Initial release of DeepVariant

.gitignore

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+# Compiled python files.
+*.pyc
+
+# Emacs temporary files
+*~
+
+# Other temporary files
+*#
+
+bazel-*
+
+**/.ipynb_checkpoints

AUTHORS

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+# This is the official list of DeepVariant authors for copyright purposes.
+# This file is distinct from the CONTRIBUTORS files.
+# See the latter for an explanation.
+
+# Names should be added to this file as:
+# Name or Organization <email address>
+# The email address is not required for organizations.
+
+Google Inc.

BUILD

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+load("//tools:zip_dir.bzl", "zip_dir")
+
+package(
+    default_visibility = [
+        "//visibility:public",
+    ],
+)
+
+test_suite(
+    name = "smoke_tests",
+    tests = [
+        "//deepvariant/core:smoke_tests",
+        "//deepvariant/environment_tests:smoke_tests",
+        "//deepvariant/testing:smoke_tests",
+    ],
+)
+
+filegroup(
+    name = "binaries",
+    srcs = [
+        "//deepvariant:binaries",
+    ],
+)
+
+exports_files(["LICENSE"])
+
+filegroup(
+    name = "licenses",
+    srcs = [
+        ":LICENSE",
+        "//third_party:abseil_cpp.LICENSE",  # redacted
+        "//third_party:boost.LICENSE",
+        "//third_party:tensorflow.LICENSE",  # redacted
+        "//third_party:tensorflow_models.LICENSE",  # redacted
+        "@com_google_protobuf//:LICENSE",
+        "@com_googlesource_code_re2//:LICENSE",
+        "@htslib//:LICENSE",
+        "@libssw//:README.md",  # SSW license embedded in the README.
+    ],
+)
+
+zip_dir(
+    name = "licenses_zip",
+    srcs = [":licenses"],
+    zipname = "licenses.zip",
+)

CONTRIBUTING.md

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+# How to Contribute
+
+Sorry, we don't take contributions to the main DeepVariant codebase at the
+moment. We expect to open the project for contributions in 1H 2018 after we
+configure continuous integration testing on github, formalize the external code
+review process, among other technical redacted
+codebase maintains its current high quality coding and testing standards.
+
+In the meantime, please feel free to fork the DeepVariant codebase and prepare
+in your fork any patches you'd eventually like to contribute and let us know
+about them so we can prioritize putting the necessary infrastructure in place
+to accept external contributions.

LICENSE

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+Copyright 2017 Google Inc.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its contributors
+   may be used to endorse or promote products derived from this software without
+   specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

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+# DeepVariant
+
+DeepVariant is an analysis pipeline that uses a deep neural network to call
+genetic variants from next-generation DNA sequencing data.
+
+# Documentation
+
+<!-- mdlint off(URL_BAD_G3DOC_PATH) -->
+
+*   [DeepVariant release notes](docs/deepvariant-release-notes.md)
+*   [Building and testing DeepVariant](docs/deepvariant-build-test.md)
+*   [DeepVariant quick start](docs/deepvariant-quick-start.md)
+*   [DeepVariant via Docker](docs/deepvariant-docker.md)
+*   [DeepVariant whole genome case study](docs/deepvariant-case-study.md)
+*   [DeepVariant exome case study](docs/deepvariant-exome-case-study.md)
+*   [DeepVariant details](docs/deepvariant-details.md)
+*   [DeepVariant model training](docs/deepvariant-model-training.md)
+
+<!-- mdlint on -->
+
+<a name="about"></a>
+## About DeepVariant
+
+redacted
+
+## Support
+
+The Genomics team in Google Brain actively supports DeepVariant and are always
+interested in improving the quality of DeepVariant. If you run into an issue, we
+recommend you follow one of two approaches to getting the issue resolved.
+
+If you have found a bug in DeepVariant - i.e., the code itself needs to be
+fixed - please report the problem on our [Issue
+tracker](https://github.com/google/deepvariant/issues). Make sure to add enough
+detail to your report that we can reproduce the problem and fix it. We encourage
+including links to snippets of BAM/VCF/etc. files that provoke the bug, if
+possible. Depending on the severity of the issue we may patch DeepVariant
+immediately with the fix or roll it into the next release.
+
+If you have general questions about DeepVariant usage, please post your question
+to [BioStars](https://www.biostars.org/), adding the tag 'deepvariant'. We
+monitor [BioStars posts tagged with
+DeepVariant](https://www.biostars.org/t/deepvariant/) and will respond as needed
+there.
+
+## Contributing
+
+Interested in contributing? See [CONTRIBUTING](CONTRIBUTING.md).
+
+## License
+
+DeepVariant is licensed under the terms of the [BSD-3-Clause license](LICENSE).
+
+## Links
+
+redacted
+
+## Acknowledgements
+
+DeepVariant happily makes use of many open source packages.  We'd like to
+specifically call out a few key ones:
+
+* [Boost Graph Library](http://www.boost.org/doc/libs/1_65_1/libs/graph/doc/index.html)
+
+* [CLIF](https://github.com/google/clif)
+
+* [GNU Parallel](https://www.gnu.org/software/parallel/)
+
+* [htslib & samtools](http://www.htslib.org/)
+
+* [numpy](http://www.numpy.org/)
+
+* [scipy](https://www.scipy.org/)
+
+* [SSW Library](https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library)
+
+* [TensorFlow and Slim](https://www.tensorflow.org/)
+
+We thank all of the developers and contributors to these packages for their
+work.
+
+
+## Disclaimer
+
+*   This is not an official Google product.

