thaplv: Tools for Haploid/Haplotype VCFs

Tools for Haploid/Haplotype VCFs (thaplv) is a software package for analyse haplotype (or haploid) data stored in the VCF format (see more information about format specifications in genomics here. The main purpose of this toolkit is include a set of efficient and fast implementations of methods for haplotypes using the GATK4 framework.

Note that this project is in early development, so there is no guarantee of maintenance in the current stage.

Requirements

• Java 8
• Git
• (Developers) Graddle 2.13 or greater

Building thaplv

For building thaplv, run ./gradlew shadowJar. The packaged jar will be in build/libs/ with the name thaplv-<version>-all.jar.

Testing thaplv

• To run all tests, run ./gradlew test. Test reports will be in build/reports/tests/index.html
• To run a subset of tests, use the test filtering provided by gradle. For example:
  • ./gradlew test --tests *SomeSpecificTest
  • ./gradlew test --tests all.in.specific.package*
• To compute coverage reports, run ./gradlew jacocoTestReport. The report will be in build/reports/jacoco/test/html/index.html

Running thaplv

For running thaplv after building, run with the command java -jar build/libs/thaplv-<version>-all.jar.

Guidelines for developers

• Pushing directly to master branch is not allowed.
• It is recomended to name branches with a short form of your name and a explanatory name. Example: dgs_fix_issue30.
• Pull requests should be reviewed before merging by other developer, and rebased/squashed by the author.
• Any new code will require unit/integration tests.
• Use org.apache.logging.log4j.Logger for logging.
• Use TestNG for testing.
• Use magicDGS Style Guide for code formatting.

Authors

• Daniel Gomez-Sanchez daniel.gomez.sanchez@hotmail.es

License

Licensed under the BSD 3-Clause License. See LICENSE.txt file.

The GATK4 framework is also licensed under the BSD 3-Clause License. See their LICENSE.tx file for more information.