Basic seeding and seed selection

[ezorita]

Description

Basic algorithms to seed input sequences and select relevant seeds.

Subtasks

• Define data structure for seeds.
• MEM seeding algorithm.
• Algorithm to check seed neighbors.
• Define data structure to pass a list of seeds for alignment. (using gstacks)
• Reseeding conditions.
• Test code for 'seed_ann_dist'.
• Test code for 'gstack_transfer_all'.
• Test code for new mapper output.

Acceptance criteria

• All MEMs in any input sequence are found.
• Seed neighbor information is also reported (when possible).
• If no neighbor annotations are available (or seed is too short) no assumption is made.

Test procedures

• Unit tests for all seeding and selection algorithms.

Dependencies

• Depends on Full stack error propagation #37