Examples with VariantCallingConfiguration au.edu.wehi.idsv.configuration.VariantCallingConfiguration used on opensource projects

Example 1 with VariantCallingConfiguration

use of au.edu.wehi.idsv.configuration.VariantCallingConfiguration in project gridss by PapenfussLab.

the class AllocateEvidence method annotate.

private VariantContextDirectedBreakpoint annotate(VariantEvidenceSupport ves) {
    VariantCallingConfiguration vc = getContext().getConfig().getVariantCalling();
    StructuralVariationCallBuilder builder = new StructuralVariationCallBuilder(getContext(), ves.variant);
    for (DirectedEvidence e : ves.support) {
        boolean shouldExclude = false;
        if (!shouldExclude) {
            builder.addEvidence(e);
        }
    }
    VariantContextDirectedBreakpoint bp = (VariantContextDirectedBreakpoint) builder.make();
    if (!vc.writeFiltered) {
        if (bp.getBreakpointQual() < vc.minScore)
            return null;
        if (bp.getBreakpointEvidenceCount() < vc.minReads)
            return null;
        if (bp.isFiltered())
            return null;
    }
    bp = (VariantContextDirectedBreakpoint) vc.applyConfidenceFilter(getContext(), bp);
    return bp;
}