# Placeholder: load py_binary
# Placeholder: load py_library
# Placeholder: load py_test
package(
default_visibility = [
"//visibility:public",
],
)
filegroup(
name = "binaries",
srcs = [
"call_variants",
"call_variants_slim",
"make_examples",
"make_examples_somatic",
"multisample_make_examples",
"runtime_by_region_vis",
"show_examples",
"train",
"vcf_stats_report",
],
)
filegroup(
name = "testdata",
testonly = True,
srcs = glob([
"testdata/input/*",
"testdata/obsolete/*",
"testdata/*",
"multiallelic_model/**",
]),
)
test_suite(
name = "gpu_tests",
tags = [
"gpu_test",
"manual",
],
tests = [
":call_variants_accelerator_test",
],
)
# Umbrella library for all the Python under DeepVariant.
py_library(
name = "deepvariant_py",
srcs = [],
deps = [
":allele_frequency",
":call_variants_lib",
":call_variants_slim_lib",
":data_providers",
":dv_utils",
":dv_vcf_constants",
":haplotypes",
":keras_modeling",
":make_examples_core",
":make_examples_lib",
":modeling",
":pileup_image",
"//deepvariant/python:allelecounter",
"//deepvariant/python:direct_phasing",
"//deepvariant/python:variant_calling",
"//deepvariant/realigner",
"//third_party/nucleus/io/python:merge_variants",
],
)
cc_library(
name = "allelecounter",
srcs = ["allelecounter.cc"],
hdrs = ["allelecounter.h"],
deps = [
":utils",
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/io:reference",
"//third_party/nucleus/protos:cigar_cc_pb2",
"//third_party/nucleus/protos:position_cc_pb2",
"//third_party/nucleus/protos:range_cc_pb2",
"//third_party/nucleus/protos:reads_cc_pb2",
"//third_party/nucleus/util:cpp_utils",
"//third_party/nucleus/util:proto_ptr",
"@com_google_absl//absl/log",
"@com_google_absl//absl/memory",
"@com_google_absl//absl/strings",
"@org_tensorflow//tensorflow/core:lib",
],
)
cc_test(
name = "allelecounter_test",
size = "small",
srcs = ["allelecounter_test.cc"],
data = ["//third_party/nucleus/testdata"],
deps = [
":allelecounter",
":utils",
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/core:statusor",
"//third_party/nucleus/io:reference",
"//third_party/nucleus/protos:cigar_cc_pb2",
"//third_party/nucleus/protos:position_cc_pb2",
"//third_party/nucleus/protos:reference_cc_pb2",
"//third_party/nucleus/testing:cpp_test_utils",
"//third_party/nucleus/testing:gunit_extras",
"//third_party/nucleus/util:cpp_utils",
"@com_google_absl//absl/container:node_hash_map",
"@com_google_absl//absl/log",
"@com_google_absl//absl/memory",
"@com_google_absl//absl/strings",
"@com_google_googletest//:gtest_main",
"@org_tensorflow//tensorflow/core:lib",
"@org_tensorflow//tensorflow/core:test",
],
)
cc_library(
name = "postprocess_variants_lib",
srcs = ["postprocess_variants.cc"],
hdrs = ["postprocess_variants.h"],
deps = [
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/protos:reference_cc_pb2",
"//third_party/nucleus/protos:variants_cc_pb2",
"//third_party/nucleus/util:cpp_utils",
"@com_google_absl//absl/strings:cord",
"@org_tensorflow//tensorflow/core:lib",
"@org_tensorflow//tensorflow/core/platform/cloud:gcs_file_system",
],
)
cc_test(
name = "postprocess_variants_lib_test",
size = "small",
srcs = ["postprocess_variants_test.cc"],
data = [
":testdata",
],
deps = [
":postprocess_variants_lib",
"//third_party/nucleus/protos:reference_cc_pb2",
"//third_party/nucleus/protos:variants_cc_pb2",
"//third_party/nucleus/testing:cpp_test_utils",
"@com_google_googletest//:gtest_main",
"@org_tensorflow//tensorflow/core:lib",
"@org_tensorflow//tensorflow/core:test",
],
)
cc_library(
name = "variant_calling",
srcs = ["variant_calling.cc"],
hdrs = ["variant_calling.h"],
deps = [
":allelecounter",
":utils",
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/core:statusor",
"//third_party/nucleus/io:vcf_reader",
"//third_party/nucleus/protos:range_cc_pb2",
"//third_party/nucleus/protos:variants_cc_pb2",
"//third_party/nucleus/util:cpp_math",
"//third_party/nucleus/util:cpp_utils",
"//third_party/nucleus/util:samplers",
"@com_google_absl//absl/container:btree",
"@com_google_absl//absl/log",
"@com_google_absl//absl/strings",
"@org_tensorflow//tensorflow/core:lib",
],
)
cc_test(
name = "variant_calling_test",
size = "small",
srcs = ["variant_calling_test.cc"],
data = [":testdata"],
deps = [
":utils",
":variant_calling",
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/io:vcf_reader",
"//third_party/nucleus/protos:variants_cc_pb2",
"//third_party/nucleus/testing:cpp_test_utils",
"//third_party/nucleus/testing:gunit_extras",
