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

Example 1 with IdsvMetrics

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

the class IdsvSamFileMetrics method getIdsvMetrics.

private static IdsvMetrics getIdsvMetrics(File idsvMetricsFiles) {
    IdsvMetrics metric = Iterators.getOnlyElement(Iterables.filter(MetricsFile.readBeans(idsvMetricsFiles), IdsvMetrics.class).iterator(), null);
    if (metric == null) {
        metric = new IdsvMetrics();
        log.error(String.format("No idsv metrics found in %s.", idsvMetricsFiles));
    }
    return metric;
}

Example 2 with IdsvMetrics

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

the class FastEmpiricalReferenceLikelihoodModel method scoreUnmappedMate.

@Override
public double scoreUnmappedMate(IdsvSamFileMetrics metrics, int mapq) {
    IdsvMetrics im = metrics.getIdsvMetrics();
    // completely unmapped read pairs are excluded for consistency with sc and dp calculation
    double score = MathUtil.prToPhred((double) im.READ_PAIRS_ONE_MAPPED / (double) (im.READ_PAIRS - im.READ_PAIRS_ZERO_MAPPED));
    score = Math.min(score, mapq);
    return score;
}

Example 3 with IdsvMetrics

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

the class IdsvSamFileMetricsCollectorTest method should_calc_max_fragment_size.

@Test
public void should_calc_max_fragment_size() {
    IdsvSamFileMetricsCollector c = new IdsvSamFileMetricsCollector(null);
    c.acceptRecord(Read(0, 1, "100M"), null);
    c.acceptRecord(RP(0, 1, 2, 1)[0], null);
    c.acceptRecord(RP(0, 1, 7, 5)[0], null);
    // should ignore this as it's not a proper pair
    SAMRecord r = RP(0, 1, 100, 5)[0];
    r.setProperPairFlag(false);
    c.acceptRecord(r, null);
    // 12345678901234567890
    // ----> <----
    c.acceptRecord(Read(0, 1, "100M"), null);
    MetricsFile<IdsvMetrics, Integer> idsv = new MetricsFile<IdsvMetrics, Integer>();
    MetricsFile<InsertSizeMetrics, Integer> is = new MetricsFile<InsertSizeMetrics, Integer>();
    MetricsFile<CigarDetailMetrics, Integer> sc = new MetricsFile<CigarDetailMetrics, Integer>();
    MetricsFile<MapqMetrics, Integer> mq = new MetricsFile<MapqMetrics, Integer>();
    c.finish(is, idsv, mq, sc);
    assertEquals(11, (int) ((IdsvMetrics) idsv.getMetrics().get(0)).MAX_PROPER_PAIR_FRAGMENT_LENGTH);
    c = new IdsvSamFileMetricsCollector(null);
    // mate before
    r = RP(0, 1, 100, 5)[1];
    c.acceptRecord(r, null);
    c.finish(is, idsv, mq, sc);
    assertEquals(11, (int) ((IdsvMetrics) idsv.getMetrics().get(0)).MAX_PROPER_PAIR_FRAGMENT_LENGTH);
}

Example 4 with IdsvMetrics

use of gridss.analysis.IdsvMetrics 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 5 with IdsvMetrics

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

the class TestHelper method IDSV.

public IdsvMetrics IDSV(Collection<SAMRecord> input) {
    IdsvSamFileMetricsCollector c = new IdsvSamFileMetricsCollector(null);
    for (SAMRecord r : input) {
        c.acceptRecord(r, null);
    }
    MetricsFile<IdsvMetrics, Integer> idsv = new MetricsFile<IdsvMetrics, Integer>();
    MetricsFile<InsertSizeMetrics, Integer> is = new MetricsFile<InsertSizeMetrics, Integer>();
    MetricsFile<CigarDetailMetrics, Integer> sc = new MetricsFile<CigarDetailMetrics, Integer>();
    MetricsFile<MapqMetrics, Integer> mqm = new MetricsFile<MapqMetrics, Integer>();
    c.finish(is, idsv, mqm, sc);
    IdsvMetrics metrics = idsv.getMetrics().get(0);
    return metrics;
}