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Initial release of DeepVariant
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‎.gitignore

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

‎AUTHORS

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

‎BUILD

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

‎CONTRIBUTING.md

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

‎LICENSE

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

‎README.md

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

‎WORKSPACE

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

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