change some to option to avoid null pointer exceptions when accessing adamrecord fields
change reference region to view end as exclusive
Merge pull request #225 from hammerlab/refpos-null

Change Some to Option to check for unmapped reads
remove duplicate mdtag field
Helper scripts to run an ADAM Console.

The idea is to set up the SPARK_CLASSPATH to point to the latest ADAM
and run spark-shell with a helper file that imports common ADAM classes.
Merge pull request #226 from hammerlab/inclusive-end

Fix ReferenceRegion from ADAMRecord
Add `-pretty` and `-o` to the `print` command

The `-pretty` option allows to pretty-print the JSON; the `-o FILE` is
for outputting to a file.
This contributes to #216.
Merge pull request #231 from hammerlab/adam-console

Helper scripts to run an ADAM Console.
Merge pull request #230 from hammerlab/mdtag-dup

Remove duplicate mdtag field
Merge pull request #232 from hammerlab/pretty_print_json_216

Add `-pretty` and `-o` to the `print` command
use adampredicate instead of unboundrecordfilter to allow filtering off RDDs on and after load
remove unused contiglength field
Merge pull request #235 from hammerlab/drop-nucleotide-field

Remove unused contiglength field
Merge pull request #234 from hammerlab/predicate-bam

Predicate to filter conversion
capture reference base, cigar element, and cigar offset during cigar processing; remove reference location in favor of reference position
Merge pull request #233 from hammerlab/refpos-reconcile

Build up reference information during cigar processing
Make ADAMVCFOutputFormat public

This commit makes the ADAMVCFOutputFormat defined in
ADAMVariationContext public and moves it to its own source file.
The alternate definition of ADAMVCFOutputFormat (unused) is
deleted.
Merge pull request #239 from massie/vcfout

Make ADAMVCFOutputFormat public
Fixes to FASTA code to properly handle indices.
Merge pull request #241 from fnothaft/fasta-long

Fixes to FASTA code to properly handle indices.