add splicing_event tables to patch schema
add splicingEvent tests for basic methods
ENSCORESW-480: updates to _objs_from_sth methods across modules
all modules take the same arguments and have the same behaviour
the only differences should be related to the columns specific to a given feature
added include_non_reference option in sort_chromosomes method
include non_reference chromosomes for mapping stats
[ENSCORESW-840]. seq_region_start from db in case of circular chromosome
[ENSCORESW-840]. seq region boundaries are fetched from the db (for slices stored in the db) in case
of circular chromosomes. This is because it is impossible to recompute the seq_region_start|end for
a feature in a circular slice since the transformation operated in method _objs_from_sth in the
corresponding adaptor is not invertible.
For some of the features (e.g. those in the Bio::EnsEMBL::FeaturePair hierarchy), we can't query
the db and the methods seq_region_start|end return undef even if the feature is on a slice.
added production database connection parameters in ConversionSupport
use production database to fetch biotype groups
[ENSCORESW-840]. The extent of the region spanned by transcripts is calculated taken into account
circular slices. In this case, do not use seq_region_start|end to compute min_start|end as the
feature might be crossing the origin of replication and the comparisons to determine min_start
and max_end might then be nonsense.
dealing with extra cases where contigs are mapped but not for the same region
still need to remove manually any mappings which would have been added before for that patch
using biotype group directly rather than list of biotypes belonging to said group
removing unwanted print out
Last change got wrongly mixed somehow. Reverting to previous commit
[ENSCORESW-840]. The extent of the region spanned by transcripts is …alculated taken into account
circular slices. In this case, do not use seq_region_start|end to compute min_start|end as the
feature might be crossing the origin of replication and the comparisons to determine min_start
and max_end might then be nonsense.