Wbiesing/fix tests

WIP to get all the travis test cases passing

 - [ ] One test case fails but doesn't result in a nonzero exit code (see end of https://s3.amazonaws.com/archive.travis-ci.org/jobs/15107105/log.txt).
- [ ] Need to fix fastq input format (zip it together into a readid file when uploading to HDFS?)
- [ ] Need to regenerate the expected outputs and **check to make sure they're correct**.  @anbangx do you want to handle this?