Implement/port ReadTransformer and ReadFilter system - enable by request

[akiezun]

ReadTransformer system needs to be available to hellbender tools. The mechanism of how it gets enabled needs to be coordinated with ReadFilters (issue #5 )

[akiezun]

For now, this request will be treated together in this issue. We may split it later.

@vdauwera - i moved it here because it's about ReadTransformers

https://www.pivotaltracker.com/story/show/70281952

ReadTransformers should be able to be added by the command line like
filters. Currently the only way to include or add a new readTransformer is
by adding a new argument to the GATK engine, and there is no way to run
only specific transformer by a walker.
When that will be done, there are readTransformers that are currently
written as filter (for example: ReassignMappingQuality) that should be
refactor to readTransformers.
Also it will be good to put all the ReadTransformers together (like the
filters).

[akiezun]

Merged this with ReadTransformers - there should be just one set of 'preprocessors'

[akiezun]

i'll grab this

[droazen]

Issues that need to be addressed as part of this ticket:

• support for arguments defined in filter classes
• PluginManager -- to port or not to port?
• performance issues with searching the classpath
• separating out the readmetrics code from the code that applies filters

[akiezun]

done for AyeAye as part of BQSR