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
quote bash vars in scripts/jenkins-test
CYA: pre-remove output files in jenkins-test

while debugging jenkins-test runs, I copied some of the files it
generates into my local ADAM_HOME; these were in turn getting copied
into the tmp dir created by jenkins-test, and causing various commands
to fail when they realized the path they were trying to output to
already exists. This seems like an unnecessary failure mode for the
jenkins-test script to be vulnerable to (namely, the existence in local
ADAM_HOME of files (untracked by git) with the same names as arbitrary
paths that jenkins-test expects to write to), especially since these
particular files are involved in tests but don’t actually live in the
git repo.
Project only the sequence when kmer/qmer counting
Merge pull request #460 from massie/kmer-projection

Project only the sequence when kmer/qmer counting
Merge pull request #459 from ryan-williams/jenkins

a few tweaks to scripts/jenkins-test