Examples of Civar

org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar
Compact Idosyncratic Variation Alignment Report.
Allows to specify variation of a sequence.

Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar

        haplotypeStrings = result;
        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;

View Full Code Here

Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar

        }
        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()));

View Full Code Here

Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar


    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+:.+$")) {

View Full Code Here

Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar

    }


    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();
    }

View Full Code Here

Examples of org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar

    private List<List<Civar.ElementOffset>> generateElementOffsetRecords(final List<String> haplotypes, final List<Civar> unrolledCivars, final int readCount, final int readLength, final int count) {


        final List<List<Civar.ElementOffset>> result = new ArrayList<>(readCount);
        for (int i = 0; i < readCount; i++) {
            int hi = i % unrolledCivars.size();
            final Civar c = unrolledCivars.get(hi);
            final String h = haplotypes.get(hi);
            int offset = h.length() <= readLength ? 0 : i % (h.length() - readLength);
            int to = Math.min(h.length(),offset + readLength);
            result.add(c.eventOffsets(reference,offset,to));
        }
        return result;
    }

View Full Code Here

TOP

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.