[ADAM-432] Run indel realignment before BQSR.
[ADAM-433] Add ability to dump BQSR observations to CSV from CLI.
Merge pull request #434 from fnothaft/realign-before-bqsr

Few transform tweaks
[ADAM-437] random nits and cleanups:

- make scalariform allow dangling parends

  sometimes I find this to be a useful way to indicate nesting:

  throw new Exception(
      “%s %s %s %s”.format(
          foo, bar baz, boo
      )
  )

- tweak comment about read-ID suffixes in FASTQ

- wrap a few long lines

- add docs to adamFastqLoad method
Merge pull request #437 from ryan-williams/nits

[ADAM-437] random nits and cleanups:
read “OQ” attr from structured SAMRecord field

converting into and out of BAM using ADAM was dropping the “OQ” attr;
HTSJDK puts it in its own field but ADAM was looking for it in the
catch-all attributes field.
Revert "[ADAM-237] Migrate to Chill serialization libraries."

This reverts commit 39821152352e6647a244d1df24facafa53aa6923.
Bump scala from 2.10.3 to 2.10.4
Merge pull request #446 from massie/serializer

Revert "[ADAM-237] Migrate to Chill serialization libraries."
Merge pull request #449 from ryan-williams/origqual

read “OQ” attr from structured SAMRecord field
[ADAM-348] Stores original position and original cigar during realignment.
Addresses issue #348 in the adam project.
Merge pull request #417 from niranjan93/NK_schema_tags

Stores original position and original cigar during realignment.
Better null handling for isSameContig utility
Merge pull request #453 from massie/is-same-contig

Better null handling for isSameContig utility
Update the contribution guidelines
Merge pull request #447 from massie/contribution

Update the contribution guidelines
[ADAM-454] Add serializers for Avro objects which don't have serializers.
Merge pull request #455 from fnothaft/add-serializers

[ADAM-454] Add serializers for Avro objects which don't have serializers
Refactor some file writing and reading logic:

- read “OQ” attr from structured SAMRecord field

  converting into and out of BAM using ADAM was dropping the “OQ”
  attr; HTSJDK puts it in its own field but ADAM was looking for it
  in the catch-all attributes field.

- style nits / long lines

- ADAMMain formatting

- apply predicate shorthand

- move adamBamLoad into ADAMContext

  I'm a little torn about this one, since I see the motivation for
  having AlignmentRecordContext own logic for things we know will be
  AlignmentRecords, but adamBamLoad also is called from and calls into
  (via implicit conversion from SparkContext back into ADAMContext)
  other things in ADAMContext that made it feel like a more natural
  fit inside of ADAMContext.

- factor out parquet-saving config

- factor multi-format saving out of Transform

- add helper for saving only aligned records

  a.k.a. BAM or ADAM records; no FASTQs
Merge pull request #450 from ryan-williams/saving

Refactor some file writing and reading logic