairs = self.load_pairs_fixture("pairs.txt")
bws_array = bwa.build_bws_array(pairs,
qtype="fastq-illumina",
src="qseq",
trim_qual=0)
for read in 0, 1:
for i in xrange(len(pairs)):
seq = bws_array[read][i]
self.assertEqual(seq.full_len, seq.clip_len,
"unexpected sequence trimming")
def build_bws_array(self):
# FIXME: plenty of UGLY code
nseq = 100
for fmt in "fastq-sanger", "fastq-illumina", "fastq-solexa":
qkey = "solexa_quality" if fmt == "fastq-solexa" else "phred_quality"
for unknown in False, True:
g = u.random_reads_generator(nseq,
fmt=fmt,
unknown=unknown,
pe=True)
bioseq_pairs, qseq_pairs = [], []
for i, read_pair in enumerate(g):
base_name = "foo-%d" % i
names = ["%s/%d" % (base_name, j) for j in 1, 2]
seq_strings = ["".join(read_pair[j][0]) for j in 0, 1]
q_strings = [
"".join(
chr(x + sg.Q_OFFSET[fmt]) for x in read_pair[j][1])
for j in 0, 1
]
bioseq_p = [
SeqRecord(Seq(seq_strings[j], single_letter_alphabet),
id=names[j],
name=names[j],
description=names[j]) for j in 0, 1
]
for j in 0, 1:
bioseq_p[j].letter_annotations[qkey] = read_pair[j][1]
bioseq_pairs.append(bioseq_p)
qseq_pairs.append([base_name])
for j in 0, 1:
for l in seq_strings, q_strings:
qseq_pairs[-1].append(l[j])
n = len(bioseq_pairs[0][0])
assert len(qseq_pairs[0][1]) == n
for src in "bioseq", "qseq":
seq_pairs = bioseq_pairs if src == "bioseq" else qseq_pairs
bwsa = bwa.build_bws_array(seq_pairs, qtype=fmt, src=src)
for j in 0, 1:
self.assertTrue(type(bwsa[j]) is bwa.bwa_seq_p_t)
for i in xrange(nseq):
bwseq = bwsa[j][i]
self.assertEqual(bwseq.len, n)
if src == "bioseq":
exp_name = bioseq_pairs[i][0].name
else:
exp_name = "%s/%d" % (qseq_pairs[i][0],
(j + 1))
self.assertEqual(len(bwseq.get_name()),
len(exp_name))
def main(argv):
try:
refseq_fname = argv[1]
read_fname = argv[2]
mate_fname = argv[3]
except IndexError:
sys.exit("Usage: %s REFSEQ_FN READ_FN MATE_FN" % sys.argv[0])
seq_list_len = 5000
max_isize = pairing_batch_size = 1000
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
pairs_flow = it.izip(read_flow, mate_flow)
res = []
while 1:
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
if len(pairs) == 0:
break
bwts = bwa.restore_index(refseq_fname)
bnsp, pacseq = bwa.restore_reference(refseq_fname)
l = len(pairs)
bwsa = bwa.build_bws_array(pairs)
logger = logging.getLogger("test")
logger.setLevel(logging.DEBUG)
counters = get_counters()
ctx = ContextStub()
visitor = MRVisitor(logger, ctx, counters)
bwa_iterator = BWAIterator(refseq_fname, gopt, popt, max_isize,
pairing_batch_size, visitor)
for read, mate in bwa_iterator.analyze(bwsa, l):
print read.get_name(), mate.get_name()
for j in 0, 1:
bwa.free_seq(l, bwsa[j])
bwa.bns_destroy(bwa_iterator.bnsp)
for cn, c in counters.iteritems():
sys.stderr.write("%s = %d\n" % (cn, c.value))
def main(argv):
try:
refseq_fname = argv[1]
read_fname = argv[2]
mate_fname = argv[3]
except IndexError:
sys.exit("Usage: %s REFSEQ_FN READ_FN MATE_FN" % sys.argv[0])
seq_list_len = 5000
max_isize = pairing_batch_size = 1000
