GitLab

For trans-spliced transcripts, augment the CDS IDs with the location, to prevent multi-row features having different seq_region names and/or strands

Allow 'special' attributes (e.g. Dbxref, Ontology_term) to be specified as a list and written as a single comma-separated value

changed attributes to use correct casing as per http://gmod.org/wiki/GFF3. Extended testcase to include transcript to test Parent attribute

as ID has to be unique, exons have no ID field, only Name

updated test module

- for ID field, concatenate object type before the stable id
- if gene biotype is protein_coding, the so term is replaced by gene

[ENSCORESW-490]. Point raised by Dan. Default GFF3 for source is . not ensembl. Using . and supporting basic features

[ENSCORESW-490]. Fixing the GFF serializer which would add an additional ; at times and now supports a custom source field. Gene and transcript now both emit this

[ENSCORESW-262]. Customised the Exon summary as hash, gene and transcript summaries have been improved. Biotype mapper can ask objects for their SO term and knows Variation objects are already annotated with a code. BioType mapper caches SO retrieval so it is a massive speed increase for large result sets.

Introduction of new FASTASerializer to replace SeqDumper's FASTA capability. Other formats remain SeqDumper's responsibility.

Introduced Utils::IO namespace along with serializer code for GFF3 and human-readable formats. Pre-release, not intended for public use.
Also added Utils::BiotypeMapper that performs ontology mappings.