remove unused test class for intermediate alignment results
remove un-used {input,param}_{id,bx} properties
Remove references to {input,param}_{id,bx}
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
Create the bridge entities more explicitly.

UR tries to find an "add_analysis_project" subroutine, which does
not exist.  So call something that does exist instead.
Merge pull request #326 from tabbott/aligner-cleanup

bwa mem aligner module cleanup
Merge pull request #322 from acoffman/remove_unused_bx_params_for_sr

Remove unused inputs_id and params_id fields in SoftwareResult
Merge pull request #330 from tmooney/explicitly_create_bridge

Create the bridge entities more explicitly.