Merge pull request #2 from PacificBiosciences/initial_release

initial release files

CHANGELOG.md

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+# v0.7.2
+Initial release.

LICENSE

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+Copyright (c) 2022, Pacific Biosciences of California, Inc.
+
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted (subject to the limitations in the
+disclaimer below) provided that the following conditions are met:
+
+ * Redistributions of source code must retain the above copyright
+   notice, this list of conditions and the following disclaimer.
+
+ * 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.
+
+ * Neither the name of Pacific Biosciences nor the names of its
+   contributors may be used to endorse or promote products derived
+   from this software without specific prior written permission.
+
+NO EXPRESS OR IMPLIED LICENSES TO ANY PARTY'S PATENT RIGHTS ARE
+GRANTED BY THIS LICENSE. THIS SOFTWARE IS PROVIDED BY PACIFIC
+BIOSCIENCES AND ITS 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 PACIFIC BIOSCIENCES OR ITS
+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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-# PharmGOAT
+# pb-StarPhase: Phase-aware pharmacogenomic diplotyper for PacBio data
+The pb-StarPhase tool will diplotype pharmacogenomic (PGx) genes from [PacBio](https://www.pacb.com/technology/) datasets.
+Key features include:
+
+* Ability to create a database from latest CPIC information
+* Ability to diplotype most genes from CPIC
+* Works on PacBio datasets from targeted and whole genome sequencing
+
+Authors: [Matt Holt](https://github.com/holtjma), [John Harting](https://github.com/jrharting), [Zev Kronenberg](https://github.com/zeeev)
+
+## Early release warning
+Please note that pb-StarPhase is in early development. 
+We are still tweaking the input and output file formats and making changes that can affect the behavior of the program.
+
+## Availability
+* [Latest release with binary](https://github.com/PacificBiosciences/pb-StarPhase/releases/latest)
+* [Auxiliary data files](./data)
+
+## Documentation
+* [Installation instructions](docs/install.md)
+* [User guide with quickstart](docs/user_guide.md)
+* [Output files](docs/user_guide.md#output-files)
+* [Methods](docs/methods.md)
+* [Performance](docs/performance.md)
+
+## Need help?
+If you notice any missing features, bugs, or need assistance with analyzing the output of pb-StarPhase, 
+please don't hesitate to open a GitHub issue.
+
+## Support information
+pb-StarPhase is a pre-release software intended for research use **only** and not for use in diagnostic procedures. 
+While efforts were made to ensure that pb-StarPhase lives up to the quality that PacBio strives for, we make no warranty regarding this software.
+
+As pb-StarPhase is **not** covered by any service level agreement or the like, please do not contact a PacBio Field Applications Scientists or PacBio Customer Service for assistance with any pb-StarPhase release. 
+Please report all issues through GitHub instead. 
+We make no warranty that any such issue will be addressed, to any extent or within any time frame.
+
+### DISCLAIMER
+THIS WEBSITE AND CONTENT AND ALL SITE-RELATED SERVICES, INCLUDING ANY DATA, ARE PROVIDED "AS IS," WITH ALL FAULTS, WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESS OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, ANY WARRANTIES OF MERCHANTABILITY, SATISFACTORY QUALITY, NON-INFRINGEMENT OR FITNESS FOR A PARTICULAR PURPOSE. YOU ASSUME TOTAL RESPONSIBILITY AND RISK FOR YOUR USE OF THIS SITE, ALL SITE-RELATED SERVICES, AND ANY THIRD PARTY WEBSITES OR APPLICATIONS. NO ORAL OR WRITTEN INFORMATION OR ADVICE SHALL CREATE A WARRANTY OF ANY KIND. ANY REFERENCES TO SPECIFIC PRODUCTS OR SERVICES ON THE WEBSITES DO NOT CONSTITUTE OR IMPLY A RECOMMENDATION OR ENDORSEMENT BY PACIFIC BIOSCIENCES.

data/README.md

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+# Auxiliary data files
+## Database files
+Databases were pre-generated for ease-of-use, sharing, and backwards compatibility when using older versions of pb-StarPhase.
+Though we will do our best to avoid breaking changes, database files are **not** guaranteed to work on versions that do not match.
+Additionally, these databases represent a snapshot in time of upstream data sources (e.g., CPIC).
+Running the same command at a later date may produce a different database with updated annotations.
+
+Each file is labeled as `{version}/cpic_{YYYYMMDD}.json` and represents a run of the following command using the specified `{version}` of pb-StarPhase on the corresponding date (`{YYYYMMDD}`):
+
+```bash
+pbstarphase build \
+    --output-db {version}/cpic_{YYYYMMDD}.json
+```