"//third_party/nucleus/util:cpp_utils",
"@com_google_absl//absl/strings",
"@com_google_googletest//:gtest_main",
"@com_google_protobuf//:protobuf",
"@org_tensorflow//tensorflow/core:lib",
"@org_tensorflow//tensorflow/core:test",
],
)
cc_library(
name = "variant_calling_multisample",
srcs = ["variant_calling_multisample.cc"],
hdrs = ["variant_calling_multisample.h"],
deps = [
":allelecounter",
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/io:vcf_reader",
"//third_party/nucleus/protos:variants_cc_pb2",
"//third_party/nucleus/util:cpp_math",
"//third_party/nucleus/util:cpp_utils",
"//third_party/nucleus/util:samplers",
"@com_google_absl//absl/container:btree",
"@com_google_absl//absl/container:flat_hash_map",
"@com_google_absl//absl/container:flat_hash_set",
"@com_google_absl//absl/container:node_hash_map",
"@com_google_absl//absl/log",
"@com_google_absl//absl/strings",
],
)
cc_test(
name = "variant_calling_multisample_somatic_test",
size = "small",
srcs = ["variant_calling_multisample_somatic_test.cc"],
deps = [
":utils",
":variant_calling_multisample",
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/protos:variants_cc_pb2",
"//third_party/nucleus/testing:gunit_extras",
"//third_party/nucleus/util:cpp_utils",
"@com_google_absl//absl/container:node_hash_map",
"@com_google_absl//absl/strings",
"@com_google_googletest//:gtest_main",
"@org_tensorflow//tensorflow/core:test",
],
)
cc_test(
name = "variant_calling_multisample_trio_test",
size = "small",
srcs = ["variant_calling_multisample_trio_test.cc"],
deps = [
":allelecounter",
":utils",
":variant_calling_multisample",
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/protos:variants_cc_pb2",
"//third_party/nucleus/testing:gunit_extras",
"//third_party/nucleus/util:cpp_utils",
"@com_google_absl//absl/container:node_hash_map",
"@com_google_absl//absl/strings",
"@com_google_googletest//:gtest_main",
"@org_tensorflow//tensorflow/core:test",
],
)
py_library(
name = "variant_caller",
srcs = ["variant_caller.py"],
srcs_version = "PY3",
deps = [
"//deepvariant/protos:deepvariant_py_pb2",
"//deepvariant/python:allelecounter",
"//deepvariant/python:variant_calling",
"//deepvariant/python:variant_calling_multisample",
"//third_party/nucleus/protos:variants_py_pb2",
"//third_party/nucleus/util:genomics_math",
"//third_party/nucleus/util:variant_utils",
"//third_party/nucleus/util:variantcall_utils",
"//third_party/nucleus/util:vcf_constants",
],
)
py_test(
name = "variant_caller_test",
size = "small",
srcs = ["variant_caller_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":py_testdata",
":variant_caller",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/util:variant_utils",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "very_sensitive_caller",
srcs = ["very_sensitive_caller.py"],
srcs_version = "PY3",
deps = [
":variant_caller",
"//deepvariant/protos:deepvariant_py_pb2",
"//deepvariant/python:allelecounter",
],
)
py_test(
name = "very_sensitive_caller_test",
size = "small",
srcs = ["very_sensitive_caller_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":py_testdata",
":very_sensitive_caller",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/testing:py_test_utils",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "vcf_candidate_importer",
srcs = ["vcf_candidate_importer.py"],
srcs_version = "PY3",
deps = [
":variant_caller",
"//deepvariant/protos:deepvariant_py_pb2",
"//deepvariant/python:allelecounter",
"//third_party/nucleus/io:vcf",
],
)
py_test(
name = "vcf_candidate_importer_test",
size = "small",
srcs = ["vcf_candidate_importer_test.py"],
data = [":testdata"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":py_testdata",
":vcf_candidate_importer",
"//deepvariant/labeler:labeled_examples_to_vcf_main_lib",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/util:variant_utils",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_test(
name = "variant_caller_trio_test",
size = "small",
srcs = ["variant_caller_trio_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":variant_caller",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/util:variant_utils",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_test(
name = "very_sensitive_caller_trio_test",
size = "small",
srcs = ["very_sensitive_caller_trio_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":very_sensitive_caller",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/testing:py_test_utils",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
