Package org.broadinstitute.gatk.utils.pairhmm

Examples of org.broadinstitute.gatk.utils.pairhmm.ActiveRegionTestDataSet

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    @DataProvider(name="trimmingData")
    public Iterator<Object[]> trimmingData() {
        final ActiveRegion activeRegion = new ActiveRegion(genomeLocParser.createGenomeLoc("chr1",1000,1100),genomeLocParser,25);
        final int length = activeRegion.getExtendedLoc().size();
        final RandomDNA rnd = new RandomDNA(13); // keep it prepoducible by fixing the seed to lucky 13.
        final ActiveRegionTestDataSet actd = new ActiveRegionTestDataSet(10,new String(rnd.nextBases(length)),new String[] {
                "Civar:*1T*" }, new String[0], new byte[0], new byte[0], new byte[0]);

        final List<Haplotype> haplotypes = actd.haplotypeList();
        for (final Haplotype h : haplotypes)
            h.setGenomeLocation(activeRegion.getExtendedLoc());

        final ReadThreadingGraph rtg = new ReadThreadingGraph(10);
        for (final Haplotype h : haplotypes)
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     */
    public static ActiveRegionTestDataSet createActiveRegionTestDataSet(final int kmerSize, final int readLength, final String variation, final int readCount, final int regionSize, final byte bq, final byte iq, final byte dq) {

        final String reference = REF.substring(0, regionSize);

        final ActiveRegionTestDataSet result = new ActiveRegionTestDataSet(kmerSize, reference,
                new String[]{"Civar:" + variation},
                new String[]{"*:" + readCount + ":" + readLength}, byteRepeat(bq, readLength), byteRepeat(dq, readLength), byteRepeat(iq, readLength));


        return result;
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                final int kmerSize = (Integer) params[0];
                final int readLength = (Integer) params[1];
                final String variation = (String) params[2];
                final int readCount = (Integer) params[3];
                final int regionSize = (Integer) params[4];
                final ActiveRegionTestDataSet dataSet = createActiveRegionTestDataSet(kmerSize, readLength, variation, readCount, regionSize, (byte) 20, (byte) 35, (byte) 35);
                return new Object[] { dataSet , kmerSize, readLength, variation, readCount, regionSize, (byte)20, (byte) 35, (byte) 35};
            }

            @Override
            public void remove() {
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Related Classes of org.broadinstitute.gatk.utils.pairhmm.ActiveRegionTestDataSet

  • htsjdk.samtools.SAMFileHeader
  • htsjdk.samtools.SAMSequenceDictionary
  • htsjdk.samtools.SAMSequenceRecord
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.ActiveRegionTestDataSetUnitTest
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResult
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResultSet
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.AssemblyResultSetUnitTest
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.Civar
  • org.broadinstitute.gatk.tools.walkers.haplotypecaller.readthreading.ReadThreadingGraph
  • org.broadinstitute.gatk.utils.GenomeLocParser
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