Update web code to support EPO_EXTENDED alignments

[twalsh-ebi]

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Description

EPO_LOW_COVERAGE alignments were renamed to EPO_EXTENDED in Ensembl release 101.

This pull request would update web code to support this renamed method type.

Views affected

These changes would affect Compara genome alignment views.

EnsEMBL::Web::Component::Compara_Alignments

Alignment tables will show the relevant EPO reference genome

Examples:

• Pig - Ningxiang region 1:101985531-102506489 on sandbox vs staging : see the "Location on Pig" column, visible on sandbox but not on staging.
• Bolivian squirrel monkey region JH378319.1:103833-103839 on sandbox vs staging : see the "Location on Human" column, visible on sandbox but not on staging. To get a sense of the difference this change makes, try clicking on the links to "Block 1" or "Block 2" on the sandbox and staging sites.

More accurate EPO-Extended alignment info will be retrieved

EPO-Extended examples:

• Primates EPO-Extended alignment of Human region 17:63992802-64238237 on sandbox vs staging
• EPO-Extended alignment of Ninxiang pig breed region 1:101985531-102006489 on sandbox vs staging
• EPO-Extended alignment of Horse region 2:55144620-55829364 on sandbox vs staging

See the legend and labelling of EPO and EPO-Extended genome assemblies in the alignment tree view.

Other alignment examples:

• Primates EPO alignment of Human region 17:63992802-64238237 on sandbox vs staging
• Mercator-Pecan alignment of Human region 17:63992802-64238237 on sandbox vs staging

Note removal of EPO-Extended legend entry.

EnsEMBL::Web::ConfigPacker

Changes in this module will prevent unwanted addition of ancestral_sequences to the species set of EPO-Extended alignments.

Example:

• Oryza punctata region 1-2000 on sandbox vs staging

Note the "Hidden and missing species" info box in the staging webpage.

Possible complications

None expected.

Merge conflicts

None detected.

Related JIRA Issues (EBI developers only)

N/A