snpEff: old EFF UNKNOWN and new ANN impact

brentp / geneimpacts

prioritize effects of variant annotations from VEP, SnpEff, et al.

MIT License

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snpEff: old EFF UNKNOWN and new ANN impact #7

Closed chapmanb closed 8 years ago

chapmanb commented 8 years ago

Fixes older EFF annotations with unknown severity
Adds protein_protein_contact in new snpEff ANN annotations (https://github.com/pcingola/SnpEff/blob/539115b3ba29fec35104f672ba6adeb0397789ab/src/main/java/org/snpeff/snpEffect/EffectType.java#L450) which is a HIGH impact change (https://github.com/pcingola/SnpEff/blob/539115b3ba29fec35104f672ba6adeb0397789ab/src/main/java/org/snpeff/snpEffect/EffectType.java#L39).

brentp commented 8 years ago

looks like you broke one of my tests (it was just added to handle empty older snpEff annotations). Can you give an example of the EFF/ANN string that causes the problem so I can add a test?

chapmanb commented 8 years ago

Brent -- sorry, I 'd missed that you'd fixed this in the interim. Your new code works for my old EFF annotation problem so I pulled that out and now only have the fix for new snpEff ANN annotations. If you'd rather close this messy branch and apply the one line fix manually that is cool -- whatever is easiest. Thanks much.

brentp commented 8 years ago

cheers. new version (0.1.0) is on pypi and I am pushing to bioconda now.