CHANGELOG: Fix for the Candidate March 2013 Reference Alignment processing profile.
The FalsePositiveVcf filter will now function properly in the reference alignment pipeline as written by this processing profile.

Filter:
Do not remove existing vcfs if it is a file and not a symlink.

FalsePositiveVcf and VarFilterSnv:
Refactor out get_samples_from_header for code re-use. Now function either on snvs.hq (in vcf format) or snvs.vcf.gz to play nicely with refalign and PC respectively.
Still pretty hacky.

FalsePositiveVcf VarFilterSnv Filter:
added _check_native_file_counts_vcf to the Filter.pm base class for validating output that involves vcf headers.
Merge branch 'fpmakebed' into gb_master