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This reverts commit 25f23f36.

This reverts commit 24c30038.
Do not attempt to update meta_coord when removing a feature, this can have bad consequences

Conflicts:

	modules/Bio/EnsEMBL/DBSQL/BaseFeatureAdaptor.pm

changes just for vega

(ii) sort_chromosomes can work with non-reference chromosomes
(iii) updated allowed_duplicated_regions for pig chr Xs and human GRCh38
(iv) methods to generate sequence alignments

[ENSCORESW-885] fix for get and update to support multispecies databases

Removed functionality to get INSDC xrefs from FlyBase; these are better determined with the xref pipeline, which attaches them to translations rather than genes.

* hotfix/comparadocumentation:
  [ENSCORESW-841] - Doxygen output. Make PerlFilter ignore additional packages in a module, to prevent confusion in Compara codebase.

[ENSCORESW-841] - Doxygen output. Make PerlFilter ignore additional packages in a module, to prevent confusion in Compara codebase.

We want people to give us bugfixes or cool features which help
everyone. So we're making the rules to contributing easier.

restore changes from c981f63d

lost during pull request #4 to f9a90829
(cherry picked from commit adcddeb2)

License and contact up-to-date for 75

use code directly in get_attrib method

A fix for the fix. Originally we started with passing through Slice
for the aligned feature but this is wrong. We need to assert the
hit feature Slice which we do not have. This change reverts the
_check_start_end_strand() method back to its original functionality.

Revert "transcript counts can now be fetched using transcript_cnt and transcript_acnt"

This reverts commit 3d9c5ad7.

* dev:
  transcript table in patch database now contains data genome_container test module updated to reflect the change

genome_container test module updated to reflect the change

* dev:
  there can be several statistics for prediction_count

Introducing a new version of our GTF dumper. Now supports
gene and transcript features, seleno markup, ccds xrefs and
a new readme.

* dev:
  corrected argument for structural_variation count