def test_realigner_end2end(self):
ref_reader = fasta.IndexedFastaReader(testdata.CHR20_FASTA)
config = realigner.realigner_config(FLAGS)
reads_realigner = realigner.Realigner(config, ref_reader)
region_str = 'chr20:10,000,000-10,009,999'
windows_count = 0
regions = ranges.RangeSet.from_regions([region_str])
for region in regions.partition(1000):
with sam.SamReader(
testdata.CHR20_BAM,
read_requirements=reads_pb2.ReadRequirements()) as sam_reader:
in_reads = list(sam_reader.query(region))
windows, out_reads = reads_realigner.realign_reads(in_reads, region)
# We should always get back all of the reads we sent in. Instead of just
# checking the lengths are the same, make sure all the read names are the
# same.
self.assertCountEqual([r.fragment_name for r in in_reads],
[r.fragment_name for r in out_reads])
# Check each window to make sure it's reasonable.
for window in windows:
# We always expect the reference sequence to be one of our haplotypes.
ref_seq = ref_reader.query(window.span)
self.assertIn(ref_seq, set(window.haplotypes))
windows_count += len(windows)
self.assertGreater(windows_count, 0)
def setUp(self):
self.ref_reader = fasta.IndexedFastaReader(testdata.CHR20_FASTA)
# redacted
FLAGS.ws_use_window_selector_model = True
self.config = realigner.realigner_config(FLAGS)
self.reads_realigner = realigner.Realigner(self.config,
self.ref_reader)
def test_realigner_end2end(self):
ref_reader = genomics_io.make_ref_reader(test_utils.CHR20_FASTA)
config = realigner.realigner_config(FLAGS)
reads_realigner = realigner.Realigner(config, ref_reader)
region_str = 'chr20:10,000,000-10,009,999'
regions = ranges.RangeSet.from_regions([region_str])
for region in regions.partition(1000):
with genomics_io.make_sam_reader(
test_utils.CHR20_BAM,
core_pb2.ReadRequirements()) as sam_reader:
in_reads = list(sam_reader.query(region))
windows, out_reads = reads_realigner.realign_reads(
in_reads, region)
# We should always get back all of the reads we sent in. Instead of just
# checking the lengths are the same, make sure all the read names are the
# same.
self.assertCountEqual([r.fragment_name for r in in_reads],
[r.fragment_name for r in out_reads])
# Make sure we assembled at least one windows in the region.
self.assertNotEqual(0, len(windows))
# Check each window to make sure it's reasonable.
for window in windows:
# We always expect the reference sequence to be one of our haplotypes.
ref_seq = ref_reader.bases(window.span)
self.assertIn(ref_seq, set(window.haplotypes))
def test_realigner_diagnostics(self, enabled, emit_reads):
# Make sure that by default we aren't emitting any diagnostic outputs.
dx_dir = test_utils.test_tmpfile('dx_enabled{}_emitreads_{}'.format(
enabled, emit_reads))
region_str = 'chr20:10046178-10046188'
region = ranges.parse_literal(region_str)
assembled_region_str = 'chr20:10046096-10046267'
reads, header = _get_reads_and_header(region)
self.config = realigner.realigner_config(FLAGS)
self.config.diagnostics.enabled = enabled
self.config.diagnostics.output_root = dx_dir
self.config.diagnostics.emit_realigned_reads = emit_reads
self.reads_realigner = realigner.Realigner(self.config,
self.ref_reader, header)
_, _ = self.reads_realigner.realign_reads(reads, region)
self.reads_realigner.diagnostic_logger.close(
) # Force close all resources.
if not enabled:
# Make sure our diagnostic output isn't emitted.
self.assertFalse(tf.io.gfile.exists(dx_dir))
else:
# Our root directory exists.
self.assertTrue(tf.io.gfile.isdir(dx_dir))
# We expect a realigner_metrics.csv in our rootdir with 1 entry in it.
metrics_file = os.path.join(
dx_dir,
self.reads_realigner.diagnostic_logger.metrics_filename)
self.assertTrue(tf.io.gfile.exists(metrics_file))
with tf.io.gfile.GFile(metrics_file) as fin:
rows = list(csv.DictReader(fin))
self.assertLen(rows, 1)
self.assertEqual(set(rows[0].keys()),
{'window', 'k', 'n_haplotypes', 'time'})
self.assertEqual(rows[0]['window'], assembled_region_str)
self.assertEqual(int(rows[0]['k']), 25)
self.assertTrue(int(rows[0]['n_haplotypes']), 2)
