AdamaJava / adamajava

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Tidyup qsnp #241

Closed ChristinaXu2017 closed 3 years ago

ChristinaXu2017 commented 3 years ago

Description

deleted the deprecated TorrentPipeline and PileupPipeline mode.
deleted MuTectPipeline which is old and wasn't used in our production pipeline for a long time.
deleted BAMPileupUtil which is not used anywhere
deleted QJumperWorker which is only required by PileupPipeline.
deleted related unit test code and an empty test file: EnsembleUtilTest.java
tidy up code.

fix issue #231.

Type of change

Delete unused code only.

How Has This Been Tested?

Unit test and regression test.

Checklist:

[X] My code follows the style guidelines of this project
[X] I have performed a self-review of my own code
[X] I have commented my code, particularly in hard-to-understand areas
[X] I have made corresponding changes to the documentation
[X] My changes generate no new warnings
[X] I have added tests that prove my fix is effective or that my feature works
[X] New and existing unit tests pass locally with my changes