[Biojava-l] Another GFF utility

[Matthew Pocock]

Hi,

I've written another GFF utility. gff.GFFMask allows
you to filter features in one file depending of if
they hit features in another file.

Are these kinds of utilities usefull to anyone?

Matthew

C:\devel\biojava-live\demos>java -classpath
.;../ant-build/biojava.jar gff.GFFMa
sk
Exception in thread "main" java.lang.Exception: Use:
GFFToFeatures [options]
    --infile in            read gff from file named in
(stdin if absent or -)
    --outfile out          write gff to file named out
(stdout if absent or -)
    --maskfile mask        read the masking gff from
file named mask (stdin if absent or -)
    --mode contain|overlap features should either be
totaly contained within or overlap the mask
    --hits accept|reject   features hitting the mask
will be accepted or rejected
    --use_seq_names y|n    mask hits should count only
if seq names match if y

        at gff.GFFMask.main(GFFMask.java:41)

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