--- a
+++ b/third_party/nucleus/util/BUILD
@@ -0,0 +1,387 @@
+# Utility routines for working with genomics data and genomics protobufs.
+
+# Placeholder: load py_library
+# Placeholder: load py_test
+
+package(
+    #default_applicable_licenses = ["//third_party/nucleus:license"],
+    default_visibility = ["//visibility:public"],
+)
+
+licenses(["notice"])
+
+py_library(
+    name = "util_py",
+    deps = [
+        ":cigar",
+        ":errors",
+        ":genomics_math",
+        ":proto_utils",
+        ":py_utils",
+        ":ranges",
+        ":sequence_utils",
+        ":struct_utils",
+        ":variant_utils",
+        ":variantcall_utils",
+        ":vcf_constants",
+        ":vis",
+    ],
+)
+
+cc_library(
+    name = "util_cpp",
+    deps = [
+        ":cpp_math",
+        ":cpp_utils",
+        ":port",
+        ":samplers",
+    ],
+)
+
+# C++ header providing portabililty macros and functions.
+cc_library(
+    name = "port",
+    hdrs = ["port.h"],
+)
+
+cc_library(
+    name = "cpp_utils",
+    srcs = ["utils.cc"],
+    hdrs = ["utils.h"],
+    deps = [
+        ":proto_ptr",
+        "//third_party/nucleus/platform:types",
+        "//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/protos:reference_cc_pb2",
+        "//third_party/nucleus/protos:struct_cc_pb2",
+        "//third_party/nucleus/protos:variants_cc_pb2",
+        "@com_google_absl//absl/log",
+        "@com_google_absl//absl/log:check",
+        "@com_google_absl//absl/strings",
+        "@org_tensorflow//tensorflow/core:lib",
+    ],
+)
+
+cc_test(
+    name = "cpp_utils_test",
+    size = "small",
+    srcs = ["utils_test.cc"],
+    deps = [
+        ":cpp_utils",
+        "//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/testing:gunit_extras",
+        "@com_google_googletest//:gtest_main",
+        "@org_tensorflow//tensorflow/core:test",
+    ],
+)
+
+py_library(
+    name = "py_utils",
+    srcs = ["utils.py"],
+    deps = ["//third_party/nucleus/util/python:utils"],
+)
+
+py_library(
+    name = "cigar",
+    srcs = ["cigar.py"],
+    deps = ["//third_party/nucleus/protos:cigar_py_pb2"],
+)
+
+py_test(
+    name = "cigar_test",
+    size = "small",
+    srcs = ["cigar_test.py"],
+    python_version = "PY3",
+    srcs_version = "PY3",
+    deps = [
+        ":cigar",
+        "//third_party/nucleus/protos:cigar_py_pb2",
+        "@absl_py//absl/testing:absltest",
+        "@absl_py//absl/testing:parameterized",
+    ],
+)
+
+py_test(
+    name = "py_utils_test",
+    size = "medium",
+    srcs = ["utils_test.py"],
+    main = "utils_test.py",
+    python_version = "PY3",
+    srcs_version = "PY3",
+    deps = [
+        ":py_utils",
+        ":ranges",
+        "//third_party/nucleus/testing:py_test_utils",
+        "@absl_py//absl/testing:absltest",
+        "@absl_py//absl/testing:parameterized",
+    ],
+)
+
+py_library(
+    name = "proto_utils",
+    srcs = ["proto_utils.py"],
+    deps = [
+        "@com_google_protobuf//:protobuf_python",
+    ],
+)
+
+cc_library(
+    name = "cpp_math",
+    srcs = ["math.cc"],
+    hdrs = ["math.h"],
+    deps = [
+        "@com_google_absl//absl/log:check",
+        "@com_google_absl//absl/strings:cord",
+    ],
+)
+
+cc_test(
+    name = "cpp_math_test",
+    size = "small",
+    srcs = ["math_test.cc"],
+    deps = [
+        ":cpp_math",
+        "@com_google_googletest//:gtest_main",
+        "@org_tensorflow//tensorflow/core:test",
+    ],
+)
+
+py_library(
+    name = "genomics_math",
+    srcs = ["genomics_math.py"],
+    deps = ["//third_party/nucleus/util/python:math"],
+)
+
+py_test(
+    name = "genomics_math_test",
+    size = "small",
+    srcs = ["genomics_math_test.py"],
+    python_version = "PY3",
+    srcs_version = "PY3",
+    deps = [
+        ":genomics_math",
+        "@absl_py//absl/testing:absltest",
+        "@absl_py//absl/testing:parameterized",
+    ],
+)
+
+py_library(
+    name = "ranges",
+    srcs = ["ranges.py"],
+    deps = [
+        "//third_party/nucleus/io:bed",
+        "//third_party/nucleus/protos:position_py_pb2",
+        "//third_party/nucleus/protos:range_py_pb2",
+        "//third_party/nucleus/protos:reference_py_pb2",
+        "//third_party/nucleus/protos:variants_py_pb2",
+        "@absl_py//absl/logging",
+    ],
+)
+
+py_test(
+    name = "ranges_test",
+    size = "small",
+    srcs = ["ranges_test.py"],
+    data = ["//third_party/nucleus/testdata"],
+    python_version = "PY3",
+    srcs_version = "PY3",
+    deps = [
+        ":ranges",
+        "//third_party/nucleus/protos:position_py_pb2",
+        "//third_party/nucleus/protos:reference_py_pb2",