# Check that our runtime is reasonable (greater than 0, less than 10 s).
self.assertTrue(0.0 < float(rows[0]['time']) < 10.0)
# As does the subdirectory for this region.
region_subdir = os.path.join(dx_dir, assembled_region_str)
self.assertTrue(tf.io.gfile.isdir(region_subdir))
# We always have a graph.dot
self.assertTrue(
tf.io.gfile.exists(
os.path.join(
region_subdir, self.reads_realigner.diagnostic_logger.
graph_filename)))
reads_file = os.path.join(
dx_dir, region_str, self.reads_realigner.diagnostic_logger.
realigned_reads_filename)
# if emit_reads=False then file should not exist and vice versa.
self.assertEqual(emit_reads, tf.io.gfile.exists(reads_file))
def test_window_selector_model_flags_failures(self):
with six.assertRaisesRegex(
self, ValueError,
'ws_min_supporting_reads should be smaller than ws_'
'max_supporting_reads.'):
FLAGS.ws_max_num_supporting_reads = 1
FLAGS.ws_min_num_supporting_reads = 2
FLAGS.ws_window_selector_model = None
FLAGS.ws_use_window_selector_model = False
_ = realigner.realigner_config(FLAGS)
with six.assertRaisesRegex(
self, ValueError, 'Cannot specify a ws_window_selector_model '
'if ws_use_window_selector_model is False.'):
FLAGS.ws_max_num_supporting_reads = -1
FLAGS.ws_min_num_supporting_reads = -1
FLAGS.ws_window_selector_model = testdata.WS_ALLELE_COUNT_LINEAR_MODEL
FLAGS.ws_use_window_selector_model = False
_ = realigner.realigner_config(FLAGS)
with six.assertRaisesRegex(
self, ValueError,
'Cannot use both ws_min_num_supporting_reads and '
'ws_use_window_selector_model flags.'):
FLAGS.ws_max_num_supporting_reads = -1
FLAGS.ws_min_num_supporting_reads = 1
FLAGS.ws_window_selector_model = None
FLAGS.ws_use_window_selector_model = True
_ = realigner.realigner_config(FLAGS)
with six.assertRaisesRegex(
self, ValueError,
'Cannot use both ws_max_num_supporting_reads and '
'ws_use_window_selector_model flags.'):
FLAGS.ws_max_num_supporting_reads = 1
FLAGS.ws_min_num_supporting_reads = -1
FLAGS.ws_window_selector_model = None
FLAGS.ws_use_window_selector_model = True
_ = realigner.realigner_config(FLAGS)
def test_window_selector_model_flags(self, model, min_supporting,
max_supporting, use_ws_model):
# This indirection is needed because the symbols in testdata are not set
# when the @parameterized decorator is called.
symbol_to_testdata = {
None: None,
'VARIANT_READS_THRESHOLD': testdata.WS_VARIANT_READS_THRESHOLD_MODEL,
'ALLELE_COUNT_LINEAR': testdata.WS_ALLELE_COUNT_LINEAR_MODEL
}
FLAGS.ws_max_num_supporting_reads = max_supporting
FLAGS.ws_min_num_supporting_reads = min_supporting
FLAGS.ws_window_selector_model = symbol_to_testdata[model]
FLAGS.ws_use_window_selector_model = use_ws_model
# We only make sure that reading the model does not crash or raise
# exceptions.
_ = realigner.realigner_config(FLAGS)
def setUp(self): self.ref_reader = fasta.IndexedFastaReader(testdata.CHR20_FASTA) self.config = realigner.realigner_config(FLAGS) self.reads_realigner = realigner.Realigner(self.config, self.ref_reader)
def shared_flags_to_options(
add_flags, flags_obj, samples_in_order, sample_role_to_train,
main_sample_index) -> deepvariant_pb2.MakeExamplesOptions:
"""Creates options from flags that are shared, along with given samples."""
