Stop fetch_all_Transcripts returning an empty list when there aren't any transcripts. The old behaviour was to return undef

store ontology term synonym xref separately from name

- Shortcut to only checkout the bioperl release we want and not pull the whole git tree

added support for ensembl-metadata

Update schema_patcher.pl

Funcgen has renamed its sql file from 'efg.sql' to 'table.sql', therefore schema_patcher.pl has to be modified to reflect this change.

Correct serializer behaviour, if an attribute for column 9 of the GFF…

Patch for release 85 adding a confident_relationship flag to the clos…

Correct serializer behaviour, if an attribute for column 9 of the GFF serializer (the misc, everything column) contains an empty array in the feature structure, skip printing the attribute rather than attribute=ARRAY(0xABCD)

Configuration to allow alignments to be exported to GFF

Allow feature boundaries to be retrieved for DNA and protein alignments (this bit of code only appears to be called when handling circular chromosomes)

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Super-tidying commit. Eliminate unnamed statement handle, don't pass fruitless object types, add some comments, change some others, collapse some code into neater forms

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Old xref connections should not be typed by the new master xref. Generate type mappings for both sets explicitly.

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Put all object types of ensembl IDs needed for a process_dependents() call into a hash. Query that every time a type is required, instead of trusting the calling code type.

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Introduce ensembl type for new xrefs, such that the new ensembl ids object_xrefs are not required to share object type with the original master xref

Kieron Taylor authored 9 years ago and Magali Ruffier committed 9 years ago

Add lookup for current xref object type for each iteration. Also syntax fixes, cleanup, and commenting.