chr: common homologous regions

This package contains functions for fast search of homologous regions shared by multiple closely related genomes. The interface of chr consists of the Intersect function and the Parameters struct:

chr.Intersect(chr.Parameters)

The function returns a slice of pointers to fasta sequences []*fasta.Sequence. The type fasta is defined in the fasta package.

Parameters

type Parameters struct {
        Reference       []*fasta.Sequence
        QueryPaths      []string
        Threshold       float64
        ShustrPval      float64
        NumThreads   	int
}

Fields of this data structure contain parameters used to call Intersect(). The parameters include:

1. reference slice of fasta sequences
2. paths to queries
3. a threshold, the minimum fraction of intersecting genomes
4. a p-value of the shustring length (needed for sus.Quantile)
5. number of threads (maximum threads used for parallel query processing)