[Bioperl-l] GuessSeqFormat GFF vs VCF

Dan Kortschak dan.kortschak at adelaide.edu.au
Mon Mar 28 21:12:55 EDT 2011


Hi All,

I'm going through the BEDTools wrapper to bring it up to date. A number
BEDTools executables now accept GFF and VCF as well as BED format input
files.

Part of the WrapperBase::CommandExts give acceptable input formats, so
I'm adding to GuessSeqFormat guessers for GFF and VCF, which from the
point of view of a stateless guesser, are indistinguishable unless (and
I don't like this idea), GFF is additionally defined as not VCF and VCF
is additionally defined as not VCF (these can be identified from the
##gff-version and ##fileformat=VCF lines).

Can people provide their thoughts on this?

cheers
Dan



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