Add ReadTools' ReadWalker implementation

magicDGS / ReadTools

A Universal Toolkit for Handling Sequence Data from Different Sequencing Platforms

https://magicdgs.github.io/ReadTools/

MIT License

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Add ReadTools' ReadWalker implementation #441

Closed magicDGS closed 6 years ago

magicDGS commented 6 years ago

For the configuration and printing of settings, should be similar to ReadToolsProgram. In addition, it should have some stuff that is always included:

Transformer for quality (ReadTools should work always on properly-formatted SAM/BAM/CRAM files).
Common help-formatter class (requires #440)

Related to #437

magicDGS commented 6 years ago

Transformer for quality requires a pre-check for the quality. We should assume that they are properly formatted and we just check if it is true.