Soft filter: over-write filter if previously PASS

vcflib / bio-vcf

Smart VCF parser DSL

MIT License

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Soft filter: over-write filter if previously PASS #32

Closed chapmanb closed 8 years ago

chapmanb commented 8 years ago

Supplement for improvements in #30

pjotrp commented 8 years ago

Hi Brad,

Is there no scenario a user would like to hang on to the PASS too? I guess you are right because PASS is not a FILTER per se.

Pj.

chapmanb commented 8 years ago

I can't think of any. In practice, PASS and '.' are equivalent. There could be a subtle distinction (passes some filter versus not assessed at all) but I've never seen any code or filtering approaches that treat these this way. You definitely don't want PASS;YourFilter which is more likely to be confusing than helpful.