GitLab

Updates so slices can handle negative strand, not finished yet, and not tested

method name changes and list to listref stuff

Removed an annoying ! from Slice
Removed duplicate declaration in Geneadaptor

Translation and TranslationAdaptor start_exon and end_exon to start_Exon and end_Exon

DBEntryAdaptor check to see if gene has a stable id before trying to used it to get info

Mapper - whitespace
Slice  - whitespace
Transcript - fetch_by_transcript to fetch_by_Transcript
AssemblyMapperAdaptor - debug line
CloneAdaptor - $clone->get_all_Contigs to @{$cone->get_all_Contigs}
DBEntryAdaptor = fetch_by_object_type  - id to $contig->dbID
ExonAdaptor - reformatting and array to arrayref for supporting_features
GeneAdaptor - fetches latest version out - need to talk with G and A about this
              each_DBLink to @$get_all_DBLinks
              get_all_Exons to array ref
              get_all_Transcripts to array ref
RawContigAdaptor - fetch_all_names
SupportingFeatureAdaptor - reformat
TranscriptAdaptor - lots of arrays to array refs

- needs testing

by their consensus seq

to table repeat_consensus

bug fix to ensure supporting features are being passed properly

removed _transform_to_slice as should use one in SeqFeature and added a check so if features are split and second half has 0 length it is skipped

bug fix

wasn't dereferencing anonyomous array and was complining about unblessed references

<     $new_exon->add_supporting_features($sf_hash{$rawContig->name()});
---
>     $new_exon->add_supporting_features(@{$sf_hash{$rawContig->name()}});

ProteinAlignFeatureAdaptor should create DnaPepAlignFeatures not PepDnaAlignFeatures; hitstrand should always be 1

Changed the way exons handle supporting features a bit

Added new SupportingFeatureAdaptor