read_reqs = reads_pb2.ReadRequirements(
keep_duplicates=flags_obj.keep_duplicates,
keep_supplementary_alignments=flags_obj.keep_supplementary_alignments,
keep_secondary_alignments=flags_obj.keep_secondary_alignments,
min_base_quality=flags_obj.min_base_quality,
min_mapping_quality=flags_obj.min_mapping_quality,
min_base_quality_mode=reads_pb2.ReadRequirements.ENFORCED_BY_CLIENT)
logging.vlog(3, 'ReadRequirements are: %s', read_reqs)
pic_options = pileup_image.default_options(read_requirements=read_reqs)
allele_counter_options = deepvariant_pb2.AlleleCounterOptions(
partition_size=flags_obj.partition_size,
read_requirements=read_reqs,
track_ref_reads=flags_obj.track_ref_reads,
normalize_reads=flags_obj.normalize_reads,
keep_legacy_behavior=flags_obj.keep_legacy_allele_counter_behavior)
options = deepvariant_pb2.MakeExamplesOptions(
exclude_contigs=exclude_contigs.EXCLUDED_HUMAN_CONTIGS,
# Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'.
random_seed=609314161,
# # Not specified by default: calling_regions = 3;
read_requirements=read_reqs,
allele_counter_options=allele_counter_options,
pic_options=pic_options,
n_cores=1,
task_id=0,
num_shards=0,
min_shared_contigs_basepairs=0.9,
sample_options=samples_in_order,
main_sample_index=main_sample_index,
sample_role_to_train=sample_role_to_train)
if add_flags:
options.mode = make_examples_core.parse_proto_enum_flag(
deepvariant_pb2.MakeExamplesOptions.Mode, flags_obj.mode.upper())
options.labeler_algorithm = make_examples_core.parse_proto_enum_flag(
deepvariant_pb2.MakeExamplesOptions.LabelerAlgorithm,
flags_obj.labeler_algorithm.upper())
options.variant_caller = make_examples_core.parse_proto_enum_flag(
deepvariant_pb2.MakeExamplesOptions.VariantCaller,
flags_obj.variant_caller.upper())
if flags_obj.ref:
options.reference_filename = flags_obj.ref
if flags_obj.confident_regions:
options.confident_regions_filename = flags_obj.confident_regions
if flags_obj.truth_variants:
options.truth_variants_filename = flags_obj.truth_variants
if flags_obj.sequencing_type:
options.pic_options.sequencing_type = make_examples_core.parse_proto_enum_flag(
deepvariant_pb2.PileupImageOptions.SequencingType,
flags_obj.sequencing_type)
if flags_obj.channels:
channel_set = flags_obj.channels.split(',')
for channel in channel_set:
if channel and channel not in dv_constants.OPT_CHANNELS:
err_msg = 'Channel "{}" is not one of the available opt channels: {}'.format(
channel, ', '.join(dv_constants.OPT_CHANNELS))
errors.log_and_raise(err_msg, errors.CommandLineError)
options.pic_options.channels[:] = channel_set
options.pic_options.num_channels += len(channel_set)
if flags_obj.multi_allelic_mode:
multi_allelic_enum = {
'include_het_alt_images':
deepvariant_pb2.PileupImageOptions.ADD_HET_ALT_IMAGES,
'exclude_het_alt_images':
deepvariant_pb2.PileupImageOptions.NO_HET_ALT_IMAGES,
}[flags_obj.multi_allelic_mode]
options.pic_options.multi_allelic_mode = multi_allelic_enum
if flags_obj.pileup_image_width:
options.pic_options.width = flags_obj.pileup_image_width
options.pic_options.alt_aligned_pileup = flags_obj.alt_aligned_pileup
options.pic_options.types_to_alt_align = flags_obj.types_to_alt_align
if flags_obj.add_supporting_other_alt_color:
options.pic_options.other_allele_supporting_read_alpha = 0.3
if flags_obj.select_variant_types:
options.select_variant_types[:] = flags_obj.select_variant_types.split(
)
for svt in options.select_variant_types:
if svt not in make_examples_core.VARIANT_TYPE_SELECTORS:
errors.log_and_raise(
'Select variant type {} not recognized. Allowed values are {}'
.format(
svt, ', '.join(
make_examples_core.VARIANT_TYPE_SELECTORS)),
