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