Add initial documentation on contributing
Merge pull request #105 from bigdatagenomics/matt-contributing

Add initial documentation on contributing
Encoding tag types in the ADAMRecord attributes, adding the 'tags' command.

This commit fixes issue 92 (https://github.com/bigdatagenomics/adam/issues/92).

The old style of encoding the "optional fields" from the SAM/BAM was to store
them as key=value pairs in the ADAMRecord.attributes string. However, this
loses information about the _type_ of the tag/value, which is necessary if
we want to reconstruct the original value type (for example, for re-exporting
BAM files from ADAM files).

This update is non-backwards-compatible, changing the format of the attributes
field to tag:type:value and introducing a new Attribute class for parsing and
handling these values.  It also adds functions to AdamRDDFunctions to allow for
filtering and subsetting of reads based on their tags, or to count the number of
distinct tags or tag-values across a set of reads.
Merge pull request #99 from genomebridge/attributeParser

Encoding tag types in the ADAMRecord attributes, adding the 'tags' command
Cleaning up change documentation.
Merge pull request #107 from fnothaft/cleanup-change-docs

Cleaning up change documentation.
Added the spark.driver.port erasure to SparkFunSuite cleanup.

We've been getting intermittent errors, with respect to Spark being unable to bind to a port,
in the context of repeated unit tests.  This apparently is a known problem, see the thread here:
  http://blog.quantifind.com/posts/spark-unit-test/
and the follow-up from Matei here:
  https://groups.google.com/forum/#!topic/spark-users/MeVzgoJXm8I

The upshot is that we need to clearProperty('spark.driver.port') when we shut down our sparkContext
after a sparkTest.
Merge pull request #104 from genomebridge/tdanford/sparkfunsuite-port

Added the port erasure to SparkFunSuite's cleanup.
fix typo in log4j config, but junk is still spewed to stdout
Remove existing BQSR implementation
Make quality scores into ints
Scaffolding for BQSR implementation
add Util.hashCombine
add stuff to Observation
Make ObservationTable ctor private
ObservationTable fixes/changes
Empirical error probability tweaks
Don't need to broadcast SnpTable; it's only referenced once
add Recalibrator skeleton
Rename PhredQualityScore to QualityScore