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

Example 6 with CigarDetailMetrics

use of gridss.analysis.CigarDetailMetrics 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());
}

Example 7 with CigarDetailMetrics

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

the class ScoringComparisonTest method printSoftClipComparison.

private void printSoftClipComparison(VariantScoringModel model1, VariantScoringModel model2) {
    List<CigarDetailMetrics> sc = CigarSizeDistributionTest.data_778();
    IdsvSamFileMetrics metrics = new IdsvSamFileMetrics(null, null, null, null, sc);
    System.out.println("Split Read:");
    System.out.println("mapq1,mapq2,sclength,score1,score2");
    for (int i = 0; i < mapq.length; i++) {
        int mapq1 = mapq[i];
        for (int j = i; j < mapq.length; j++) {
            int mapq2 = mapq[j];
            for (int scLength = 0; scLength < sc.size(); scLength += 5) {
                System.out.println(String.format("%d,%d,%d,%f,%f", mapq1, mapq2, scLength, model1.scoreSplitRead(metrics, scLength, mapq1, mapq2), model2.scoreSplitRead(metrics, scLength, mapq1, mapq2)));
            }
        }
    }
    System.out.println("SoftClip:");
    System.out.println("mapq1,sclength,score1,score2");
    for (int i = 0; i < mapq.length; i++) {
        int mapq1 = mapq[i];
        for (int scLength = 0; scLength < sc.size(); scLength += 5) {
            System.out.println(String.format("%d,%d,%f,%f", mapq1, scLength, model1.scoreSoftClip(metrics, scLength, mapq1), model2.scoreSoftClip(metrics, scLength, mapq1)));
        }
    }
}