bigdatagenomics/adam — pull request #467 by ryan-williams (2014-11-07 01:28:48+00:00)
Title: [ADAM-436] Optionally output original qualities to fastq

Some improvements to fastq-writing flow / `adam2fastq`:
* optionally write out original qualities or "recalibrated" ones
* run `adam2fastq` through the single-or-paired-fastq interface based on the number of file arguments passed
* fix a bug where the projection was leaving out needed fields
* add an optional additional sanity check when writing paired-fastq