Compute the global bin mask from a set of reference samples

Identifies bins with sufficient coverage across all reference samples. Bins where the summed normalized coverage is less than 5% of the median are masked out. Mirrors newref_tools.get_mask() in upstream WisecondorX.

Usage

.get_mask(samples)

Arguments

samples

List of sample objects (each a named list of integer vectors keyed by chromosome "1"–"24").

Value

A list with two elements:

mask

Logical vector of length sum(bins_per_chr); TRUE for bins with sufficient coverage.

bins_per_chr

Integer vector of length 24 giving the number of bins per chromosome.