cc_library(
name = "utils",
srcs = ["utils.cc"],
hdrs = ["utils.h"],
deps = [
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/protos:variants_cc_pb2",
"//third_party/nucleus/util:cpp_utils",
"@com_google_absl//absl/strings",
"@org_tensorflow//tensorflow/core:lib",
],
)
cc_test(
name = "utils_test",
size = "small",
srcs = ["utils_test.cc"],
deps = [
":utils",
"//third_party/nucleus/testing:cpp_test_utils",
"//third_party/nucleus/testing:gunit_extras",
"@com_google_googletest//:gtest_main",
"@org_tensorflow//tensorflow/core:test",
],
)
py_library(
name = "make_examples_lib",
srcs = ["make_examples.py"],
srcs_version = "PY3",
deps = [
":dv_constants",
":logging_level",
":make_examples_core",
":make_examples_options",
"//deepvariant/protos:deepvariant_py_pb2",
"//deepvariant/python:allelecounter",
"//deepvariant/python:direct_phasing",
"//third_party/nucleus/io/python:hts_verbose",
"//third_party/nucleus/protos:reads_py_pb2",
"//third_party/nucleus/util:errors",
"//third_party/nucleus/util:proto_utils",
"@absl_py//absl:app",
"@absl_py//absl/flags",
],
)
cc_library(
name = "direct_phasing",
srcs = ["direct_phasing.cc"],
hdrs = ["direct_phasing.h"],
deps = [
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/core:statusor",
"//third_party/nucleus/protos:reads_cc_pb2",
"//third_party/nucleus/protos:variants_cc_pb2",
"//third_party/nucleus/util:proto_ptr",
"@com_google_absl//absl/container:btree",
"@com_google_absl//absl/container:flat_hash_map",
"@com_google_absl//absl/container:flat_hash_set",
"@com_google_absl//absl/hash",
"@com_google_absl//absl/log",
"@com_google_absl//absl/status",
"@com_google_absl//absl/strings",
],
)
cc_test(
name = "direct_phasing_test",
size = "small",
srcs = ["direct_phasing_test.cc"],
deps = [
":direct_phasing",
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/protos:variants_cc_pb2",
"//third_party/nucleus/testing:cpp_test_utils",
"@com_google_absl//absl/strings",
"@com_google_googletest//:gtest_main",
"@org_tensorflow//tensorflow/core:test",
],
)
py_library(
name = "make_examples_core",
srcs = ["make_examples_core.py"],
srcs_version = "PY3",
deps = [
":allele_frequency",
":dv_constants",
":dv_utils",
":dv_utils_using_clif",
":dv_vcf_constants",
":pileup_image",
":resources_main_lib",
":variant_caller",
":vcf_candidate_importer",
":very_sensitive_caller",
"//deepvariant/labeler:customized_classes_labeler",
"//deepvariant/labeler:haplotype_labeler",
"//deepvariant/labeler:positional_labeler",
"//deepvariant/protos:deepvariant_py_pb2",
"//deepvariant/python:allelecounter",
"//deepvariant/python:direct_phasing",
"//deepvariant/realigner",
"//deepvariant/vendor:timer",
"//third_party/nucleus/io:fasta",
"//third_party/nucleus/io:sam",
"//third_party/nucleus/io:sharded_file_utils",
"//third_party/nucleus/io:tfrecord",
"//third_party/nucleus/io:vcf",
"//third_party/nucleus/io/python:hts_verbose",
"//third_party/nucleus/protos:range_py_pb2",
"//third_party/nucleus/protos:reads_py_pb2",
"//third_party/nucleus/protos:variants_py_pb2",
"//third_party/nucleus/util:py_utils",
"//third_party/nucleus/util:ranges",
"//third_party/nucleus/util:struct_utils",
"//third_party/nucleus/util:variant_utils",
"@absl_py//absl/logging",
"@com_google_protobuf//:protobuf_python",
],
)
py_test(
name = "make_examples_core_test",
size = "large",
srcs = ["make_examples_core_test.py"],
data = [":testdata"],
python_version = "PY3",
shard_count = 2,
srcs_version = "PY3",
deps = [
":dv_constants",
":dv_utils",
":dv_utils_using_clif",
":make_examples_core",
":make_examples_lib",
":py_testdata",
"//deepvariant/labeler:variant_labeler",
"//deepvariant/protos:deepvariant_py_pb2",
"//deepvariant/protos:realigner_py_pb2",
"//third_party/nucleus/io:fasta",
"//third_party/nucleus/io:vcf",
"//third_party/nucleus/protos:reads_py_pb2",
"//third_party/nucleus/protos:reference_py_pb2",
"//third_party/nucleus/testing:py_test_utils",
"//third_party/nucleus/util:ranges",
"//third_party/nucleus/util:variant_utils",
"@absl_py//absl/flags",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:flagsaver",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "make_examples_options",
srcs = ["make_examples_options.py"],
srcs_version = "PY3",
deps = [
":dv_constants",
":exclude_contigs",
":make_examples_core",
":pileup_image",
"//deepvariant/protos:deepvariant_py_pb2",
"//deepvariant/python:allelecounter",
"//deepvariant/python:direct_phasing",
"//deepvariant/realigner",
