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
fix mutect format: FA => FREQ
change FA->FREQ and some checks
comments from Luca
adding 'move to' info at _fix_mutect_vcf
remove Exc, not apply here
SGE: Moved from minimum mem/core ratio to median
rename function and improve docstring
Numpy dependency removed and left of median implemented
Scalpel CHI2 filtering added using bcftools. Common InDels REJECTed by bcftools.
Merge pull request #465 from lpantano/master

Convert FA to FREQ in FORMAT fields of MuTect VCFs
Merge pull request #446 from lbeltrame/varscan-reject-vcf

Add REJECT filter to non-somatic records in VarScan2
bcftools command obtained by config_utils.get_program in scalpel.py
Merge pull request #476 from mjafin/scalpel_filter

Scalpel CHI2 filtering added using bcftools. Common InDels REJECTed by b...