New program FilterVcf that provides simple hard filtering functionality for VCFs.
Merge pull request #95 from broadinstitute/tf_hard_filtering

New program FilterVcf that provides simple hard filtering functionality ...
consider soft clipping at the ends of reads when clipping reads that
overhang the reference
Merge pull request #97 from broadinstitute/nh_off_the_end_clip_fix

consider soft clipping at the ends of reads when clipping reads that
Added a button  to the explain-flags.html page. This button switches the flag from the flag of a read, to that of its mate (as much as can be infered).