moving duplicated code to common
moving duplicated code to common
moving redundant stuff to common
consolidating alignment functions
Update addsv.py

typo in description ?
Update addsv.py

typo
Merge pull request #17 from gillet/patch-2

Update addsv.py
Merge pull request #16 from gillet/patch-1

Thanks!
tweaking randomsites.py, add option to avoid ref N bases
tweaking randomsites.py, add option to avoid ref N bases
unify aligners, note new alignment selection syntax
fix checkoptions error, update docs
preliminary bowtie2 supoprt for snv/indel
preliminary bowtie2 supoprt for snv/indel
add --maxdepth parameter
add --ignorepileup, needed for RNA spikein
Merge remote branch 'upstream/master'

Conflicts:
	addindel.py
	addsnv.py