GitLab

fix for ChainedAssemblyMapper to map using the destination slice if one is provided http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-108

<ensembl-dev@ebi.ac.uk> to <dev@ensembl.org>.

Formatting of SYNOPSIS code.

Passes unit tests.

added use of method bind_param_generic_fetch to allow binding parameters when using the generic fetch method

In all the feature adaptors, use either _create_feature() or
_create_feature_fast() from BaseFeatureAdaptor in _objs_from_sth() to
create features.

added order as an optional argument to list_dbIDs, mosy useful for genes and transcripts so caching is maximised

modified execute calls to make compatible with other databases. Need to use bind_param first, with the type of the parameter, and execute later

documentation of fetch_by_region-method fixed

WAS :         $slice = $sa->fetch_by_region('x', 100000, 200000);
CHANGED TO :  $slice = $sa->fetch_by_region('chromosome','x', 100000, 200000);

allow prediction transcripts to be computed in slice coords and transformed to raw contig coords - untested

fixes RepeatFeatureAdaptor::fetch_by_dbID

where all my transcripts were disappearing to.

I'm assuming it still works for slices.  I don't have slice tests yet.

Refactored PredictionTranscriptAdaptor to inherit from BaseAlignFeature (and fixed some bugs)
Altered RepeatFeatureAdaptor slightly for changed BaseAlignFeature implementation