updated ur submodule to 9b115b4
Updated class browser cache.
Updated `genome` tab completion.
Updated `gmt` tab completion.
Fix Bsmap tests
new Genome::File::Vcf functionality

add some methods to manipulte entries.
add writer class
updated ur submodule to 87fd68f
Add methods to update header data (INFO, FORMAT, FILTER)
add some inline POD to Genome::File::Vcf::Entry
set is_output on output_file in ProcessValidationIndels
add 'filter_calls_involving_only' to Vcf::Entry

$entry->filter_calls_involving_only(
    filter_name => "BORING",
    alleles => ["A", "AC"]
    )

apples the genotype filter BORING to any calls in the entry that involve
only the alleles A and/or AC.
Merge remote-tracking branch: upstream/master