Write maximal cliques

Added physics definition

Added physics button

Dissertation incorporated

Corrected example

example changes

Short record

MANE HGVS annotation

Minor issues

Removed excessive columns

Added dissertation results

Commented option to remove unpaired reads

VarScan corrections

added varscan annotation

quit varscan testing

VarScan2 added

Ignore duplication

Clean version for publication with random shuffle

gitignore updated

unimportant

Homology work tried

Minor changes

minor_issues