Add REJECT filter to non-somatic records in VarScan2

Like the work done in FreeBayes, this patch adds a REJECT filter to
non-somatic records (i.e., everything with a Somatic Status - SS - not
equal to 2) produced by VarScan2.

It includes some duplicated code from FreeBayes, which could be moved to
vcfutils.
Merge remote-tracking branch 'upstream/master' into varscan-reject-vcf
Move move_vcf to vcfutils to reduce code duplication
Port to the new location of move_vcf
Add a couple of FIXMEs / TODOs
Merge remote-tracking branch 'upstream/master' into varscan-reject-vcf
Add missing shutil
Use the bgzipped file name for adding the filter

Previous code used the original return value from combine_variants, and
thus the file was without the right extension, causing file_exists() in
the reject calling function to close early, preventing any REJECT records
to be written
Merge pull request #446 from lbeltrame/varscan-reject-vcf

Add REJECT filter to non-somatic records in VarScan2