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
pairs_flow = it.izip(read_flow, mate_flow)
res = []
while 1:
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
if len(pairs) == 0:
break
bwts = bwa.restore_index(refseq_fname)
bnsp, pacseq = bwa.restore_reference(refseq_fname)
l = len(pairs)
bwsa = bwa.build_bws_array(pairs)
logger = logging.getLogger("test")
logger.setLevel(logging.DEBUG)
counters = get_counters()
ctx = ContextStub()
visitor = MRVisitor(logger, ctx, counters)
bwa_iterator = BWAIterator(refseq_fname, gopt, popt, max_isize,
pairing_batch_size, visitor)
for read, mate in bwa_iterator.analyze(bwsa, l):
print read.get_name(), mate.get_name()
for j in 0, 1:
bwa.free_seq(l, bwsa[j])
bwa.bns_destroy(bwa_iterator.bnsp)
for cn, c in counters.iteritems():
sys.stderr.write("%s = %d\n" % (cn, c.value))
def run_bwa_py_sampe(refseq_fname, read_fname, mate_fname):
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
pairs = [x for x in it.izip(read_flow, mate_flow)]
print_meminfo("AFTER READING PAIRS")
bwsa = bwa.build_bws_array(pairs)
print_meminfo("AFTER BUILDING BWSA")
bwts = bwa.restore_index(refseq_fname)
print_meminfo("AFTER RESTORING INDEX")
bnsp, pacseq = bwa.restore_reference(refseq_fname)
print_meminfo("AFTER RESTORING REFERENCE")
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
ii, last_ii = bwa.isize_info_t(), bwa.isize_info_t()
last_ii.avg = -1.0
l = len(pairs)
print_meminfo("AFTER INIT OPT & II")
bwa.cal_sa_reg_gap(0, bwts, l, bwsa[0], gopt)
bwa.cal_sa_reg_gap(0, bwts, l, bwsa[1], gopt)
print_meminfo("AFTER CAL_SA_REG_GAP")
cnt_chg = bwa.cal_pac_pos_pe(bwts, l, bwsa, ii, popt, gopt, last_ii)
print_meminfo("AFTER CAL_PAC_POS_PE")
bwa.paired_sw(bnsp, pacseq, l, bwsa, popt, ii)
print_meminfo("AFTER PAIRED_SW")
bwa.refine_gapped(bnsp, l, bwsa[0], pacseq)
bwa.refine_gapped(bnsp, l, bwsa[1], pacseq)
print_meminfo("AFTER REFINE_GAPPED")
for k in xrange(l):
v1 = bwa.analyze_hit(gopt[0], bnsp, bwsa[0][k], bwsa[1][k])
v2 = bwa.analyze_hit(gopt[0], bnsp, bwsa[1][k], bwsa[0][k])
print_meminfo("AFTER ANALYZE_HIT")
# deallocate seq & ref data
for i in 0, 1:
bwa.free_seq(l, bwsa[i])
bwa.bwt_destroy(bwts[i])
bwa.bns_destroy(bnsp)
print_meminfo("AFTER DEALLOC")
del pacseq
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
print_meminfo("AFTER DEL PACSEQ")
del pairs
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
print_meminfo("AFTER DEL PAIRS")
def build_bws_array(self):
# FIXME: plenty of UGLY code
nseq = 100
for fmt in "fastq-sanger", "fastq-illumina", "fastq-solexa":
qkey = "solexa_quality" if fmt == "fastq-solexa" else "phred_quality"
for unknown in False, True:
g = u.random_reads_generator(nseq, fmt=fmt, unknown=unknown, pe=True)
bioseq_pairs, qseq_pairs = [], []
for i, read_pair in enumerate(g):
base_name = "foo-%d" % i
names = ["%s/%d" % (base_name, j) for j in 1, 2]
seq_strings = ["".join(read_pair[j][0]) for j in 0, 1]
q_strings = ["".join(chr(x+sg.Q_OFFSET[fmt]) for x in read_pair[j][1])
for j in 0, 1]
