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CLI & mappability filter for region join, custom exceptions #421

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CLI & mappability filter for region join, custom exceptions #421

wants to merge 7 commits into from

Commits on Feb 16, 2015

  1. Adding CountReads object and ReadCounter CLI option.

    @tdanford
    tdanford committed Feb 16, 2015
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  2. Adding hasReferenceRegion to ReferenceMapping

    @tdanford
    tdanford committed Feb 16, 2015
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  3. [ADAM-420] Adding a package for custom exceptions. 

    Including UnmappedException as the first (typed) custom exception.

This is so we can include/report better error messages from within ADAM
processes.
    @tdanford
    tdanford committed Feb 16, 2015
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  4. [ADAM-297] RegionJoin filters for mappability 

    There are two changes here:

1. RegionJoin.partitionAndJoin now pre-filters all records on either
side of the join with a check that the records are mappable, and doesn't
try to join those that aren't.

2. RegionJoin attempts to catch the NPE that comes from having
non-mappable records sneak through, and throws an UnmappedException
instead.
    @tdanford
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  5. Changed RegionJoin to BroadcastRegionJoin

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    tdanford committed Feb 16, 2015
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  6. Add an include for FlatGenotype 

    (don't know how/why this was dropped)
    @tdanford
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  7. Added a ReferenceMapping for Variant and Genotype. 

    Also, fixed some imports in the CountReads class.
    @tdanford
    tdanford committed Feb 16, 2015
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