Examples with SequentialCoverageAnnotator au.edu.wehi.idsv.SequentialCoverageAnnotator used on opensource projects

Example 1 with SequentialCoverageAnnotator

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

the class AnnotateReferenceCoverage method iterator.

@Override
public CloseableIterator<VariantContextDirectedBreakpoint> iterator(CloseableIterator<VariantContextDirectedBreakpoint> calls, ExecutorService threadpool) {
    ProcessingContext context = getContext();
    List<SAMEvidenceSource> sources = getSamEvidenceSources();
    AssemblyEvidenceSource asm = getAssemblySource();
    int windowSize = SAMEvidenceSource.maximumWindowSize(context, sources, asm);
    return new SequentialCoverageAnnotator<VariantContextDirectedBreakpoint>(context, sources, calls, 2 * windowSize + WINDOW_SIZE_SAFETY_MARGIN, threadpool);
}