bioseq_p = [SeqRecord(Seq(seq_strings[j], single_letter_alphabet),
id=names[j],
name=names[j],
description=names[j]) for j in 0, 1]
for j in 0, 1:
bioseq_p[j].letter_annotations[qkey] = read_pair[j][1]
bioseq_pairs.append(bioseq_p)
qseq_pairs.append([base_name])
for j in 0, 1:
for l in seq_strings, q_strings:
qseq_pairs[-1].append(l[j])
n = len(bioseq_pairs[0][0])
assert len(qseq_pairs[0][1]) == n
for src in "bioseq", "qseq":
seq_pairs = bioseq_pairs if src == "bioseq" else qseq_pairs
bwsa = bwa.build_bws_array(seq_pairs, qtype=fmt, src=src)
for j in 0, 1:
self.assertTrue(type(bwsa[j]) is bwa.bwa_seq_p_t)
for i in xrange(nseq):
bwseq = bwsa[j][i]
self.assertEqual(bwseq.len, n)
if src == "bioseq":
exp_name = bioseq_pairs[i][0].name
else:
exp_name = "%s/%d" % (qseq_pairs[i][0], (j+1))
self.assertEqual(len(bwseq.get_name()), len(exp_name))
def main(argv):
try:
refseq_fname = argv[1]
read_fname = argv[2]
mate_fname = argv[3]
except IndexError:
sys.exit("Usage: %s REFSEQ_FN READ_FN MATE_FN" % sys.argv[0])
seq_list_len = 10000
max_isize = pairing_batch_size = 10000
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
pairs_flow = it.izip(read_flow, mate_flow)
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
bwts = bwa.restore_index(refseq_fname)
bnsp, pacseq = bwa.restore_reference(refseq_fname)
l = len(pairs)
bwsa = bwa.build_bws_array(pairs)
bwa_iterator = BWAIterator(refseq_fname, gopt, popt, max_isize,
pairing_batch_size)
pairs = [p for p in bwa_iterator.analyze(bwsa, l)]
print "READ POS GAPO GAPE MM STRAND SCORE CIGAR"
for read, mate in pairs:
if read.n_multi > 0:
print
multi_list = [m for m in read.itermulti()]
for m in multi_list:
print read.get_name(), m.pos, m.n_gapo, m.n_gape, m.n_mm, m.strand, \
m.score, m.get_cigar(read.len)
for j in 0, 1:
bwa.free_seq(l, bwsa[j])
bwa.bns_destroy(bwa_iterator.bnsp)
def main(argv):
try:
refseq_fname = argv[1]
read_fname = argv[2]
mate_fname = argv[3]
except IndexError:
sys.exit("Usage: %s REFSEQ_FN READ_FN MATE_FN" % sys.argv[0])
seq_list_len = 10000
max_isize = pairing_batch_size = 10000
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
pairs_flow = it.izip(read_flow, mate_flow)
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
bwts = bwa.restore_index(refseq_fname)
bnsp, pacseq = bwa.restore_reference(refseq_fname)
l = len(pairs)
bwsa = bwa.build_bws_array(pairs)
bwa_iterator = BWAIterator(refseq_fname, gopt, popt, max_isize,
pairing_batch_size)
pairs = [p for p in bwa_iterator.analyze(bwsa, l)]
print "READ POS GAPO GAPE MM STRAND SCORE CIGAR"
for read, mate in pairs:
if read.n_multi > 0:
print
multi_list = [m for m in read.itermulti()]
for m in multi_list:
print read.get_name(), m.pos, m.n_gapo, m.n_gape, m.n_mm, m.strand, \
m.score, m.get_cigar(read.len)
for j in 0, 1:
bwa.free_seq(l, bwsa[j])
bwa.bns_destroy(bwa_iterator.bnsp)
def build_bws_array_with_trim_qual(self):
pairs = self.load_pairs_fixture("pairs.txt")
bws_array = bwa.build_bws_array(pairs, qtype="fastq-illumina", src="qseq", trim_qual=15)