"//third_party/nucleus/io:sharded_file_utils",
"//third_party/nucleus/io/python:hts_verbose",
"//third_party/nucleus/protos:reads_py_pb2",
"//third_party/nucleus/util:errors",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
],
)
py_binary(
name = "make_examples",
srcs = [
"make_examples.py",
],
main = "make_examples.py",
python_version = "PY3",
deps = [
":dv_constants",
":logging_level",
":make_examples_core",
":make_examples_options",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io/python:hts_verbose",
"//third_party/nucleus/util:errors",
"//third_party/nucleus/util:proto_utils",
"@absl_py//absl/flags",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
"@absl_py//absl:app",
],
)
cc_library(
name = "merge_phased_reads_lib",
srcs = [
"merge_phased_reads.cc",
],
hdrs = [
"merge_phased_reads.h",
],
deps = [
"@com_google_absl//absl/container:flat_hash_map",
"@com_google_absl//absl/container:flat_hash_set",
"@com_google_absl//absl/log",
"@com_google_absl//absl/log:check",
"@com_google_absl//absl/status",
"@com_google_absl//absl/status:statusor",
"@com_google_absl//absl/strings",
"@com_google_absl//absl/strings:str_format",
"@com_googlesource_code_re2//:re2",
],
)
cc_binary(
name = "merge_phased_reads",
srcs = [
"merge_phased_reads_main.cc",
],
deps = [
":merge_phased_reads_lib",
"@com_google_absl//absl/flags:flag",
"@com_google_absl//absl/log:check",
],
)
cc_test(
name = "merge_phased_reads_test",
size = "small",
srcs = [
"merge_phased_reads_test.cc",
],
deps = [
":merge_phased_reads_lib",
"@com_google_absl//absl/hash:hash_testing",
"@com_google_absl//absl/status",
"@com_google_absl//absl/status:statusor",
"@com_google_absl//absl/strings",
"@com_google_googletest//:gtest_main",
"@org_tensorflow//tensorflow/core:test",
],
)
py_library(
name = "make_examples_somatic_lib",
srcs = [
"make_examples_somatic.py",
],
srcs_version = "PY2AND3",
deps = [
":dv_constants",
":logging_level",
":make_examples_core",
":make_examples_options",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io/python:hts_verbose",
"//third_party/nucleus/util:errors",
"//third_party/nucleus/util:proto_utils",
"@absl_py//absl/flags",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
"@absl_py//absl:app",
],
)
py_binary(
name = "make_examples_somatic",
srcs = [
"make_examples_somatic.py",
],
main = "make_examples_somatic.py",
python_version = "PY3",
deps = [
":dv_constants",
":logging_level",
":make_examples_core",
":make_examples_options",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io/python:hts_verbose",
"//third_party/nucleus/util:errors",
"//third_party/nucleus/util:proto_utils",
"@absl_py//absl/flags",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
"@absl_py//absl:app",
],
)
py_test(
name = "make_examples_somatic_test",
srcs = ["make_examples_somatic_test.py"],
data = [":testdata"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":make_examples_somatic_lib",
":py_testdata",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:flagsaver",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "allele_frequency",
srcs = ["allele_frequency.py"],
srcs_version = "PY3",
deps = [
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io:vcf",
"//third_party/nucleus/util:ranges",
"//third_party/nucleus/util:variant_utils",
"@absl_py//absl/logging",
],
)
py_test(
name = "allele_frequency_test",
srcs = ["allele_frequency_test.py"],
data = [":testdata"],
python_version = "PY3",
deps = [
":allele_frequency",
":py_testdata",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io:fasta",
"//third_party/nucleus/io:vcf",
"//third_party/nucleus/protos:variants_py_pb2",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_test(
name = "make_examples_test",
size = "large",
srcs = ["make_examples_test.py"],
data = [":testdata"],
python_version = "PY3",
shard_count = 2,
srcs_version = "PY3",
deps = [
":dv_utils",
":make_examples_core",
":make_examples_lib",
":py_testdata",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io:tfrecord",
"//third_party/nucleus/io:vcf",
"//third_party/nucleus/protos:reads_py_pb2",
"//third_party/nucleus/protos:reference_py_pb2",
"//third_party/nucleus/protos:variants_py_pb2",
"//third_party/nucleus/testing:py_test_utils",
"//third_party/nucleus/util:ranges",
"//third_party/nucleus/util:variant_utils",
"//third_party/nucleus/util:variantcall_utils",
"//third_party/nucleus/util:vcf_constants",
