Examples with SimpleInterval org.broadinstitute.hellbender.utils.SimpleInterval used on opensource projects

Example 11 with SimpleInterval

use of org.broadinstitute.hellbender.utils.SimpleInterval in project gatk by broadinstitute.

the class ReCapSegCallerUnitTest method testMakeCalls.

@Test
public void testMakeCalls() {
    final List<Target> targets = new ArrayList<>();
    final List<String> columnNames = Arrays.asList("Sample");
    final List<Double> coverage = new ArrayList<>();
    //add amplification targets
    for (int i = 0; i < 10; i++) {
        final SimpleInterval interval = new SimpleInterval("chr", 100 + 2 * i, 101 + 2 * i);
        targets.add(new Target(interval));
        coverage.add(ParamUtils.log2(2.0));
    }
    //add deletion targets
    for (int i = 0; i < 10; i++) {
        final SimpleInterval interval = new SimpleInterval("chr", 300 + 2 * i, 301 + 2 * i);
        targets.add(new Target(interval));
        coverage.add(ParamUtils.log2(0.5));
    }
    //add targets that don't belong to a segment
    for (int i = 1; i < 10; i++) {
        final SimpleInterval interval = new SimpleInterval("chr", 400 + 2 * i, 401 + 2 * i);
        targets.add(new Target(interval));
        coverage.add(ParamUtils.log2(1.0));
    }
    //add obviously neutral targets with some small spread
    for (int i = -5; i < 6; i++) {
        final SimpleInterval interval = new SimpleInterval("chr", 500 + 2 * i, 501 + 2 * i);
        targets.add(new Target(interval));
        coverage.add(ParamUtils.log2(0.01 * i + 1));
    }
    //add spread-out targets to a neutral segment (mean near zero)
    for (int i = -5; i < 6; i++) {
        final SimpleInterval interval = new SimpleInterval("chr", 700 + 2 * i, 701 + 2 * i);
        targets.add(new Target(interval));
        coverage.add(ParamUtils.log2(0.1 * i + 1));
    }
    final RealMatrix coverageMatrix = new Array2DRowRealMatrix(targets.size(), 1);
    coverageMatrix.setColumn(0, coverage.stream().mapToDouble(x -> x).toArray());
    final int n = targets.size();
    final int m = coverageMatrix.getRowDimension();
    final ReadCountCollection counts = new ReadCountCollection(targets, columnNames, coverageMatrix);
    List<ModeledSegment> segments = new ArrayList<>();
    //amplification
    segments.add(new ModeledSegment(new SimpleInterval("chr", 100, 200), 100, ParamUtils.log2(2.0)));
    //deletion
    segments.add(new ModeledSegment(new SimpleInterval("chr", 300, 400), 100, ParamUtils.log2(0.5)));
    //neutral
    segments.add(new ModeledSegment(new SimpleInterval("chr", 450, 550), 100, ParamUtils.log2(1)));
    //neutral
    segments.add(new ModeledSegment(new SimpleInterval("chr", 650, 750), 100, ParamUtils.log2(1)));
    List<ModeledSegment> calls = ReCapSegCaller.makeCalls(counts, segments);
    Assert.assertEquals(calls.get(0).getCall(), ReCapSegCaller.AMPLIFICATION_CALL);
    Assert.assertEquals(calls.get(1).getCall(), ReCapSegCaller.DELETION_CALL);
    Assert.assertEquals(calls.get(2).getCall(), ReCapSegCaller.NEUTRAL_CALL);
    Assert.assertEquals(calls.get(3).getCall(), ReCapSegCaller.NEUTRAL_CALL);
}

Example 12 with SimpleInterval

use of org.broadinstitute.hellbender.utils.SimpleInterval in project gatk by broadinstitute.

the class ReadCountCollectionUnitTest method newInstanceInfo.

