def testSimple(self):
"""
A simple example must work as expected.
"""
counts = Counter()
counts['A'] += 1
counts['G'] += 2
self.assertEqual('A:1 G:2', baseCountsToStr(counts))
def testSimple(self):
"""
A simple example must work as expected.
"""
counts = Counter()
counts['A'] += 1
counts['G'] += 2
self.assertEqual('A:1 G:2',
baseCountsToStr(counts))
for column in sam.pileup(reference=referenceId):
bases = Counter()
for read in column.pileups:
if filterRead(read):
base = read.alignment.query_sequence[read.query_position]
bases[base] += 1
baseCount = sum(bases.values())
if printStats:
counts.append(baseCount)
if printOffsets:
print(
'%d: %d %s' %
(column.reference_pos + 1, baseCount, baseCountsToStr(bases)))
if printStats:
referenceLength = referenceLengths[referenceId]
print('Reference id: %s' % referenceId)
print('Reference length: %d' % referenceLength)
print('Bases covered: %s' % pct(len(counts), referenceLength))
print('Min coverage depth: %d' %
(0 if len(counts) < referenceLength else min(counts)))
if counts:
# Don't use Python3 default= option on max. Trying to keep Python 2
# compatibility.
print('Max coverage depth: %d' % max(counts))
else:
print('Max coverage depth: 0')
print('Mean coverage depth: %.3f' % (sum(counts) / referenceLength))