Adjustments for #76 , rename certain options to be more explicit#81

Merged

apeltzer merged 16 commits intodevfrom

rename_bam_flags

Nov 19, 2018

Commits on Nov 5, 2018

Commits on Nov 7, 2018

Fix syntax error
apeltzer
committed

Commits on Nov 17, 2018

Merge branch 'dev' into rename_bam_flags
apeltzer
authored

Commits on Nov 19, 2018

Add better bam filtering / extraction protocol

Alexander Peltzer
authored and
Alexander Peltzer
committed
Small typo fix

Alexander Peltzer
authored and
Alexander Peltzer
committed
Add gz to fastq

Alexander Peltzer
authored and
Alexander Peltzer
committed
Speed up using pigz!

Alexander Peltzer
authored and
Alexander Peltzer
committed
Better help function :)

Alexander Peltzer
authored and
Alexander Peltzer
committed
Update usage as well in docs

Alexander Peltzer
authored and
Alexander Peltzer
committed
Update defaults

Alexander Peltzer
authored and
Alexander Peltzer
committed

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