"//third_party/nucleus/util:vis",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:flagsaver",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "call_variants_slim_lib",
srcs = ["call_variants_slim.py"],
srcs_version = "PY3",
deps = [
":data_providers",
":dv_utils",
":logging_level",
":modeling",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io:tfrecord",
"//third_party/nucleus/protos:variants_py_pb2",
"//third_party/nucleus/util:errors",
"//third_party/nucleus/util:proto_utils",
"//third_party/nucleus/util:variant_utils",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
],
)
py_binary(
name = "call_variants_slim",
srcs = ["call_variants_slim.py"],
python_version = "PY3",
deps = [
":call_variants_slim_main_lib",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
],
)
py_library(
name = "keras_modeling",
srcs = ["keras_modeling.py"],
srcs_version = "PY3",
deps = [
":dv_constants",
":dv_utils",
":dv_utils_using_clif",
"@absl_py//absl/logging",
],
)
py_test(
name = "keras_modeling_test",
size = "large",
srcs = ["keras_modeling_test.py"],
deps = [
":dv_config",
":dv_constants",
":keras_modeling",
"//third_party/nucleus/testing:py_test_utils",
"@absl_py//absl/testing:absltest",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
],
)
py_binary(
name = "call_variants",
srcs = ["call_variants.py"],
python_version = "PY3",
deps = [
"call_variants_lib",
":dv_config",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
],
)
py_binary(
name = "train",
srcs = [
"train.py",
],
main = "train.py",
deps = [
":data_providers",
":dv_constants",
":dv_utils",
":keras_modeling",
"//third_party/nucleus/io:sharded_file_utils",
"@absl_py//absl:app",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
],
)
py_binary(
name = "train_inceptionv3",
srcs = [
"train_inceptionv3.py",
],
main = "train_inceptionv3.py",
deps = [
":average_model_checkpoint_patched",
":data_providers",
":dv_constants",
":dv_utils",
":keras_modeling",
"//third_party/nucleus/io:sharded_file_utils",
"@absl_py//absl:app",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
],
)
py_library(
name = "call_variants_lib",
srcs = ["call_variants.py"],
srcs_version = "PY3",
deps = [
":dv_utils",
":keras_modeling",
":logging_level",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io:sharded_file_utils",
"//third_party/nucleus/io:tfrecord",
"//third_party/nucleus/protos:variants_py_pb2",
"//third_party/nucleus/util:errors",
"//third_party/nucleus/util:proto_utils",
"//third_party/nucleus/util:variant_utils",
"//third_party/nucleus/util:vis",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
],
)
py_test(
name = "call_variants_test",
size = "large",
srcs = ["call_variants_test.py"],
data = [":testdata"],
deps = [
":call_variants_lib",
":dv_utils",
":keras_modeling",
":py_testdata",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io:sharded_file_utils",
"//third_party/nucleus/io:tfrecord",
"@absl_py//absl/flags",
"@absl_py//absl/testing:absltest", # buildcleaner: keep
"@absl_py//absl/testing:flagsaver",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "call_variants_slim_main_lib",
srcs = [
"call_variants_slim.py",
],
deps = [
":call_variants_slim_lib",
"@absl_py//absl/flags",
],
)
py_test(
name = "call_variants_slim_test",
size = "large",
srcs = ["call_variants_slim_test.py"],
args = ["--use_tpu=false"],
data = [":testdata"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":call_variants_slim_main_lib",
":dv_utils",
":modeling",
":py_testdata",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io:tfrecord",
"//third_party/nucleus/testing:py_test_utils",
"//third_party/nucleus/util:variant_utils",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:flagsaver",
"@absl_py//absl/testing:parameterized",
],
)
py_test(
name = "call_variants_accelerator_test",
size = "large",
srcs = ["call_variants_accelerator_test.py"],
data = [":testdata"],
python_version = "PY3",
srcs_version = "PY3",
tags = [
"gpu_test",
"manual",
"notap",
],
deps = [
":call_variants_slim_main_lib",
":modeling",
":py_testdata",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "pileup_image",
srcs = ["pileup_image.py"],
srcs_version = "PY3",
deps = [
":dv_constants",
":sample",
"//deepvariant/protos:deepvariant_py_pb2",
"//deepvariant/python:pileup_image_native",
"//third_party/nucleus/io:fasta",
"//third_party/nucleus/io:sam",
"//third_party/nucleus/protos:reads_py_pb2",
"//third_party/nucleus/protos:variants_py_pb2",
"//third_party/nucleus/util:ranges",
"@absl_py//absl/logging",
],
