Changes for version 1.1 - 2012-04-13
- Changed the default API of Bio::GFF3::LowLevel::Parser to support multi-loc features. In order to be able to group feature lines that hand in some cases it would not be possibleave the same ID attribute, it now returns arrayrefs that are groups of the formerly-returned hashrefs.
- HOWEVER, there is a backward-compatibility layer that back-converts the features to the conform to the return types in 1.1. Existing users of this code should not be adversely affected.
- Add better support for Derives_from: feature line hashrefs now have a derived_features attribute holding an arrayref of the features that Derives_from this one.
- Remove assumptions in the parser about child features coming after their parents in the file. The GFF3 specification does not require this.
- gff3_from_fasta - make GFF3 from fasta sequences
- Bio::GFF3::LowLevel - fast, low-level functions for parsing and formatting GFF3
- Bio::GFF3::LowLevel::Parser - a fast, low-level gff3 parser
- Bio::GFF3::LowLevel::Parser::1_0_backcompat - compatibility layer to support Bio::GFF3::LowLevel::Parser 1.0 API
- Bio::GFF3::Transform::FromFasta - make gff3 for the sequences in a fasta file