Request: support for GTF/GFF format

[magicDGS]

Support for GTF/GFF formats

GTF and GFF are the usual formats for annotations in the genome, and even the TabixFormat includes a GFF default. Thus, I wonder if it could be possible to implement a Feature and FeatureCodec for these formats. I found that the IGV team have implemented a GFFCodec and GFFFeature which could be ported to htsjdk.

I'm planning to implement it for my personal use, but if you think that this could be interesting for other API clients, I can contribute with it.

[lbergelson]

Thanks for pointing that out Pierre. It's important to note thought that
the IGV implementation is LGPL which may not be universally acceptable to
all users.

On Tue, Mar 22, 2016 at 1:46 PM, Pierre Lindenbaum <[email protected]

wrote:

FYI: there is one in IGV:
http://data.broadinstitute.org/igv/projects/downloads/IGVDistribution_2.1.11/src/org/broad/igv/feature/tribble/GFFCodec.java

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#537 (comment)

[magicDGS]

I also noted it in the description... should I add the link pointing to the file?

[lbergelson]

Oh, sorry @magicDGS. I saw your comment and Pierre's at the same time and didn't read yours carefully enough.

[magicDGS]

Closing - it sounds better to address this in htsjdk-next-beta