def _reference_model_options(p_error, max_gq, gq_resolution=1):
return deepvariant_pb2.VariantCallerOptions(
sample_name='UNKNOWN',
p_error=p_error,
max_gq=max_gq,
gq_resolution=gq_resolution,
ploidy=2)
def test_call_from_allele_counter(self):
ref = fasta.IndexedFastaReader(testdata.CHR20_FASTA)
sam_reader = sam.SamReader(testdata.CHR20_BAM)
size = 1000
region = ranges.make_range('chr20', 10000000, 10000000 + size)
allele_counter = _allelecounter.AlleleCounter(
ref.c_reader, region,
deepvariant_pb2.AlleleCounterOptions(partition_size=size))
caller = variant_calling.VariantCaller(
deepvariant_pb2.VariantCallerOptions(min_count_snps=2,
min_count_indels=2,
min_fraction_snps=0.12,
min_fraction_indels=0.12,
sample_name='sample_name',
p_error=0.001,
max_gq=50,
gq_resolution=1,
ploidy=2))
# Grab all of the reads in our region and add them to the allele_counter.
reads = list(sam_reader.query(region))
self.assertNotEmpty(reads)
for read in reads:
allele_counter.add(read)
# Get the candidates records for this whole region.
candidates = caller.calls_from_allele_counter(allele_counter)
# We should have at least some candidates and some gvcf records.
self.assertNotEmpty(candidates)
# Each candidate should be a DeepVariantCall.
for candidate in candidates:
self.assertIsInstance(candidate, deepvariant_pb2.DeepVariantCall)
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 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
