Handle large number of SNVs.

[junseonghwan]

Currently, re-assigning an SNV results in computation of single cell cache.

• For any SNVs that do not have single cell coverage, sampling assignment should not trigger single cell cache update.
• Only the cells that have reads at the SNV being re-assigned need to update cache.
• Write a test for single cell cache computation.
• Single cell data to store vector of integers, which index the bulk data. This can speed up computation of cache by computing likelihood at SNVs for which the cell has reads.

[junseonghwan]

Keep track of two separate vectors of SNVs, one with single cell coverage and one without.

If new nodes are created as a result of assigning SNVs without single cell coverage, the single cell likelihood now has a new node to consider for assignment. Therefore, not updating cache for re-assignment of these SNVs can invalidate the single cell likelihood.

However, the cache will be correctly updated for next SNV to be re-assigned with single cell coverage.

[junseonghwan]

• Interface class to handle processing of configuration file and manage data objects.
• BulkDatum to store Locus.
• SingleCellData to store vector<size_t>, indexing bulk data vector for which is has reads.

[junseonghwan]

Run a simulated experiments with 1000 somatic SNVs with dropout equal to 0.99 (majority of the somatic SNVs are not going to have single cell coverage).

• Introduce sparsity parameter for simulated data.

[junseonghwan]

Single cell likelihood calculation: need a fast way to check for presence/absence of mutation s at node v.

• Get the node that the SNV s is assigned to, call it u.
• Check if u is an ancestor of v or u == v.

[junseonghwan]

It turns out that unordered_map does not have O(1) access time, which results in becoming a bottleneck for performance when storing loglikelihood values for each cell at each node.

We can move single cell cache to each node. Each node can store a vector of double values, one for each cell.

[junseonghwan]

Accessing Eigen matrix is taking quite a bit of time. Pre-compute and store the single cell likelihood as a vector of vector.