sequences = [ bws_array[read][i] for i in xrange(5) for read in 0,1 ]
clipped = map(lambda seq: seq.full_len > seq.clip_len, sequences)
self.assertTrue(any(clipped))
def run_bwa_py_sampe(refseq_fname, read_fname, mate_fname, seq_list_len=None):
size_list = []
resident_list = []
failed_ii = 0
read_flow = Bio.SeqIO.parse(open(read_fname), "fastq-illumina")
mate_flow = Bio.SeqIO.parse(open(mate_fname), "fastq-illumina")
# pairs = [x for x in it.izip(read_flow, mate_flow)]
pairs_flow = it.izip(read_flow, mate_flow)
while 1:
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
if len(pairs) == 0:
break
size, resident = print_meminfo("AFTER READING PAIRS")
size_list.append(size)
resident_list.append(resident)
bwsa = bwa.build_bws_array(pairs)
size, resident = print_meminfo("AFTER BUILDING BWSA")
size_list.append(size)
resident_list.append(resident)
bwts = bwa.restore_index(refseq_fname)
size, resident = print_meminfo("AFTER RESTORING INDEX")
size_list.append(size)
resident_list.append(resident)
bnsp, pacseq = bwa.restore_reference(refseq_fname)
size, resident = print_meminfo("AFTER RESTORING REFERENCE")
size_list.append(size)
resident_list.append(resident)
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
ii, last_ii = bwa.isize_info_t(), bwa.isize_info_t()
last_ii.avg = -1.0
l = len(pairs)
size, resident = print_meminfo("AFTER INIT OPT & II")
size_list.append(size)
resident_list.append(resident)
bwa.cal_sa_reg_gap(0, bwts, l, bwsa[0], gopt)
bwa.cal_sa_reg_gap(0, bwts, l, bwsa[1], gopt)
size, resident = print_meminfo("AFTER CAL_SA_REG_GAP")
size_list.append(size)
resident_list.append(resident)
cnt_chg = bwa.cal_pac_pos_pe(bwts, l, bwsa, ii, popt, gopt, last_ii)
size, resident = print_meminfo("AFTER CAL_PAC_POS_PE")
size_list.append(size)
resident_list.append(resident)
# sys.stderr.write("ii=%f\n" % ii.avg)
if ii.avg < 0.0:
failed_ii += 1
bwa.paired_sw(bnsp, pacseq, l, bwsa, popt, ii)
size, resident = print_meminfo("AFTER PAIRED_SW")
size_list.append(size)
resident_list.append(resident)
bwa.refine_gapped(bnsp, l, bwsa[0], pacseq)
bwa.refine_gapped(bnsp, l, bwsa[1], pacseq)
size, resident = print_meminfo("AFTER REFINE_GAPPED")
size_list.append(size)
resident_list.append(resident)
for k in xrange(l):
v1 = bwa.analyze_hit(gopt[0], bnsp, bwsa[0][k], bwsa[1][k])
v2 = bwa.analyze_hit(gopt[0], bnsp, bwsa[1][k], bwsa[0][k])
size, resident = print_meminfo("AFTER ANALYZE_HIT")
size_list.append(size)
resident_list.append(resident)
# deallocate seq & ref data
for i in 0, 1:
bwa.free_seq(l, bwsa[i])
bwa.bwt_destroy(bwts[i])
bwa.bns_destroy(bnsp)
size, resident = print_meminfo("AFTER DEALLOC")
size_list.append(size)
resident_list.append(resident)
del pacseq
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
size, resident = print_meminfo("AFTER DEL PACSEQ")
size_list.append(size)
resident_list.append(resident)
del pairs
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
size, resident = print_meminfo("AFTER DEL PAIRS")
size_list.append(size)
