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

Example 1 with VariantContextWindowedSortingIterator

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

the class VcfTransformCommandLineProgram method getAllCalls.

public Iterator<IdsvVariantContext> getAllCalls(File file, CloseableIterator<VariantContextDirectedBreakpoint> breakpointCalls) {
    VCFFileReader vcfReader = new VCFFileReader(file, false);
    CloseableIterator<VariantContext> it = vcfReader.iterator();
    Iterator<IdsvVariantContext> idsvIt = Iterators.transform(it, variant -> IdsvVariantContext.create(getContext(), null, variant));
    Iterator<IdsvVariantContext> nonbpIt = Iterators.filter(idsvIt, variant -> !(variant instanceof VariantContextDirectedBreakpoint));
    // sort back to nominal VCF position
    Iterator<VariantContextDirectedBreakpoint> bpit = new VariantContextWindowedSortingIterator<>(getContext(), SAMEvidenceSource.maximumWindowSize(getContext(), getSamEvidenceSources(), getAssemblySource()), breakpointCalls);
    Iterator<IdsvVariantContext> mergedIt = Iterators.mergeSorted(ImmutableList.of(bpit, nonbpIt), IdsvVariantContext.ByLocationStart);
    return new AutoClosingIterator<>(mergedIt, vcfReader, it);
}