broadinstitute / hellbender / 195
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lbergelson 
Adding a dataflow pipeline for Read only tools
This includes wrappers to present SAMRecords to the tools themselves
Also adding 4 simple tools as examples
  FlagStatsDataflow
    It makes use of dataflow's built in hierarchical aggregation
  CountBases
    Simple walker that makes use of the SAMRecord conversion
  CountReads
    Does what it says
  PrintReads
    This is a very limited version of our print reads walker
    It prints SAMRecords as strings to an unordered text file
    It could potentially be useful as method for examining bam output before we have a proper bam writer

These tools exist in two parts:
  A transform extending from PTransformSAM (A subclass of PTransform<Read,O> which facilitates conversion to SAMRecord
  A command line tool implementing a complete pipeline
    These pipelines can apply arbitrary ReadFilters / ReadTransformers which are applied before the main transform
    (a list of transforms and a list of filters can be applied, it's currently not handled very efficiently though, better to pre-comine them into a single meta transform)

Currently, only tests which use local files are running on travis.
There is code included to run on files in buckets, but the tests for it are currently disabled due to travis configuration issues (will be resolved in a seperate ticket)

Some changes were made to existing classes to make them Serialize properly
Some test files were moved to help normalize test data locations (although not all tests are normalized, should be done in separate ticket)
  the new storage locations are based on the complete package name rather than just the tool name

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Jobs
ID Job ID Ran Files Coverage
1 195.1 (TERM=dumb) 0
70.86
 Travis Job 195.1
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