)
py_test(
name = "pileup_image_test",
size = "small",
srcs = ["pileup_image_test.py"],
data = [":testdata"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":dv_constants",
":make_examples_core",
":pileup_image",
":py_testdata",
"//deepvariant/protos:deepvariant_py_pb2",
"//deepvariant/python:pileup_image_native",
"//third_party/nucleus/io:fasta",
"//third_party/nucleus/protos:variants_py_pb2",
"//third_party/nucleus/util:ranges",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
cc_library(
name = "pileup_image_native",
srcs = ["pileup_image_native.cc"],
hdrs = ["pileup_image_native.h"],
deps = [
":pileup_channel_lib",
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/protos:cigar_cc_pb2",
"//third_party/nucleus/protos:position_cc_pb2",
"//third_party/nucleus/protos:reads_cc_pb2",
"//third_party/nucleus/protos:struct_cc_pb2",
"//third_party/nucleus/protos:variants_cc_pb2",
"//third_party/nucleus/util:proto_ptr",
"@com_google_absl//absl/log",
"@com_google_absl//absl/log:check",
"@org_tensorflow//tensorflow/core:lib",
],
)
cc_library(
name = "pileup_channel_lib",
hdrs = ["pileup_channel_lib.h"],
deps = [
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/protos:cigar_cc_pb2",
"//third_party/nucleus/protos:position_cc_pb2",
"//third_party/nucleus/protos:reads_cc_pb2",
"//third_party/nucleus/protos:struct_cc_pb2",
"//third_party/nucleus/protos:variants_cc_pb2",
"@com_google_absl//absl/container:btree",
"@com_google_absl//absl/log",
"@com_google_absl//absl/log:check",
],
)
cc_test(
name = "pileup_channel_lib_test",
srcs = ["pileup_channel_lib_test.cc"],
deps = [
":pileup_channel_lib",
"//deepvariant/protos:deepvariant_cc_pb2",
"//third_party/nucleus/protos:cigar_cc_pb2",
"//third_party/nucleus/protos:reads_cc_pb2",
"//third_party/nucleus/protos:struct_cc_pb2",
"//third_party/nucleus/testing:cpp_test_utils",
"//third_party/nucleus/util:cpp_utils",
"@com_google_googletest//:gtest_main",
"@org_tensorflow//tensorflow/core:test",
],
)
py_library(
name = "postprocess_variants_py_lib",
srcs = ["postprocess_variants.py"],
data = glob([
"multiallelic_model/**",
]),
srcs_version = "PY3",
deps = [
# END_INTERNAL
":dv_vcf_constants",
":logging_level",
":dv_utils",
":dv_constants",
":haplotypes",
"//deepvariant/protos:deepvariant_py_pb2",
"//deepvariant/python:postprocess_variants",
"//third_party/nucleus/io:sharded_file_utils",
"//third_party/nucleus/io:tabix",
"//third_party/nucleus/io:tfrecord",
"//third_party/nucleus/io:vcf",
"//third_party/nucleus/io/python:merge_variants",
"//third_party/nucleus/protos:reference_py_pb2",
"//third_party/nucleus/protos:struct_py_pb2",
"//third_party/nucleus/protos:variants_py_pb2",
"//third_party/nucleus/util:errors",
"//third_party/nucleus/util:genomics_math",
"//third_party/nucleus/util:proto_utils",
"//third_party/nucleus/util:struct_utils",
"//third_party/nucleus/util:variant_utils",
"//third_party/nucleus/util:variantcall_utils",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
],
)
py_binary(
name = "postprocess_variants",
srcs = [
"postprocess_variants.py",
],
main = "postprocess_variants.py",
python_version = "PY3",
deps = [
":postprocess_variants_py_lib",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
],
)
py_test(
name = "postprocess_variants_test",
size = "medium",
srcs = ["postprocess_variants_test.py"],
data = [":testdata"],
python_version = "PY3",
srcs_version = "PY3",
tags = ["requires-net:external"],
deps = [
":dv_constants",
":dv_vcf_constants",
":postprocess_variants_py_lib",
":py_testdata",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io:fasta",
"//third_party/nucleus/io:tfrecord",
"//third_party/nucleus/io:vcf",
"//third_party/nucleus/protos:reference_py_pb2",
"//third_party/nucleus/protos:struct_py_pb2",
"//third_party/nucleus/protos:variants_py_pb2",
"//third_party/nucleus/testing:py_test_utils",
"//third_party/nucleus/util:genomics_math",
"//third_party/nucleus/util:struct_utils",
"//third_party/nucleus/util:variant_utils",
"//third_party/nucleus/util:variantcall_utils",
"//third_party/nucleus/util:vcf_constants",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:flagsaver",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "py_testdata",
testonly = True,
srcs = ["testdata.py"],
srcs_version = "PY3",
deps = [
"//third_party/nucleus/testing:py_test_utils",
],
)
py_library(
name = "data_providers",
srcs = ["data_providers.py"],
srcs_version = "PY3",
deps = [
":dv_constants",
":dv_utils",
