Examples with InsertSizeDistribution gridss.analysis.InsertSizeDistribution used on opensource projects

Example 1 with InsertSizeDistribution

use of gridss.analysis.InsertSizeDistribution in project gridss by PapenfussLab.

the class EmpiricalReferenceLikelihoodModelTest method should_score_read_pairs_correctly.

@Test
public void should_score_read_pairs_correctly() {
    IdsvSamFileMetrics metrics = new IdsvSamFileMetrics(new InsertSizeMetrics() {

        {
            MEAN_INSERT_SIZE = 2;
            MEDIAN_INSERT_SIZE = 2;
            MIN_INSERT_SIZE = 1;
            MAX_INSERT_SIZE = 3;
            MEDIAN_ABSOLUTE_DEVIATION = 1;
        }
    }, new IdsvMetrics() {

        {
            MAX_READ_LENGTH = 100;
            MAX_PROPER_PAIR_FRAGMENT_LENGTH = 2;
            MIN_PROPER_PAIR_FRAGMENT_LENGTH = 2;
            READ_PAIRS = 13;
            READ_PAIRS_ONE_MAPPED = 2;
            READ_PAIRS_ZERO_MAPPED = 1;
            READ_PAIRS_BOTH_MAPPED = READ_PAIRS - READ_PAIRS_ONE_MAPPED - READ_PAIRS_ZERO_MAPPED;
            READS = 2 * READ_PAIRS;
            MAPPED_READS = READS - READ_PAIRS_ONE_MAPPED - 2 * READ_PAIRS_ZERO_MAPPED;
        }
    }, new MapqMetrics() {

        {
        }
    }, new InsertSizeDistribution(new int[] { 1, 2, 3 }, new double[] { 1, 8, 1 }), new ArrayList<CigarDetailMetrics>());
    assertEquals(10, model.scoreReadPair(metrics, 3, 1000, 1000), 0.001);
}

Example 2 with InsertSizeDistribution

use of gridss.analysis.InsertSizeDistribution in project gridss by PapenfussLab.

the class GcSinglePassSamProgram method getReadPairConcordanceCalculator.

public ReadPairConcordanceCalculator getReadPairConcordanceCalculator() {
    if (!rpccInitialised) {
        // Read metrics file
        InsertSizeDistribution isd = null;
        if (INSERT_SIZE_METRICS != null) {
            if (!INSERT_SIZE_METRICS.exists()) {
                log.warn("Missing " + INSERT_SIZE_METRICS);
            } else {
                isd = InsertSizeDistribution.create(INSERT_SIZE_METRICS);
            }
        }
        rpcc = ReadPairConcordanceCalculator.create(READ_PAIR_CONCORDANCE_METHOD, FIXED_READ_PAIR_CONCORDANCE_MIN_FRAGMENT_SIZE, FIXED_READ_PAIR_CONCORDANCE_MAX_FRAGMENT_SIZE, READ_PAIR_CONCORDANT_PERCENT, isd, null);
        rpccInitialised = true;
    }
    return rpcc;
}

Example 3 with InsertSizeDistribution

use of gridss.analysis.InsertSizeDistribution in project gridss by PapenfussLab.

the class ProcessStructuralVariantReadsCommandLineProgram method getReadPairConcordanceCalculator.

public ReadPairConcordanceCalculator getReadPairConcordanceCalculator() {
    if (!rpccInitialised) {
        // Read metrics file
        InsertSizeDistribution isd = null;
        if (INSERT_SIZE_METRICS != null) {
            if (!INSERT_SIZE_METRICS.exists()) {
                log.warn("Missing " + INSERT_SIZE_METRICS);
            } else {
                isd = InsertSizeDistribution.create(INSERT_SIZE_METRICS);
            }
        }
        rpcc = ReadPairConcordanceCalculator.create(READ_PAIR_CONCORDANCE_METHOD, FIXED_READ_PAIR_CONCORDANCE_MIN_FRAGMENT_SIZE, FIXED_READ_PAIR_CONCORDANCE_MAX_FRAGMENT_SIZE, READ_PAIR_CONCORDANT_PERCENT, isd, null);
        rpccInitialised = true;
    }
    return rpcc;
}

Example 4 with InsertSizeDistribution

use of gridss.analysis.InsertSizeDistribution in project gridss by PapenfussLab.

the class IdsvSamFileMetricsTest method wrapper_inner_metrics.

@Test
public void wrapper_inner_metrics() {
    IdsvMetrics im = new IdsvMetrics();
    InsertSizeMetrics ism = new InsertSizeMetrics();
    MapqMetrics mqm = new MapqMetrics();
    List<CigarDetailMetrics> sc = new ArrayList<CigarDetailMetrics>();
    InsertSizeDistribution isd = new InsertSizeDistribution(new int[] { 1 }, new double[] { 1 });
    IdsvSamFileMetrics metrics = new IdsvSamFileMetrics(ism, im, mqm, isd, sc);
    assertEquals(im, metrics.getIdsvMetrics());
    assertEquals(isd, metrics.getInsertSizeDistribution());
    assertEquals(ism, metrics.getInsertSizeMetrics());
    assertEquals(sc, metrics.getCigarDetailMetrics());
    assertEquals(mqm, metrics.getMapqMetrics());
}