errors.CommandLineError)
num_shards, examples, candidates, gvcf, runtime_by_region = (
sharded_file_utils.resolve_filespecs(
flags_obj.task, flags_obj.examples or '', flags_obj.candidates
or '', flags_obj.gvcf or '', flags_obj.runtime_by_region
or ''))
options.examples_filename = examples
options.candidates_filename = candidates
options.gvcf_filename = gvcf
options.include_med_dp = flags_obj.include_med_dp
options.task_id = flags_obj.task
options.num_shards = num_shards
options.runtime_by_region = runtime_by_region
options.parse_sam_aux_fields = make_examples_core.resolve_sam_aux_fields(
flags_obj=flags_obj)
if flags_obj.aux_fields_to_keep:
options.aux_fields_to_keep[:] = flags_obj.aux_fields_to_keep.split(
',')
else:
options.aux_fields_to_keep = None
options.use_original_quality_scores = flags_obj.use_original_quality_scores
if flags_obj.add_hp_channel:
options.pic_options.num_channels += 1
options.pic_options.add_hp_channel = True
if flags_obj.hp_tag_for_assembly_polishing < 0:
errors.log_and_raise(
'--hp_tag_for_assembly_polishing has to be set to a positive int.',
errors.CommandLineError)
if (flags_obj.hp_tag_for_assembly_polishing > 0
and not flags_obj.sort_by_haplotypes):
errors.log_and_raise(
'--hp_tag_for_assembly_polishing requires --sort_by_haplotypes to be '
'set ', errors.CommandLineError)
options.pic_options.sort_by_haplotypes = flags_obj.sort_by_haplotypes
options.pic_options.hp_tag_for_assembly_polishing = flags_obj.hp_tag_for_assembly_polishing
if flags_obj.write_run_info:
options.run_info_filename = examples + _RUN_INFO_FILE_EXTENSION
options.calling_regions.extend(
make_examples_core.parse_regions_flag(flags_obj.regions))
options.exclude_calling_regions.extend(
make_examples_core.parse_regions_flag(flags_obj.exclude_regions))
options.realigner_enabled = flags_obj.realign_reads
options.realigner_options.CopyFrom(
realigner.realigner_config(flags_obj))
if (options.mode == deepvariant_pb2.MakeExamplesOptions.TRAINING
and flags_obj.training_random_emit_ref_sites != NO_RANDOM_REF):
options.sample_options[
main_sample_index].variant_caller_options.fraction_reference_sites_to_emit = (
flags_obj.training_random_emit_ref_sites)
if (flags_obj.use_allele_frequency and not flags_obj.population_vcfs):
errors.log_and_raise(
'If use_allele_frequency is set then population_vcfs '
'must be provided.', errors.CommandLineError)
if flags_obj.use_allele_frequency:
options.use_allele_frequency = flags_obj.use_allele_frequency
options.pic_options.num_channels += 1
options.pic_options.use_allele_frequency = True
if flags_obj.population_vcfs:
options.population_vcf_filenames.extend(
re.split(',| ', flags_obj.population_vcfs))
options.max_reads_per_partition = flags_obj.max_reads_per_partition
options.use_ref_for_cram = flags_obj.use_ref_for_cram
options.hts_block_size = flags_obj.hts_block_size
options.logging_every_n_candidates = flags_obj.logging_every_n_candidates
options.customized_classes_labeler_classes_list = flags_obj.customized_classes_labeler_classes_list
options.customized_classes_labeler_info_field_name = flags_obj.customized_classes_labeler_info_field_name
return options
def default_options(add_flags=True, flags_obj=None):
"""Creates a DeepVariantOptions proto populated with reasonable defaults.
Args:
add_flags: bool. defaults to True. If True, we will push the value of
certain FLAGS into our options. If False, those option fields are left
uninitialized.
flags_obj: object. If not None, use as the source of flags,
else use global FLAGS.
Returns:
deepvariant_pb2.DeepVariantOptions protobuf.
Raises:
ValueError: If we observe invalid flag values.
