Report PASS for PASS in Filter column instead of empty list

[jblachly]

See Issue #153 which was closed by the reporter after a developer suggested that existing behavior (which is to return an empty list for FILTER, when the filter column contains "PASS".

I was surprised by this behavior, instead expecting parser to pass through what was in the VCF file -- returning an empty list for '.' but reporting a string if a string is there). I wanted to suggest again that this behavior be changed to report "PASS" for the following reason.

This point is subtle but important: PASS carries semantic meaning and should be passed through -- the VCF specification(1) allows an empty string in the FILTER column to signify that filters have not been applied. This makes "PASS" distinct from the empty string.

Current behavior does not conform to the VCF specification, in that it does not differentiate between the empty value and PASS. I therefore recommend that ["PASS"] should be returned, instead of the empty list. I am happy to issue a pull request if extra hands are needed for this.

(1) VCF 4.1 specs page 4, item#7