quote bash vars in scripts/jenkins-test
CYA: pre-remove output files in jenkins-test

while debugging jenkins-test runs, I copied some of the files it
generates into my local ADAM_HOME; these were in turn getting copied
into the tmp dir created by jenkins-test, and causing various commands
to fail when they realized the path they were trying to output to
already exists. This seems like an unnecessary failure mode for the
jenkins-test script to be vulnerable to (namely, the existence in local
ADAM_HOME of files (untracked by git) with the same names as arbitrary
paths that jenkins-test expects to write to), especially since these
particular files are involved in tests but don’t actually live in the
git repo.
Project only the sequence when kmer/qmer counting
Merge pull request #460 from massie/kmer-projection

Project only the sequence when kmer/qmer counting
Merge pull request #459 from ryan-williams/jenkins

a few tweaks to scripts/jenkins-test
Some cleanups of Predicate logic

- simplify PredicateUtils wrapper

- wrap some long lines

- wrapper for FieldCondition[Boolean] creation

- AlignmentRecordCondition creation conv. wrappers

- add supplementaryAlignment to AlignmentRecordField
Merge pull request #457 from ryan-williams/predicates

A few random Predicate-related cleanups
Add paired-fastq writing functionality

- converting read to FASTQ optionally adds suffix

- opt. verification step when reading paired-FASTQs

- add method for outputting paired-FASTQ files

- add persistence to paired FASTQ writing

- round-trip test of paired-FASTQ reading & writing

- add bam2fastq command for outputting paired-fastqs

- rename bam2fastq to adam2fastq

- use ValidationStringency in Adam2Fastq

- adam2fastq asserts equal #s of first-/second-reads
Merge pull request #438 from ryan-williams/paired-fastq

Add ability to save paired-FASTQ files
Remove unused val from Reads2Ref