Update web code to support EPO_EXTENDED alignments

[twalsh-ebi]

Requirements

• Filling out the template is required. Any pull request that does not include enough information to be efficiently reviewed may be rejected.
• Please consider which branch this is to be submitted against. This is usually obvious, however if it is to be applied to both a release branch nn and master then please submit it against postreleasefix/nn and let us merge it into to the two branches.

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

With the changes in this module:

• Alignment tables will show the relevant EPO reference genome
• More accurate EPO-Extended alignment info will be retrieved

EnsEMBL::Web::ConfigPacker

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

EnsEMBL::Draw::GlyphSet::genetree_legend

The EPO/EPO-Extended legend entry will only be shown for EPO-Extended text alignment views.

Possible complications

None expected.

Merge conflicts

None detected.

Related JIRA Issues (EBI developers only)

N/A