remove unused test class for intermediate alignment results
refactor sam header creation in alignment result

I'm planning to make some changes that want access to the read group
information in the generated sam header, so I pulled the relevant code
out into a function and added some more specific tests about sam header
generation.
trailing whitespace

DO NOT WANT
add some tests for bwamem alignment module
add more tests for bwa mem aligner module

I need a test that actually aligns something.
add methods for finding faidx / bwa indexed fastas
more cleanup of paths that were using str concat everywhere
Merge pull request #326 from tabbott/aligner-cleanup

bwa mem aligner module cleanup