Introduce Nathan's unit tests and notes.

Conflicts:
	modules/Bio/EnsEMBL/DBSQL/GeneAdaptor.pm

Update eukaryota.pm

Added method documentation to explains why they get overridden

Overwrite transcript_names_from_gene method for all Ensembl Genomes species so it doesn't add '-201' suffix to the gene names.

we should not import our own annotation

these are being set when importing the LRGs

Self-syntenies: construct MLSS correctly.

Restore read coverage support

A warning more verbose, allow no alias, formatting

When retrieving the MLSS for self-synteny we must only specify the
species once so that we get one back.

Restore read_coverage data support removed in 75. Also support the has_coverage field and the downstream effects on rendered sequence of secondary strains - strains with no explicit read coverage data are represented in lowercase where there is no genotype call available.

code (e.g. Ensembl web) creates features without an adaptor.
In case of circular slices, return seq_region_start|end from the db only if
an adaptor is available.
If there is no adaptor it will try to do the normal calculation rather than die.

using internal_id as unique key instead

Other than some very minor formatting changes, the two changes here:
a) make a warning more verbose (I missed the meaning of the output)
b) allow the config file to have no alias value without causing an error.

Master

Kieron Taylor authored 11 years ago and Magali Ruffier committed 10 years ago

[ENSCORESW-816] Patch attempting to fix reused contigs being destroyed as duplicates. Also formatting changes.

Andy Yates authored 11 years ago and Magali Ruffier committed 10 years ago

Removed the duplicate removal detection. We really can have these now. I would prefer a better way to detect them though

initial PostgreSQL support