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
Merge pull request #458 from massie/reads2ref

Remove unused val from Reads2Ref
small cleanup of SAM vs. BAM file-writing
init SAM/BAM header on each partition