Fixes related to problems with samtools & bowtie2

-see issues #73, #72, #69, #68
-added new samtools and bowtie2 binaries which should work on more systems
-added checks for samtools and bowtie2 binaries; if binaries don't work instructions for replacing them are provided

Merge pull request #67 from snayfach/dev

Alignment mode changes

Merge pull request #62 from snayfach/dev

Major pull from Dev

Removed debug comment

Accidentally left a comment in code that caused mpileup to not run

Merge pull request #36 from snayfach/dev

Dev

Merge pull request #34 from snayfach/dev

Dev

Merge pull request #33 from snayfach/dev

Print full command and database path with parameters

Fixed bug with bz2 files. Added check for file compression