Variant

VAGrENT models different variant types as different classes. These classes are simple data containers with a few data validation rules. All variant are expected to be plotted to a reference genome sequence. The main classes are:-

• Sanger::CGP::Vagrent::Data::Substitution
• Sanger::CGP::Vagrent::Data::Insertion
• Sanger::CGP::Vagrent::Data::Deletion
• Sanger::CGP::Vagrent::Data::ComplexIndel

All these classes inherit from:-

• Sanger::CGP::Vagrent::Data::AbstractGenomicPosition
• Sanger::CGP::Vagrent::Data::AbstractVariation

The data needed to populate these objects are as follows

• Species
• Genome
• Chromosome/Contig
• Minimum position
• Maximum position
• Wild type sequence
• Variant sequence

All coordinates are expected to be inclusive (ie first and last affected wild type position), except for Insertions whos coordinates are exclusive (ie the position between which the insertion occurred)