org.hammerlab.guacamole.jointcaller.evidence
If we are going to consider only one allele at this site, pick the best one.
If we are going to consider only one allele at this site, pick the best one.
TODO: this should probably do something more sophisticated.
Comparisons between ranges.
Comparisons between ranges. Order is DESCENDING (i.e. reversed) from by start.
Name of the reference contig
Name of the reference contig
The end position on the genome, *exclusive*.
The end position on the genome, *exclusive*. Must be non-negative.
Iterate through elements in the range.
Iterate through elements in the range.
Number of elements in the range.
Number of elements in the range.
Return a new instance containing only the calls that pass filters.
Does the region overlap another reference region
Does the region overlap another reference region
another region on the genome
True if the the regions overlap
Does the region overlap the given locus, with halfWindowSize padding?
Does the region overlap the given locus, with halfWindowSize padding?
Start position on the genome, inclusive.
Start position on the genome, inclusive. Must be non-negative.
A grouping of AlleleEvidenceAcrossSamples instances (one for each allele) at the same site.
Currently not much is done here, and we just write out VCF entries for all the called alleles separately. Later we may want to use this as a place to decide which if any of a number of alleles called at the same site should be written out.