+        "//third_party/nucleus/protos:variants_py_pb2",
+        "//third_party/nucleus/testing:py_test_utils",
+        "@absl_py//absl/testing:absltest",
+        "@absl_py//absl/testing:parameterized",
+    ],
+)
+
+py_library(
+    name = "variantcall_utils",
+    srcs = ["variantcall_utils.py"],
+    deps = [
+        ":vcf_constants",
+        "//third_party/nucleus/protos:struct_py_pb2",
+        "//third_party/nucleus/protos:variants_py_pb2",
+    ],
+)
+
+py_test(
+    name = "variantcall_utils_test",
+    size = "small",
+    srcs = ["variantcall_utils_test.py"],
+    python_version = "PY3",
+    srcs_version = "PY3",
+    deps = [
+        ":variantcall_utils",
+        "//third_party/nucleus/protos:struct_py_pb2",
+        "//third_party/nucleus/protos:variants_py_pb2",
+        "@absl_py//absl/testing:absltest",
+        "@absl_py//absl/testing:parameterized",
+    ],
+)
+
+py_library(
+    name = "variant_utils",
+    srcs = ["variant_utils.py"],
+    deps = [
+        ":ranges",
+        ":variantcall_utils",
+        ":vcf_constants",
+        "//third_party/nucleus/protos:struct_py_pb2",
+        "//third_party/nucleus/protos:variants_py_pb2",
+    ],
+)
+
+py_test(
+    name = "variant_utils_test",
+    size = "small",
+    srcs = ["variant_utils_test.py"],
+    python_version = "PY3",
+    srcs_version = "PY3",
+    deps = [
+        ":ranges",
+        ":variant_utils",
+        "//third_party/nucleus/protos:variants_py_pb2",
+        "//third_party/nucleus/testing:py_test_utils",
+        "@absl_py//absl/testing:absltest",
+        "@absl_py//absl/testing:parameterized",
+    ],
+)
+
+py_library(
+    name = "struct_utils",
+    srcs = ["struct_utils.py"],
+    deps = [
+        "//third_party/nucleus/protos:struct_py_pb2",
+    ],
+)
+
+py_test(
+    name = "struct_utils_test",
+    srcs = ["struct_utils_test.py"],
+    python_version = "PY3",
+    srcs_version = "PY3",
+    deps = [
+        ":struct_utils",
+        "//third_party/nucleus/protos:struct_py_pb2",
+        "//third_party/nucleus/protos:variants_py_pb2",
+        "@absl_py//absl/testing:absltest",
+        "@absl_py//absl/testing:parameterized",
+    ],
+)
+
+py_library(
+    name = "vcf_constants",
+    srcs = ["vcf_constants.py"],
+    deps = [
+        ":struct_utils",
+        "//third_party/nucleus/protos:variants_py_pb2",
+    ],
+)
+
+py_test(
+    name = "vcf_constants_test",
+    srcs = ["vcf_constants_test.py"],
+    python_version = "PY3",
+    srcs_version = "PY3",
+    deps = [
+        ":struct_utils",
+        ":vcf_constants",
+        "//third_party/nucleus/protos:variants_py_pb2",
+        "@absl_py//absl/testing:absltest",
+        "@absl_py//absl/testing:parameterized",
+    ],
+)
+
+py_library(
+    name = "errors",
+    srcs = ["errors.py"],
+    deps = [
+        "@absl_py//absl/logging",
+    ],
+)
+
+py_test(
+    name = "errors_test",
+    srcs = ["errors_test.py"],
+    python_version = "PY3",
+    srcs_version = "PY3",
+    deps = [
+        ":errors",
+        "@absl_py//absl/testing:absltest",
+        "@absl_py//absl/testing:parameterized",
+    ],
+)
+
+cc_library(
+    name = "samplers",
+    hdrs = ["samplers.h"],
+    deps = [
+        "//third_party/nucleus/platform:types",
+        "@com_google_absl//absl/log:check",
+    ],
+)
+
+cc_test(
+    name = "samplers_test",
+    size = "small",
+    srcs = ["samplers_test.cc"],
+    deps = [
+        ":samplers",
+        "//third_party/nucleus/testing:cpp_test_utils",
+        "@com_google_googletest//:gtest_main",
+        "@org_tensorflow//tensorflow/core:test",
+    ],
+)
+
+py_library(
+    name = "sequence_utils",
+    srcs = ["sequence_utils.py"],
+)
+
+py_test(
+    name = "sequence_utils_test",
+    srcs = ["sequence_utils_test.py"],
+    python_version = "PY3",
+    srcs_version = "PY3",
+    deps = [
+        ":sequence_utils",
+        "@absl_py//absl/testing:absltest",
+        "@absl_py//absl/testing:parameterized",
+    ],
+)
+
+cc_library(
+    name = "proto_ptr",
+    hdrs = [
+        "proto_ptr.h",
+    ],
+)
+
+py_library(
+    name = "vis",
+    srcs = ["vis.py"],
+    deps = ["//third_party/nucleus/protos:variants_py_pb2"],
+)
+
+py_test(
+    name = "vis_test",
+    size = "small",
+    srcs = ["vis_test.py"],
+    python_version = "PY3",
+    srcs_version = "PY3",
+    deps = [
+        ":vis",
+        "//third_party/nucleus/protos:variants_py_pb2",
+        "//third_party/nucleus/testing:py_test_utils",
+        "@absl_py//absl/testing:absltest",
+        "@absl_py//absl/testing:parameterized",
+    ],
+)