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Catherine Stones
cathy-stones/
deepvariant-r1.6.1
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# Placeholder: load py_library

# Placeholder: load py_test

# Placeholder: load py_binary



package(

    default_visibility = [

        "//visibility:public",

    ],

)



filegroup(

    name = "binaries",

    srcs = [

        "make_examples",

        "//deepvariant:call_variants",

        "//deepvariant:postprocess_variants",

        "//deepvariant:vcf_stats_report",

    ],

)



py_library(

    name = "dt_constants",

    srcs = ["dt_constants.py"],

    srcs_version = "PY2AND3",

)



py_library(

    name = "py_testdata",

    testonly = True,

    srcs = ["testdata.py"],

    srcs_version = "PY2AND3",

    deps = [

        "//third_party/nucleus/testing:py_test_utils",

    ],

)



py_library(

    name = "make_examples_lib",

    srcs = ["make_examples.py"],

    srcs_version = "PY2AND3",

    deps = [

        ":dt_constants",

        "//deepvariant:logging_level",

        "//deepvariant:make_examples_core",

        "//deepvariant:make_examples_options",

        "//deepvariant/protos:deepvariant_py_pb2",

        "//deepvariant/python:allelecounter",

        "//third_party/nucleus/io/python:hts_verbose",

        "//third_party/nucleus/protos:reads_py_pb2",

        "//third_party/nucleus/protos:variants_py_pb2",

        "//third_party/nucleus/util:errors",

        "//third_party/nucleus/util:proto_utils",

        "@absl_py//absl:app",

        "@absl_py//absl/flags",

    ],

)



py_binary(

    name = "make_examples",

    srcs = [

        "make_examples.py",

    ],

    main = "make_examples.py",

    python_version = "PY3",

    deps = [

        ":dt_constants",

        "//deepvariant/protos:deepvariant_py_pb2",

        "//deepvariant:logging_level",

        "//deepvariant:make_examples_core",

        "//deepvariant:make_examples_options",

        "//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_test",

    size = "large",

    srcs = ["make_examples_test.py"],

    data = [":testdata"],

    python_version = "PY3",

    shard_count = 2,

    srcs_version = "PY2AND3",

    deps = [

        ":make_examples_lib",

        ":py_testdata",

        "//deepvariant:dv_utils",

        "//deepvariant:make_examples_core",

        "//deepvariant/labeler:variant_labeler",

        "//deepvariant/protos:deepvariant_py_pb2",

        "//third_party/nucleus/io:fasta",

        "//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",

        "@absl_py//absl/flags",

        "@absl_py//absl/logging",

        "@absl_py//absl/testing:absltest",

        "@absl_py//absl/testing:flagsaver",

        "@absl_py//absl/testing:parameterized",

    ],

)