":keras_modeling",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io:sharded_file_utils",
"@absl_py//absl/logging",
"@com_google_protobuf//:protobuf_python",
],
)
py_library(
name = "data_providers_test_lib",
testonly = True,
srcs = ["data_providers_test.py"],
srcs_version = "PY3",
deps = [
":data_providers",
":dv_config",
":dv_constants",
":dv_utils",
":py_testdata",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io:tfrecord",
"//third_party/nucleus/testing:py_test_utils",
"//third_party/nucleus/util:variant_utils",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_test(
name = "data_providers_test",
size = "medium",
srcs = ["data_providers_test.py"],
data = [":testdata"],
main = "data_providers_test.py",
python_version = "PY3",
srcs_version = "PY3",
deps = [
":data_providers_test_lib",
],
)
py_library(
name = "haplotypes",
srcs = ["haplotypes.py"],
srcs_version = "PY3",
deps = [
"//third_party/nucleus/util:genomics_math",
"//third_party/nucleus/util:variant_utils",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
],
)
py_test(
name = "haplotypes_test",
size = "small",
srcs = ["haplotypes_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":haplotypes",
"//third_party/nucleus/testing:py_test_utils",
"@absl_py//absl/flags",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:flagsaver",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "modeling",
srcs = ["modeling.py"],
srcs_version = "PY3",
deps = [
":data_providers",
":dv_utils",
"//third_party/nucleus/util:variant_utils",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
],
)
py_test(
name = "modeling_test",
size = "large",
srcs = ["modeling_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":dv_constants",
":dv_utils",
":dv_utils_using_clif",
":modeling",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "dv_utils",
srcs = ["dv_utils.py"],
srcs_version = "PY3",
deps = [
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io:sharded_file_utils",
"//third_party/nucleus/io:tfrecord",
"//third_party/nucleus/protos:variants_py_pb2",
"@absl_py//absl/logging",
],
)
py_test(
name = "dv_utils_test",
size = "small",
srcs = ["dv_utils_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":dv_utils",
":py_testdata",
"//third_party/nucleus/io:tfrecord",
"//third_party/nucleus/protos:variants_py_pb2",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "dv_utils_using_clif",
srcs = ["dv_utils_using_clif.py"],
srcs_version = "PY3",
deps = [
":dv_utils",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/protos:variants_py_pb2",
"//third_party/nucleus/util:ranges",
"//third_party/nucleus/util:variant_utils",
],
)
py_test(
name = "dv_utils_using_clif_test",
size = "small",
srcs = ["dv_utils_using_clif_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":dv_utils_using_clif",
":py_testdata",
"//third_party/nucleus/protos:variants_py_pb2",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "logging_level",
srcs = ["logging_level.py"],
deps = ["@absl_py//absl/flags"],
)
py_library(
name = "exclude_contigs",
srcs = ["exclude_contigs.py"],
)
py_test(
name = "exclude_contigs_test",
size = "small",
srcs = ["exclude_contigs_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":exclude_contigs",
"@absl_py//absl/testing:absltest",
],
)
py_library(
name = "dv_constants",
srcs = ["dv_constants.py"],
srcs_version = "PY3",
)
py_library(
name = "dv_vcf_constants",
srcs = ["dv_vcf_constants.py"],
srcs_version = "PY3",
deps = [
"//third_party/nucleus/protos:variants_py_pb2",
"//third_party/nucleus/util:vcf_constants",
],
)
py_test(
name = "dv_vcf_constants_test",
size = "small",
srcs = ["dv_vcf_constants_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":dv_vcf_constants",
"//third_party/nucleus/protos:reference_py_pb2",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_binary(
name = "resources",
srcs = ["resources.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [":resources_main_lib"],
)
py_library(
name = "resources_main_lib",
srcs = ["resources.py"],
srcs_version = "PY3",
deps = ["//deepvariant/protos:resources_py_pb2"],
)
py_test(
name = "resources_test",
srcs = ["resources_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":resources_main_lib",
"@absl_py//absl/testing:absltest",
],
)
py_binary(
name = "vcf_stats_report",
srcs = ["vcf_stats_report.py"],
main = "vcf_stats_report.py",
python_version = "PY3",
srcs_version = "PY3",
deps = [
":vcf_stats_report_lib",
