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
[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.
Updating CHANGES.md for our 0.14.0 release
[maven-release-plugin] prepare release adam-parent-0.14.0
[maven-release-plugin] prepare for next development iteration
[ADAM-387] fix some deprecation warnings

- move from deprecated SAMFileReader to SamReader
- move off of a deprecated scalatest method
Merge pull request #387 from ryan-williams/deprecations
Added "read pairs that cross chromosomes" to MarkDuplicatesSuite
Merge pull request #380 from nfergu/markduplicateschanges

Rewrite of MarkDuplicates which seems to improve performance
[ADAM-237] Migrate to Chill serialization libraries.
Merge pull request #391 from fnothaft/chill-serializers

[ADAM-237] Migrate to Chill serialization libraries.