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

Example 1 with FileSystemContext

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

the class ComputeCoverage method initIntervalCoverageAccumulator.

private IntervalCoverageAccumulator initIntervalCoverageAccumulator() {
    SAMSequenceDictionary dictionary = getReference().getSequenceDictionary();
    if (VCF == null) {
        return new IntervalCoverageAccumulator(COVERAGE_METHOD, dictionary, BIN_SIZE, null);
    } else {
        try (VCFFileReader vcfReader = new VCFFileReader(VCF, false)) {
            try (CloseableIterator<VariantContext> it = vcfReader.iterator()) {
                GenomicProcessingContext pc = new GenomicProcessingContext(new FileSystemContext(TMP_DIR.get(0), MAX_RECORDS_IN_RAM), REFERENCE_SEQUENCE, getReference());
                Iterator<IdsvVariantContext> idsvIt = Iterators.transform(it, variant -> IdsvVariantContext.create(pc, null, variant));
                Iterator<VariantContextDirectedEvidence> bpit = Iterators.filter(idsvIt, VariantContextDirectedEvidence.class);
                return new IntervalCoverageAccumulator(COVERAGE_METHOD, dictionary, BIN_SIZE, bpit);
            }
        }
    }
}

Example 2 with FileSystemContext

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

the class SimulationGenerator method getProcessingContext.

protected GenomicProcessingContext getProcessingContext() {
    GenomicProcessingContext pc = new GenomicProcessingContext(new FileSystemContext(TMP_DIR.get(0), new File("."), MAX_RECORDS_IN_RAM), REFERENCE, null);
    pc.setCommandLineProgram(this);
    return pc;
}