GitLab

method to use is get_seq_region_id()

satisfies perl critic

Replaced all instantiations of pairs of circular slices with a call to the
above method.

An option from the command-line (-current-schema-no-cvs) allows to load the
schema from the file system instead of fetching it from the CVS repository.

we do not want to retrieve all symlinks of the slice, just the slice itself

constructor of its parent (Storable) which is neglecting a lot of the UnmappedObject specific
attributes which instead are assigned and dealt with in the UnmappedObject constructor.
This hasn't been an issue so far as there doesn't seem to be any code calling this new_fast
implementation.

Improvements to documentation, describing the presence of forward and reverse strand features in the results of get_all_* methods.

newer and maintained versions are in ensembl-production checkout

Removed new_fast method already inherited from parent (Feature) class and after MiscFeatureAdaptor attribute default initialisation

eliminate the need for a specialised MiscFeature::new_fast implementation.

get_all_Transcripts no longer returns the naked cache to user scripts. Protection from obliterating transcripts by manipulating the cache from outside of the object.

ENSCORESW-517: cdna2genomic returns 'genomic' coordinates which are relative to the slice of the feature
if the slice is not the whole chromosome, we need to adjust by adding the transcript->slice->start to the cdna2genomic return value, -1
if the slice is the whole chromosome, we add 1-1, so nothing changes
all test cases still pass with the modification

was not tested by PAR, as patches are stored on scaffolds, ie a different coord system

to provide correct comparison with initial seq_region_name, fetch the seq_region_name from the seq_region_id

removing copy from ensembl-core

new version now in ensembl-production

removing ensembl-core copy

removing ensembl-core version