helper to get SAM output as a string
add adam `view` command

similar to `samtools view`
add -c, -o flags, plus opt. printing SAM to stdout
add "disjunction" -g / -G options to `adam view`

-f and -F do positive and negative conjunctions, but in at least one
situation I've wanted to do an "or": give me all reads in this file
where the read is unmapped *or* the mate is unmapped.
expose non-file-saving bits of `adam transform`
expose non-file-saving bits of `adam view`
Add a test for new `view` command

- includes a SAM file with one read for each of the 700 possible
  flag-field values allowed by HTSJDK’s and ADAM’s SAM parsing code
  paths.
- bonus: includes `make-flag-values-sam.py` script used to generate the
  aforementioned SAM file.
- concern: ViewSuite test takes about 30s to run on my laptop; how much
  do we care about test-running latency? Is there an obviously quicker
  way to run a similar test to what I have here?
working examples on .sam included in repo
adam-local becomes adam-submit
link raw sam test file
count_kmer examle
Merge pull request #466 from allenday/master

working examples on .sam included in repo
Merge pull request #451 from ryan-williams/view

add `adam view` command, analogous to `samtools view`
fastq-writing bug-fixes and cleanups

- unify code-paths for single-/paired-fastq writing

  also use recalibrated qualities

- shorten `-validation` argument to adam2fastq

- add first/second-in-pair to adam2fastq projection

  these are necessary for outputting “/1”/“/2”!

- optional extra pair-checking to adam2fastq

- add extra check to fastq test suite

- whitespaces
Merge pull request #467 from ryan-williams/fastq

[ADAM-436] Optionally output original qualities to fastq
Fixed typo on MAVEN_OPTS quotation mark
Merge pull request #471 from neurons/fix_readme

Fixed typo on MAVEN_OPTS quotation mark
Consolidate documentation into a single location in source.

This system uses `pandoc` to convert Markdown into PDF and HTML
for each release. These currents docs were taken from our Wiki
and README.
Merge pull request #474 from massie/docs

Consolidate documentation into a single location in source.
added ReferenceMapping for Genotype

added filterByOverlappingRegion for GenotypeRDDFunctions