private ReadCountCollectionInfo newInstanceInfo(final int columnCount, final int targetCount, final boolean withIntervals) {
    final Random rdn = new Random((11 + columnCount) * (13 * targetCount) * (withIntervals ? 37 : 9));
    final List<String> columnNames = new ArrayList<>(columnCount);
    for (int i = 0; i < columnCount; i++) {
        columnNames.add("col_" + Math.abs(rdn.nextInt()) + "_" + i);
    }
    final List<String> targetNames;
    targetNames = new ArrayList<>(targetCount);
    for (int j = 0; j < targetCount; j++) {
        targetNames.add("tgt_" + Math.abs(rdn.nextInt()) + "_" + j);
    }
    final double[][] counts = new double[targetCount][columnCount];
    for (int i = 0; i < counts.length; i++) {
        for (int j = 0; j < counts[i].length; j++) {
            counts[i][j] = rdn.nextGaussian();
        }
    }
    final List<SimpleInterval> intervals;
    if (withIntervals) {
        intervals = new ArrayList<>(targetCount);
        int start = 1;
        for (int j = 0; j < targetCount; j++) {
            final int newStart = start + rdn.nextInt(100);
            final int newEnd = newStart + 1 + rdn.nextInt(200);
            intervals.add(new SimpleInterval("seq1", newStart, newEnd));
            start = newEnd + 1;
        }
    } else {
        intervals = null;
    }
    return new ReadCountCollectionInfo(columnCount, targetCount, columnNames, targetNames, intervals, counts);
}

Example 13 with SimpleInterval

use of org.broadinstitute.hellbender.utils.SimpleInterval in project gatk by broadinstitute.

the class SegmentUtilsUnitTest method testUnionSegments.

/**
     * Test for {@link SegmentUtils#unionSegments}.  Expected behavior:
     * <p>
     * On chr1 {@link SegmentUtils#collectBreakpointsByContig} gives:
     * </p>
     *      <p>
     *      1, 5, 10, 20, 40, 40, 42, 90, 91, 115, 125, 140.
     *      </p>
     * <p>
     * Then {@link SegmentUtils#constructUntrimmedSegments} finds the segments:
     * </p>
     *      <p>
     *      [1, 4], [5, 10], [11, 19], [20, 40], [41, 41], [42, 89], [90, 91], [92, 114], [115, 125], [126, 140].
     *      </p>
     * <p>
     * and returns the non-empty segments:
     * </p>
     *      <p>
     *      [1, 4], [5, 10], [20, 40], [42, 89], [90, 91], [92, 114], [115, 125], [126, 140].
     *      </p>
     * <p>
     * Then {@link SegmentUtils#mergeSpuriousStartsAndEnds} merges the last segment left to form [115, 140],
     * and {@link SegmentMergeUtils#mergeSpuriousMiddles} randomly merges segment [92, 114] left or right.
     * </p>
     * <p>
     * Finally, {@link SegmentUtils#trimInterval} gives:
     * </p>
     *      <p>
     *      [1, 10], [20, 40], [42, 42], [90, 114], [115, 140] (if [92, 114] merged left) or
     *      </p>
     *      <p>
     *      [1, 10], [20, 40], [42, 42], [90, 91], [92, 140] (if [92, 114] merged right)
     *      </p>
     * <p>
     * The remaining empty segment on chr2 is retained.
     */
@Test
public void testUnionSegments() {
    final String sampleName = "placeholder_sample_name";
    final List<Target> targets = new ArrayList<Target>();
    targets.add(new Target("t1", new SimpleInterval("chr1", 1, 10)));
    targets.add(new Target("t2", new SimpleInterval("chr1", 20, 30)));
    targets.add(new Target("t3", new SimpleInterval("chr1", 31, 40)));
    targets.add(new Target("t4", new SimpleInterval("chr1", 90, 100)));
    targets.add(new Target("t5", new SimpleInterval("chr1", 110, 120)));
    targets.add(new Target("t6", new SimpleInterval("chr1", 130, 140)));
    final RealMatrix zeroCoverageMatrix = new Array2DRowRealMatrix(targets.size(), 1);
    final ReadCountCollection counts = new ReadCountCollection(targets, Collections.singletonList(sampleName), zeroCoverageMatrix);
    final AllelicCount snp1 = new AllelicCount(new SimpleInterval("chr1", 5, 5), 0, 1);
    final AllelicCount snp2 = new AllelicCount(new SimpleInterval("chr1", 40, 40), 0, 1);
    final AllelicCount snp3 = new AllelicCount(new SimpleInterval("chr1", 42, 42), 0, 1);
    final AllelicCount snp4 = new AllelicCount(new SimpleInterval("chr1", 91, 91), 0, 1);
    final AllelicCount snp5 = new AllelicCount(new SimpleInterval("chr1", 115, 115), 0, 1);
    final AllelicCount snp6 = new AllelicCount(new SimpleInterval("chr1", 125, 125), 0, 1);
    final AllelicCount snp7 = new AllelicCount(new SimpleInterval("chr2", 10, 10), 0, 1);
    final List<AllelicCount> snps = Arrays.asList(snp1, snp2, snp3, snp4, snp5, snp6, snp7);
    final List<SimpleInterval> targetSegments = Arrays.asList(new SimpleInterval("chr1", 1, 10), new SimpleInterval("chr1", 20, 40), new SimpleInterval("chr1", 90, 140));
    final List<SimpleInterval> snpSegments = Arrays.asList(new SimpleInterval("chr1", 5, 40), new SimpleInterval("chr1", 42, 91), new SimpleInterval("chr1", 115, 125), new SimpleInterval("chr2", 10, 10));
    final List<SimpleInterval> unionedSegments = SegmentUtils.unionSegments(targetSegments, snpSegments, new Genome(counts, snps));
    final List<SimpleInterval> expectedLeft = Arrays.asList(new SimpleInterval("chr1", 1, 10), new SimpleInterval("chr1", 20, 40), new SimpleInterval("chr1", 42, 42), new SimpleInterval("chr1", 90, 114), new SimpleInterval("chr1", 115, 140), new SimpleInterval("chr2", 10, 10));
    final List<SimpleInterval> expectedRight = Arrays.asList(new SimpleInterval("chr1", 1, 10), new SimpleInterval("chr1", 20, 40), new SimpleInterval("chr1", 42, 42), new SimpleInterval("chr1", 90, 91), new SimpleInterval("chr1", 92, 140), new SimpleInterval("chr2", 10, 10));
    Assert.assertTrue(unionedSegments.equals(expectedLeft) || unionedSegments.equals(expectedRight));
}

