[ADAM-356] Refactor packages for org.bdgenomics.adam.rdd contents

o Moving indel realignment code into a consistent package.
o Moving read specific RDD transformations into a new rdd.read package.
o Move SummarizeGenotypes into the rdd.variation package.
o Moving pileup aggregator into a new rdd.pileup package.
o Breaking read RDD functions/context into rdd.read package.
o Moving contig rdd functions/context into own rdd.contig package.
o Moving pileup and pileup RDD functions into own rdd.pileup package.
[ADAM-372][ADAM-371][ADAM-365] ADAM Spark interaction is more canonical

Removed SparkArgs and SparkCommand
Spark config should be ADAM-independent
Added bin/ with scripts for submitting jobs to spark-submit and also using spark-shell and pyspark
Fixes #372, fixes #371, and fixes #365.
Merge pull request #374 from laserson/refactor-cli

[ADAM-372][ADAM-371][ADAM-365] Refactoring CLI to simplify and integrate with Spark model better
[ADAM-377] Update to Jenkins scripts and README.
Rewrite of MarkDuplicates which seems to improve performance
Moved methods around to make diffing with the previous version easier
Modified loops in markReadsInBucket to use collection.foreach
Merge pull request #377 from fnothaft/register-serializers

[ADAM-377] Update to Jenkins scripts and README.
[ADAM-369] Improve debug output for indel realigner
Merge pull request #369 from fnothaft/realigner-md-tag-msg

[ADAM-369] Improve debug output for indel realigner
bump scalatest to 2.2.2

mostly to pick up wildcard test-suite handling, e.g.:

    $ mvn test -Dsuites="*MdTag*"

(hammerlab has a helper around this for even more convenience; see
https://github.com/hammerlab/internal-tools/blob/master/scripts/mvn-utils/mvn-test)
Merge branch 'scalatest-fix' into upstream-master

This is a re-merge of the (re-based) 'bump scalatest to 2.2.2' branch
into master, since I (tdanford) messed up the merge the first time.
[ADAM-383] MdTag handles CigarOperator.{EQ,X}
Merge pull request #383 from ryan-williams/mdtags

Make Mdtags handle '=' and 'X' cigar operators
[ADAM-379] Fix the position of the jar path in the submit.
This accordingly with the spark documentation: http://spark.apache.org/docs/latest/submitting-applications.html.

That is, the jar must come after the `options` like --master and so on, but mainly --class. Otherwise, no `main` can be found in the JAR.
Merge pull request #379 from med-at-scale/fix-adam-submit
[ADAM-360] Upgrade to Spark 1.1.0.
Merge pull request #378 from fnothaft/spark-1.1.0

[ADAM-360] Upgrade to Spark 1.1.0.
[ADAM-375] Upgrade to Hadoop-BAM 7.0.0.
Merge pull request #376 from fnothaft/htsjdk-migration

[ADAM-375] Upgrade to Hadoop-BAM 7.0.0.