Examples of optionalizeAll()

Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar.optionalizeAll()

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        return result;
    }

    private List<String> expandAllCombinations(final String cigarString, final String reference) {
        final Civar civar = Civar.fromCharSequence(cigarString);
        final List<Civar> unrolledCivars = civar.optionalizeAll().unroll();
        List<String> result = new ArrayList<>(unrolledCivars.size());
        for (final Civar c : unrolledCivars) {
            result.add(c.applyTo(reference));
        }
        return result;
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Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar.optionalizeAll()

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        return result;
    }

    private List<Haplotype> expandAllHaplotypeCombinations(final String civarString, final String reference) {
        final Civar civar = Civar.fromCharSequence(civarString);
        final List<Civar> unrolledCivars = civar.optionalizeAll().unroll();
        List<Haplotype> result = new ArrayList<>(unrolledCivars.size());
        for (final Civar c : unrolledCivars) {
            final String baseString = c.applyTo(reference);
            final Haplotype haplotype = new Haplotype(baseString.getBytes(),baseString.equals(reference));
            haplotype.setGenomeLocation(genomeLocParser.createGenomeLoc("chr1",1,reference.length()));
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Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar.optionalizeAll()

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    public List<List<Civar.ElementOffset>> readEventOffsetList() {
        if (haplotypeCigars.length != 1 || !haplotypeCigars[0].startsWith("Civar:"))
            throw new UnsupportedOperationException();
        if (readEventOffsetList == null) {
            final Civar civar = Civar.fromCharSequence(haplotypeCigars[0].substring(6));
            final List<Civar> unrolledCivars = civar.optionalizeAll().unroll();

            readEventOffsetList = new ArrayList<>(readCigars.length);
            int count = 0;
            for (final String descr : readCigars) {
                if (descr.matches("^\\d+:\\d+:.+$")) {
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Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar.optionalizeAll()

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    public List<Civar> unrolledCivars() {
        if (haplotypeCigars.length != 1 || !haplotypeCigars[0].startsWith("Civar:"))
            throw new UnsupportedOperationException();
        final Civar civar = Civar.fromCharSequence(haplotypeCigars[0].substring(6));
        return civar.optionalizeAll().unroll();
    }

    public void introduceErrors(final Random rnd) {
        final List<GATKSAMRecord> reads = readList();
        final ArrayList<GATKSAMRecord> result = new ArrayList<>(reads.size());
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