Example 14 with SimpleInterval

use of org.broadinstitute.hellbender.utils.SimpleInterval in project gatk by broadinstitute.

the class TargetCollectionUnitTest method testTargetByLocationExactMatch.

@Test(dataProvider = "targetDBData")
public void testTargetByLocationExactMatch(final TargetCollection<SimpleInterval> targetCollection) {
    for (int i = 0; i < targetCollection.targetCount(); i++) {
        final SimpleInterval si = targetCollection.target(i);
        Assert.assertEquals(targetCollection.target(si), si);
    }
}

Example 15 with SimpleInterval

use of org.broadinstitute.hellbender.utils.SimpleInterval in project gatk by broadinstitute.

the class TargetCollectionUnitTest method testTargetByLocationAmbiguousOverlapping.

@Test(dataProvider = "twoOrMoreTargetDBData")
public void testTargetByLocationAmbiguousOverlapping(final TargetCollection<SimpleInterval> targetCollection) {
    for (int i = 0; i < targetCollection.targetCount() - 1; i++) {
        final int start = targetCollection.target(i).getEnd() - 1;
        final int end = targetCollection.target(i + 1).getStart() + 1;
        final SimpleInterval loc = TargetsToolsTestUtils.createInterval(targetCollection.target(i).getContig(), start, end);
        try {
            targetCollection.target(loc);
            Assert.fail("expected exception. Index == " + i);
        } catch (final TargetCollection.AmbiguousTargetException ex) {
        // ok.
        } catch (final Throwable t) {
            Assert.fail("wrong exception: ", t);
        }
    }
}