qualimap and fastqc folders added
added fastqc and qualimap scripts
format update

removed extra tabs
format update
format update
adding fastqc and qualimap update
adding fastqc and qualimap calls
added fastqc and qualimap folder paths
should work with qualimap folder in path
Added sam to bam and sorting using samtools
Added sam to bam and sorting using samtools
format fixed and debugging done
format update and debugging done
Delete __init__.pyc
Delete pipeline.pyc
Delete coverage.pyc
Delete abstractAnalysis.pyc
Delete __init__.pyc
Delete indels.pyc
Delete substitutions.pyc