Fixes related to problems with samtools & bowtie2

-see issues snayfach#73, snayfach#72, snayfach#69, snayfach#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 snayfach#67 from snayfach/dev

Alignment mode changes

Merge pull request snayfach#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 snayfach#36 from snayfach/dev

Dev

Merge pull request snayfach#34 from snayfach/dev

Dev

Merge pull request snayfach#33 from snayfach/dev

Print full command and database path with parameters

Fixed bug with bz2 files. Added check for file compression