pull request changes
Moved ebola.fasta from TestLasta folder to general input folder, and made appropriate adjustments to tests already using the file.  Added test case for "bwa index".
Resolved issue #20 by adding post_download_ret argument to DownloadPackage.
Merge pull request #21 from broadinstitute/irwin-issue20

Resolved issue #20 by adding post_download_ret argument to DownloadPacka...
Added bwa aln test + ability to specify some commandline argument to dirrectly follow bwa to allow for pipes and dirrecting output
Merge branch 'master' of github.com:broadinstitute/viral-ngs into hml-bwa
fixed spacing/tab issue in file.py
fix python 2 to 3 encoding compatiblity issue
Merge pull request #19 from broadinstitute/hml-bwa

Hml bwa
Merge branch 'master' of github.com:broadinstitute/viral-ngs into hml-80-complete

Conflicts:
	tools/__init__.py
	tools/bwa.py