Examples with Segment org.apache.commons.math3.geometry.euclidean.twod.Segment used on opensource projects

Example 6 with Segment

use of org.apache.commons.math3.geometry.euclidean.twod.Segment in project gatk-protected by broadinstitute.

the class SNPSegmenter method writeSegmentFile.

/**
     * Write segment file based on maximum-likelihood estimates of the minor allele fraction at SNP sites,
     * assuming the specified allelic bias.  These estimates are converted to target coverages,
     * which are written to a temporary file and then passed to {@link RCBSSegmenter}.
     * @param snps                  TargetCollection of allelic counts at SNP sites
     * @param sampleName            sample name
     * @param outputFile            segment file to write to and return
     * @param allelicBias           allelic bias to use in estimate of minor allele fraction
     */
public static void writeSegmentFile(final TargetCollection<AllelicCount> snps, final String sampleName, final File outputFile, final double allelicBias) {
    Utils.validateArg(snps.totalSize() > 0, "Must have a positive number of SNPs to perform SNP segmentation.");
    try {
        final File targetsFromSNPCountsFile = File.createTempFile("targets-from-snps", ".tsv");
        final List<Target> targets = snps.targets().stream().map(ac -> new Target(name(ac), ac.getInterval())).collect(Collectors.toList());
        final RealMatrix minorAlleleFractions = new Array2DRowRealMatrix(snps.targetCount(), 1);
        minorAlleleFractions.setColumn(0, snps.targets().stream().mapToDouble(ac -> ac.estimateMinorAlleleFraction(allelicBias)).toArray());
        ReadCountCollectionUtils.write(targetsFromSNPCountsFile, new ReadCountCollection(targets, Collections.singletonList(sampleName), minorAlleleFractions));
        //segment SNPs based on observed log_2 minor allele fraction (log_2 is applied in CBS.R)
        RCBSSegmenter.writeSegmentFile(sampleName, targetsFromSNPCountsFile.getAbsolutePath(), outputFile.getAbsolutePath(), false);
    } catch (final IOException e) {
        throw new UserException.CouldNotCreateOutputFile("Could not create temporary output file during " + "SNP segmentation.", e);
    }
}

Example 7 with Segment

use of org.apache.commons.math3.geometry.euclidean.twod.Segment in project gatk-protected by broadinstitute.

the class CNLOHCaller method calculateVarianceOfCopyNeutralSegmentMeans.

/**
     * Attempt to get an idea of segment mean variance near copy neutral.
     *
     * @param segments Never {@code null}
     * @return variance of segment mean (in CR space) of segments that are "close enough" to copy neutral.
     *   Zero if no segments are "close enough"
     */
private double calculateVarianceOfCopyNeutralSegmentMeans(final List<ACNVModeledSegment> segments, final double meanBiasInCR) {
    Utils.nonNull(segments);
    // Only consider values "close enough" to copy neutral (CR == 1).
    final double neutralCR = 1 + meanBiasInCR;
    final double[] neutralSegmentMeans = segments.stream().mapToDouble(ACNVModeledSegment::getSegmentMeanInCRSpace).filter(m -> Math.abs(m - neutralCR) < CLOSE_ENOUGH_TO_COPY_NEUTRAL_IN_CR).toArray();
    return new Variance().evaluate(neutralSegmentMeans);
}

Example 8 with Segment

use of org.apache.commons.math3.geometry.euclidean.twod.Segment in project gatk-protected 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 9 with Segment

use of org.apache.commons.math3.geometry.euclidean.twod.Segment in project graphysica by Graphysica.

the class Aire method distance.

@Override
public double distance(@NotNull final Vector2D curseur, @NotNull final Repere repere) {
    if (positionDansAire(curseur, repere)) {
        return 0;
    }
    Vector2D premierPoint = null;
    Vector2D point1 = null;
    Vector2D point2;
    double distance = Double.MAX_VALUE;
    int i = 0;
    final Iterator<ObjectProperty<Vector2D>> iteration = points.iterator();
    while (i < points.size()) {
        if (i == 0) {
            point1 = repere.positionVirtuelle(iteration.next().getValue());
            premierPoint = point1;
        }
        i++;
        if (i < points.size()) {
            point2 = repere.positionVirtuelle(iteration.next().getValue());
        } else {
            point2 = premierPoint;
        }
        distance = Math.min(distance, new Segment(point1, point2, null).distance(curseur));
        point1 = point2;
    }
    return distance;
}

Example 10 with Segment

use of org.apache.commons.math3.geometry.euclidean.twod.Segment in project graphysica by Graphysica.

the class SegmentDroite method distance.

@Override
public double distance(@NotNull final Vector2D curseur, @NotNull final Repere repere) {
    final Vector2D p1 = repere.positionVirtuelle(getPoint1());
    final Vector2D p2 = repere.positionVirtuelle(getPoint2());
    return new Segment(p1, p2, null).distance(curseur);
}