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

removed extra tabs
format update
format update
adding fastqc and qualimap update
Merge pull request #1 from ifiddes/master

merging in kmer counting.
Update pipeline.sh

Resolving conflicts.
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
Temporarily removing the sonlib module
Fixing sonlib submodule
Delete pipeline.pyc
Merge branch 'development'