"""
if not flags_obj:
flags_obj = FLAGS
read_reqs = reads_pb2.ReadRequirements(
min_base_quality=10,
min_mapping_quality=10,
min_base_quality_mode=reads_pb2.ReadRequirements.ENFORCED_BY_CLIENT)
pic_options = pileup_image.default_options(read_requirements=read_reqs)
allele_counter_options = deepvariant_pb2.AlleleCounterOptions(
partition_size=flags_obj.partition_size, read_requirements=read_reqs)
if flags_obj.sample_name:
sample_name = flags_obj.sample_name
elif flags_obj.reads:
with sam.SamReader(flags_obj.reads) as sam_reader:
sample_name = extract_sample_name_from_sam_reader(sam_reader)
else:
sample_name = _UNKNOWN_SAMPLE
variant_caller_options = deepvariant_pb2.VariantCallerOptions(
min_count_snps=flags_obj.vsc_min_count_snps,
min_count_indels=flags_obj.vsc_min_count_indels,
min_fraction_snps=flags_obj.vsc_min_fraction_snps,
min_fraction_indels=flags_obj.vsc_min_fraction_indels,
# Not specified by default: fraction_reference_sites_to_emit,
# Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'.
random_seed=1400605801,
sample_name=sample_name,
p_error=0.001,
max_gq=50,
gq_resolution=flags_obj.gvcf_gq_binsize,
ploidy=2)
options = deepvariant_pb2.DeepVariantOptions(
exclude_contigs=exclude_contigs.EXCLUDED_HUMAN_CONTIGS,
# Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'.
random_seed=609314161,
# # Not specified by default: calling_regions = 3;
read_requirements=read_reqs,
allele_counter_options=allele_counter_options,
variant_caller_options=variant_caller_options,
pic_options=pic_options,
n_cores=1,
task_id=0,
num_shards=0,
min_shared_contigs_basepairs=0.9,
)
if add_flags:
options.mode = parse_proto_enum_flag(
deepvariant_pb2.DeepVariantOptions.Mode, flags_obj.mode.upper())
options.labeler_algorithm = parse_proto_enum_flag(
deepvariant_pb2.DeepVariantOptions.LabelerAlgorithm,
flags_obj.labeler_algorithm.upper())
if flags_obj.ref:
options.reference_filename = flags_obj.ref
if flags_obj.reads:
options.reads_filename = flags_obj.reads
if flags_obj.confident_regions:
options.confident_regions_filename = flags_obj.confident_regions
if flags_obj.truth_variants:
options.truth_variants_filename = flags_obj.truth_variants
if flags_obj.downsample_fraction != NO_DOWNSAMPLING:
options.downsample_fraction = flags_obj.downsample_fraction
if flags_obj.multi_allelic_mode:
multi_allelic_enum = {
'include_het_alt_images':
deepvariant_pb2.PileupImageOptions.ADD_HET_ALT_IMAGES,
'exclude_het_alt_images':
deepvariant_pb2.PileupImageOptions.NO_HET_ALT_IMAGES,
}[flags_obj.multi_allelic_mode]
options.pic_options.multi_allelic_mode = multi_allelic_enum
if flags_obj.pileup_image_height:
options.pic_options.height = flags_obj.pileup_image_height
if flags_obj.pileup_image_width:
options.pic_options.width = flags_obj.pileup_image_width
num_shards, examples, candidates, gvcf = io_utils.resolve_filespecs(
flags_obj.task, flags_obj.examples or '', flags_obj.candidates or '',
flags_obj.gvcf or '')
options.examples_filename = examples
options.candidates_filename = candidates
options.gvcf_filename = gvcf
options.calling_regions.extend(parse_regions_flag(flags_obj.regions))
options.exclude_calling_regions.extend(
parse_regions_flag(flags_obj.exclude_regions))
options.task_id = flags_obj.task
options.num_shards = 0 if num_shards is None else num_shards
options.realigner_enabled = flags_obj.realign_reads
if options.realigner_enabled:
options.realigner_options.CopyFrom(realigner.realigner_config(flags_obj))
options.max_reads_per_partition = flags_obj.max_reads_per_partition
if (options.mode == deepvariant_pb2.DeepVariantOptions.TRAINING and
flags_obj.training_random_emit_ref_sites != NO_RANDOM_REF):
options.variant_caller_options.fraction_reference_sites_to_emit = (
flags_obj.training_random_emit_ref_sites)
return options
def test_realigner_diagnostics(self, enabled, emit_reads):
# Make sure that by default we aren't emitting any diagnostic outputs.
dx_dir = test_utils.test_tmpfile('dx')
region_str = 'chr20:10046179-10046188'
region = ranges.parse_literal(region_str)
assembled_region_str = 'chr20:10046109-10046257'
reads = _get_reads(region)
self.config = realigner.realigner_config(FLAGS)
self.config.diagnostics.enabled = enabled
self.config.diagnostics.output_root = dx_dir
self.config.diagnostics.emit_realigned_reads = emit_reads
self.reads_realigner = realigner.Realigner(self.config,
self.ref_reader)
_, realigned_reads = self.reads_realigner.realign_reads(reads, region)
self.reads_realigner.diagnostic_logger.close(
) # Force close all resources.