resident_list.append(resident)
return max(size_list), max(resident_list), failed_ii
def run_bwa_py_sampe(refseq_fname, read_fname, mate_fname, seq_list_len=None):
size_list = []
resident_list = []
failed_ii = 0
read_flow = Bio.SeqIO.parse(open(read_fname), 'fastq-illumina')
mate_flow = Bio.SeqIO.parse(open(mate_fname), 'fastq-illumina')
#pairs = [x for x in it.izip(read_flow, mate_flow)]
pairs_flow = it.izip(read_flow, mate_flow)
while 1:
pairs = list(it.islice(pairs_flow, 0, seq_list_len))
if len(pairs) == 0:
break
size, resident = print_meminfo("AFTER READING PAIRS")
size_list.append(size)
resident_list.append(resident)
bwsa = bwa.build_bws_array(pairs)
size, resident = print_meminfo("AFTER BUILDING BWSA")
size_list.append(size)
resident_list.append(resident)
bwts = bwa.restore_index(refseq_fname)
size, resident = print_meminfo("AFTER RESTORING INDEX")
size_list.append(size)
resident_list.append(resident)
bnsp, pacseq = bwa.restore_reference(refseq_fname)
size, resident = print_meminfo("AFTER RESTORING REFERENCE")
size_list.append(size)
resident_list.append(resident)
gopt, popt = bwa.gap_init_opt(), bwa.pe_init_opt()
ii, last_ii = bwa.isize_info_t(), bwa.isize_info_t()
last_ii.avg = -1.0
l = len(pairs)
size, resident = print_meminfo("AFTER INIT OPT & II")
size_list.append(size)
resident_list.append(resident)
bwa.cal_sa_reg_gap(0, bwts, l, bwsa[0], gopt)
bwa.cal_sa_reg_gap(0, bwts, l, bwsa[1], gopt)
size, resident = print_meminfo("AFTER CAL_SA_REG_GAP")
size_list.append(size)
resident_list.append(resident)
cnt_chg = bwa.cal_pac_pos_pe(bwts, l, bwsa, ii, popt, gopt, last_ii)
size, resident = print_meminfo("AFTER CAL_PAC_POS_PE")
size_list.append(size)
resident_list.append(resident)
#sys.stderr.write("ii=%f\n" % ii.avg)
if ii.avg < 0.0:
failed_ii += 1
bwa.paired_sw(bnsp, pacseq, l, bwsa, popt, ii)
size, resident = print_meminfo("AFTER PAIRED_SW")
size_list.append(size)
resident_list.append(resident)
bwa.refine_gapped(bnsp, l, bwsa[0], pacseq)
bwa.refine_gapped(bnsp, l, bwsa[1], pacseq)
size, resident = print_meminfo("AFTER REFINE_GAPPED")
size_list.append(size)
resident_list.append(resident)
for k in xrange(l):
v1 = bwa.analyze_hit(gopt[0], bnsp, bwsa[0][k], bwsa[1][k])
v2 = bwa.analyze_hit(gopt[0], bnsp, bwsa[1][k], bwsa[0][k])
size, resident = print_meminfo("AFTER ANALYZE_HIT")
size_list.append(size)
resident_list.append(resident)
# deallocate seq & ref data
for i in 0, 1:
bwa.free_seq(l, bwsa[i])
bwa.bwt_destroy(bwts[i])
bwa.bns_destroy(bnsp)
size, resident = print_meminfo("AFTER DEALLOC")
size_list.append(size)
resident_list.append(resident)
del pacseq
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
size, resident = print_meminfo("AFTER DEL PACSEQ")
size_list.append(size)
resident_list.append(resident)
del pairs
n_unreachable = gc.collect()
logging.debug("n_unreachable = %d" % n_unreachable)
size, resident = print_meminfo("AFTER DEL PAIRS")
size_list.append(size)
resident_list.append(resident)
return max(size_list), max(resident_list), failed_ii
