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
adam `view` command
helper to get SAM output as a string
add -c, -o flags, plus opt. printing SAM to stdout
Add a test for new `view` command

- includes a SAM file with one read for each of the 1000 possible
  flag-field values allowed by HTSJDK’s SAM parsing code.
- 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?