if not enabled:
# Make sure our diagnostic output isn't emitted.
self.assertFalse(tf.gfile.Exists(dx_dir))
else:
# Our root directory exists.
self.assertTrue(tf.gfile.IsDirectory(dx_dir))
# We expect a realigner_metrics.csv in our rootdir with 1 entry in it.
metrics_file = os.path.join(
dx_dir,
self.reads_realigner.diagnostic_logger.metrics_filename)
self.assertTrue(tf.gfile.Exists(metrics_file))
with tf.gfile.FastGFile(metrics_file) as fin:
rows = list(csv.DictReader(fin))
self.assertEqual(len(rows), 1)
self.assertEqual(set(rows[0].keys()),
{'window', 'k', 'n_haplotypes', 'time'})
self.assertEqual(rows[0]['window'], assembled_region_str)
self.assertEqual(int(rows[0]['k']), 25)
self.assertTrue(int(rows[0]['n_haplotypes']), 2)
# Check that our runtime is reasonable (greater than 0, less than 10 s).
self.assertTrue(0.0 < float(rows[0]['time']) < 10.0)
# As does the subdirectory for this region.
region_subdir = os.path.join(dx_dir, assembled_region_str)
self.assertTrue(tf.gfile.IsDirectory(region_subdir))
# We always have a graph.dot
self.assertTrue(
tf.gfile.Exists(
os.path.join(
region_subdir, self.reads_realigner.diagnostic_logger.
graph_filename)))
reads_file = os.path.join(
dx_dir, region_str, self.reads_realigner.diagnostic_logger.
realigned_reads_filename)
if emit_reads:
self.assertTrue(tf.gfile.Exists(reads_file))
reads_from_dx = io_utils.read_tfrecords(
reads_file, reads_pb2.Read)
self.assertCountEqual(reads_from_dx, realigned_reads)
else:
self.assertFalse(tf.gfile.Exists(reads_file))
def setUp(self):
self.ref_reader = genomics_io.make_ref_reader(test_utils.CHR20_FASTA)
self.config = realigner.realigner_config(FLAGS)
self.reads_realigner = realigner.Realigner(self.config,
self.ref_reader)
def default_options(add_flags=True, flags=None):
"""Creates a DeepVariantOptions proto populated with reasonable defaults.
Args:
add_flags: bool. defaults to True. If True, we will push the value of
certain FLAGS into our options. If False, those option fields are left
uninitialized.
flags: object. If not None, use as the source of flags,
else use global FLAGS.
Returns:
deepvariant_pb2.DeepVariantOptions protobuf.
Raises:
ValueError: If we observe invalid flag values.
"""
if not flags:
flags = FLAGS
read_reqs = core_pb2.ReadRequirements(
min_base_quality=10,
min_mapping_quality=10,
min_base_quality_mode=core_pb2.ReadRequirements.ENFORCED_BY_CLIENT)
pic_options = pileup_image.default_options(read_requirements=read_reqs)
allele_counter_options = deepvariant_pb2.AlleleCounterOptions(
partition_size=flags.partition_size, read_requirements=read_reqs)
if flags.sample_name:
sample_name = flags.sample_name
elif flags.reads:
sample_name = extract_sample_name_from_reads(flags.reads)
else:
sample_name = _UNKNOWN_SAMPLE
variant_caller_options = deepvariant_pb2.VariantCallerOptions(
min_count_snps=flags.vsc_min_count_snps,
min_count_indels=flags.vsc_min_count_indels,
min_fraction_snps=flags.vsc_min_fraction_snps,
min_fraction_indels=flags.vsc_min_fraction_indels,
# Not specified by default: fraction_reference_sites_to_emit,
# Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'.