"@absl_py//absl/flags",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
],
)
py_library(
name = "vcf_stats_report_lib",
srcs = ["vcf_stats_report.py"],
srcs_version = "PY3",
deps = [
":vcf_stats",
"//third_party/nucleus/io:vcf",
"//third_party/nucleus/util:errors",
],
)
py_library(
name = "vcf_stats",
srcs = ["vcf_stats.py"],
srcs_version = "PY3",
deps = [
":vcf_stats_vis",
"//third_party/nucleus/util:variant_utils",
"//third_party/nucleus/util:variantcall_utils",
"@absl_py//absl/logging",
],
)
py_test(
name = "vcf_stats_test",
srcs = ["vcf_stats_test.py"],
data = [":testdata"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":py_testdata",
":vcf_stats",
"//third_party/nucleus/io:vcf",
"//third_party/nucleus/testing:py_test_utils",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "vcf_stats_vis",
srcs = ["vcf_stats_vis.py"],
srcs_version = "PY3",
)
py_test(
name = "vcf_stats_vis_test",
srcs = ["vcf_stats_vis_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":vcf_stats_vis",
"//third_party/nucleus/testing:py_test_utils",
"@absl_py//absl/testing:absltest",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
],
)
py_binary(
name = "show_examples",
srcs = ["show_examples.py"],
python_version = "PY3",
deps = [
":show_examples_lib",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
],
)
py_library(
name = "show_examples_lib",
srcs = ["show_examples.py"],
srcs_version = "PY3",
deps = [
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io:sharded_file_utils",
"//third_party/nucleus/io:tfrecord",
"//third_party/nucleus/protos:variants_py_pb2",
"//third_party/nucleus/util:errors",
"//third_party/nucleus/util:ranges",
"//third_party/nucleus/util:vis",
"@absl_py//absl:app",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
],
)
py_test(
name = "show_examples_test",
srcs = ["show_examples_test.py"],
data = [":testdata"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":py_testdata",
":show_examples_lib",
"//third_party/nucleus/testing:py_test_utils",
"@absl_py//absl/flags",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:flagsaver",
"@absl_py//absl/testing:parameterized",
],
)
py_library(
name = "average_model_checkpoint_patched",
srcs = ["average_model_checkpoint_patched.py"],
)
py_library(
name = "dv_config",
srcs = ["dv_config.py"],
)
py_library(
name = "dashboard_utils",
srcs = ["dashboard_utils.py"],
srcs_version = "PY3",
)
py_test(
name = "dashboard_utils_test",
srcs = ["dashboard_utils_test.py"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":dashboard_utils",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_binary(
name = "runtime_by_region_vis",
srcs = ["runtime_by_region_vis.py"],
python_version = "PY3",
deps = [
":runtime_by_region_vis_lib",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
],
)
py_library(
name = "runtime_by_region_vis_lib",
srcs = ["runtime_by_region_vis.py"],
srcs_version = "PY3",
deps = [
":dashboard_utils",
"//third_party/nucleus/io:sharded_file_utils",
"@absl_py//absl:app",
"@absl_py//absl/flags",
],
)
py_test(
name = "runtime_by_region_vis_test",
srcs = ["runtime_by_region_vis_test.py"],
data = [":testdata"],
python_version = "PY3",
srcs_version = "PY3",
deps = [
":py_testdata",
":runtime_by_region_vis_lib",
"@absl_py//absl/testing:absltest",
"@absl_py//absl/testing:parameterized",
],
)
py_binary(
name = "multisample_make_examples",
srcs = [
"multisample_make_examples.py",
],
main = "multisample_make_examples.py",
python_version = "PY3",
deps = [
":logging_level",
":make_examples_core",
":make_examples_options",
"//deepvariant/protos:deepvariant_py_pb2",
"//third_party/nucleus/io/python:hts_verbose",
"//third_party/nucleus/util:errors",
"//third_party/nucleus/util:proto_utils",
"@absl_py//absl/flags",
# TODO: Figure out why we need this dep.
"@absl_py//absl/testing:parameterized", # buildcleaner: keep
"@absl_py//absl:app",
],
)
py_library(
name = "sample",
srcs = ["sample.py"],
srcs_version = "PY3",
deps = [
":variant_caller",
"//deepvariant/protos:deepvariant_py_pb2",
"//deepvariant/python:allelecounter",
"//third_party/nucleus/io:sam",
"//third_party/nucleus/protos:reads_py_pb2",
],
)
py_library(
name = "convert_to_saved_model_lib",
srcs = ["convert_to_saved_model.py"],
deps = [
":dv_utils",
":keras_modeling",
"@absl_py//absl:app",
"@absl_py//absl/flags",
"@absl_py//absl/logging",
],
)
py_binary(
name = "convert_to_saved_model",
srcs = ["convert_to_saved_model.py"],
python_version = "PY3",
deps = [
":convert_to_saved_model_lib",
],
)