def setUp(self):
seed.init()
# Add global setup here
pass
epsilon = args.epsilon
debug = logging.DEBUG if args.debug else logging.INFO
formatter = logging.Formatter("%(asctime)s %(message)s")
handler = logging.StreamHandler(sys.stderr)
handler.setFormatter(formatter)
handler.setLevel(debug)
logger = logging.getLogger()
logger.setLevel(debug)
logger.addHandler(handler)
g = sv_io.read_genome(genome)
rds = sv_io.read_reads(reads)
sfx = seed.init(g, rds)
alignement.setScores(match, mismatch, insdel)
k = int(round(math.log(len(g), 4)))
m = len(g)
cnt = 1
for r in rds:
logger.info('read %d', cnt)
cnt += 1
n = len(r)
minerr = ('', '', '', float('inf'))
for i in range(0, n-k):
logger.debug('seed %d %s', i, r[i:i+k])
indexes = seed.find(r[i:i+k], sfx, g)
for idx in indexes:
rstart = i+k
def setUp(self):
seed.init()
# Add global setup here
pass