random_seed=1400605801,
sample_name=sample_name,
p_error=0.001,
max_gq=50,
gq_resolution=1,
ploidy=2)
options = deepvariant_pb2.DeepVariantOptions(
exclude_contigs=[
# The two canonical names for the contig representing the human
# mitochondrial sequence.
'chrM',
'MT',
# From hs37d5.
# (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/phase2_reference_assembly_sequence/README_human_reference_20110707) # pylint:disable=line-too-long
'GL000207.1',
'GL000226.1',
'GL000229.1',
'GL000231.1',
'GL000210.1',
'GL000239.1',
'GL000235.1',
'GL000201.1',
'GL000247.1',
'GL000245.1',
'GL000197.1',
'GL000203.1',
'GL000246.1',
'GL000249.1',
'GL000196.1',
'GL000248.1',
'GL000244.1',
'GL000238.1',
'GL000202.1',
'GL000234.1',
'GL000232.1',
'GL000206.1',
'GL000240.1',
'GL000236.1',
'GL000241.1',
'GL000243.1',
'GL000242.1',
'GL000230.1',
'GL000237.1',
'GL000233.1',
'GL000204.1',
'GL000198.1',
'GL000208.1',
'GL000191.1',
'GL000227.1',
'GL000228.1',
'GL000214.1',
'GL000221.1',
'GL000209.1',
'GL000218.1',
'GL000220.1',
'GL000213.1',
'GL000211.1',
'GL000199.1',
'GL000217.1',
'GL000216.1',
'GL000215.1',
'GL000205.1',
'GL000219.1',
'GL000224.1',
'GL000223.1',
'GL000195.1',
'GL000212.1',
'GL000222.1',
'GL000200.1',
'GL000193.1',
'GL000194.1',
'GL000225.1',
'GL000192.1',
'NC_007605',
'hs37d5',
],
# Fixed random seed produced with 'od -vAn -N4 -tu4 < /dev/urandom'.
random_seed=609314161,
# # Not specified by default: calling_regions = 3;
read_requirements=read_reqs,
allele_counter_options=allele_counter_options,
variant_caller_options=variant_caller_options,
pic_options=pic_options,
n_cores=1,
task_id=0,
num_shards=0,
min_shared_contigs_basepairs=0.9,
)
if add_flags:
if flags.mode == 'training':
options.mode = deepvariant_pb2.DeepVariantOptions.TRAINING
elif flags.mode == 'calling':
options.mode = deepvariant_pb2.DeepVariantOptions.CALLING
else:
raise ValueError('Unexpected mode', flags.mode)
if flags.ref:
options.reference_filename = flags.ref
if flags.reads:
options.reads_filename = flags.reads
if flags.confident_regions:
options.confident_regions_filename = flags.confident_regions
if flags.truth_variants:
options.truth_variants_filename = flags.truth_variants
if flags.downsample_fraction != NO_DOWNSAMPLING:
options.downsample_fraction = flags.downsample_fraction
if flags.multi_allelic_mode:
multi_allelic_enum = {
'include_het_alt_images':
deepvariant_pb2.PileupImageOptions.ADD_HET_ALT_IMAGES,
'exclude_het_alt_images':
deepvariant_pb2.PileupImageOptions.NO_HET_ALT_IMAGES,
}[flags.multi_allelic_mode]
options.pic_options.multi_allelic_mode = multi_allelic_enum
if flags.pileup_image_height:
options.pic_options.height = flags.pileup_image_height
if flags.pileup_image_width:
options.pic_options.width = flags.pileup_image_width
num_shards, examples, candidates, gvcf = io_utils.resolve_filespecs(
flags.task, flags.examples or '', flags.candidates or '',
flags.gvcf or '')
options.examples_filename = examples
options.candidates_filename = candidates
options.gvcf_filename = gvcf
# redacted
regions_flag = flags.regions
if isinstance(regions_flag, str):
regions_flag = regions_flag.split()
options.calling_regions.extend(regions_flag)
options.task_id = flags.task
options.num_shards = 0 if num_shards is None else num_shards
if flags.realign_reads:
options.realigner_enabled = True
options.realigner_options.CopyFrom(
realigner.realigner_config(flags))
options.max_reads_per_partition = flags.max_reads_per_partition
if (options.mode == deepvariant_pb2.DeepVariantOptions.TRAINING
and flags.training_random_emit_ref_sites != NO_RANDOM_REF):
options.variant_caller_options.fraction_reference_sites_to_emit = (
flags.training_random_emit_ref_sites)
return options