WORKSPACE

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+workspace(name = "genomics")
+
+# Abseil libraries
+git_repository(
+    name = "com_google_absl_py",
+    # redacted
+    commit = "e7e488817ecce91d290d7fcce997b8dda1c6ee77",
+    remote = "https://github.com/abseil/abseil-py.git",
+)
+# Note: com_google_absl (the C++ abseil library) is provided by TensorFlow.
+
+# Note: we are using a post-1.6 build release that fixes a double-free.
+new_http_archive(
+    name = "htslib",
+    build_file = "third_party/htslib.BUILD",
+    sha256 = "7743e379fa27fdbaa81d4efc97adc5e0b2c5ade3cd09a93e311ea0c6b3a4ddf6",
+    strip_prefix = "htslib-57fa9be5255475b2cf9331db32848590a8ea8eb9",
+    urls = [
+        "https://github.com/samtools/htslib/archive/57fa9be5255475b2cf9331db32848590a8ea8eb9.zip"
+    ],
+)
+
+new_http_archive(
+    name = "libssw",
+    build_file = "third_party/libssw.BUILD",
+    sha256 = "10b9305e5a580ee5319f736d3581916f6c873ef4475bd0c0e564c2934334732c",
+    strip_prefix = "Complete-Striped-Smith-Waterman-Library-1.0",
+    urls = [
+        "https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/archive/v1.0.tar.gz",
+    ],
+)
+
+# Import tensorflow.  Note path.
+local_repository(
+    name = "org_tensorflow",
+    path = "../tensorflow",
+)
+
+# Required boilerplate for tf_workspace(), apparently.
+http_archive(
+    name = "io_bazel_rules_closure",
+    sha256 = "25f5399f18d8bf9ce435f85c6bbf671ec4820bc4396b3022cc5dc4bc66303609",
+    strip_prefix = "rules_closure-0.4.2",
+    urls = [
+        "http://mirror.bazel.build/github.com/bazelbuild/rules_closure/archive/0.4.2.tar.gz",  # 2017-08-29
+        "https://github.com/bazelbuild/rules_closure/archive/0.4.2.tar.gz",
+    ],
+)
+
+# Import all of the tensorflow dependencies.
+load("@org_tensorflow//tensorflow:workspace.bzl", "tf_workspace")
+
+tf_workspace(tf_repo_name = "org_tensorflow")
+
+# Pull in slim.
+# slim is  located inside the tensorflow/models repository.
+# The slim subdirectory in the tensorflow/models repository has its own
+# WORKSPACE file so we need to strip a prefix to make it the root of the
+# repository.
+# The prefix is "models-<commit>/slim"
+# where commit is the full commit.
+# Pin to the lastest version that builds for now. See b/68431494#comment4.
+http_archive(
+    name = "org_tensorflow_slim",
+    strip_prefix = "models-6d140f139cf02ceb87afa76024c4b502a556a3e5/slim",
+    urls = ["https://github.com/tensorflow/models/archive/6d140f1.tar.gz"],
+)
+
+new_local_repository(
+    name = "clif",
+    build_file = "third_party/clif.BUILD",
+    path = "/usr/local",
+)