Removed unneeded files.
Added quality trimming (Q=10) to cutadapt statement
Remove trailing blank/newlines from sequence strings when counting read lengths
Merge branch 'trim_quals'
Fixed output formatting bug
Fixed logging output error
Bugfix: python != bash
Bugfix: argument passing error
Change alignment output name from .sam to .bam to match output format
Changed miRBase output alignment name
Added png extension to output file name.
Adding quick script to get read lengths of mapped reads
Added initial fastqc support, changed readlink -f to readlink -m to handle weird uppmax filesystem symbolic links
Improved logging, added temp directory processing, improved error handling
Adding fastqc bugfix and better annotation flow control
Fixed runtime calculation (was backwards)
Merge pull request #1 from mariogiov/master

baaaaaaash