use of org.broadinstitute.hdf5.HDF5File in project gatk-protected by broadinstitute.
the class NormalizeSomaticReadCountsIntegrationTest method assertBetaHatsRobustToOutliers.
/**
* Asserts that the calculation of beta hats is not significantly affected by zero-coverage outlier counts
* We perform this check by randomly setting some coverages to zero in copy ratio space (-infinity in log space).
* betaHats imputes 0 in log space (1 in copy ratio space) whenever coverage is below a certain low threshold
* and should thus be robust to this type of noise.
*/
private void assertBetaHatsRobustToOutliers(final ReadCountCollection preTangentNormalized, final File ponFile) {
try (final HDF5File ponReader = new HDF5File(ponFile)) {
final PCACoveragePoN pon = new HDF5PCACoveragePoN(ponReader);
final List<String> ponTargets = pon.getPanelTargetNames();
final RealMatrix input = reorderTargetsToPoNOrder(preTangentNormalized, ponTargets);
// randomly set some entries to zero in copy-ratio space (-infinity in log space)
final Random random = new Random(13);
final double noiseProportion = 0.01;
final RealMatrix noisyInput = input.copy();
noisyInput.walkInOptimizedOrder(new DefaultRealMatrixChangingVisitor() {
@Override
public double visit(final int row, final int column, final double value) {
return random.nextDouble() < noiseProportion ? Double.NEGATIVE_INFINITY : value;
}
});
final RealMatrix betaHats = PCATangentNormalizationUtils.calculateBetaHats(pon.getReducedPanelPInverseCounts(), input, PCATangentNormalizationUtils.EPSILON);
final RealMatrix noisyBetaHats = PCATangentNormalizationUtils.calculateBetaHats(pon.getReducedPanelPInverseCounts(), noisyInput, PCATangentNormalizationUtils.EPSILON);
final RealMatrix difference = betaHats.subtract(noisyBetaHats);
difference.walkInOptimizedOrder(new DefaultRealMatrixPreservingVisitor() {
@Override
public void visit(final int row, int column, double value) {
Assert.assertEquals(value, 0, 0.01);
}
});
}
}
use of org.broadinstitute.hdf5.HDF5File in project gatk-protected by broadinstitute.
the class HDF5LibraryUnitTest method testMakeNaNDouble.
@Test()
public void testMakeNaNDouble() throws IOException {
final File testFile = File.createTempFile("hdf5", ".hd5");
HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE);
file.makeGroup("test-group/double-group");
Assert.assertTrue(file.makeDouble("test-group/double-group/my-double", Double.NaN));
System.err.println(testFile);
file.close();
final long time = System.currentTimeMillis();
Assert.assertTrue(testFile.length() > 0);
Assert.assertTrue(testFile.lastModified() <= time);
file = new HDF5File(testFile, HDF5File.OpenMode.READ_ONLY);
final double theDouble = file.readDouble("test-group/double-group/my-double");
Assert.assertTrue(Double.isNaN(theDouble));
file.close();
}
use of org.broadinstitute.hdf5.HDF5File in project gatk-protected by broadinstitute.
the class HDF5LibraryUnitTest method testReMakeDoubleArray.
@Test()
public void testReMakeDoubleArray() throws IOException {
final File testFile = File.createTempFile("hdf5", ".hd5");
HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE);
file.makeGroup("test-group/double-group");
final double[] testValues1 = new double[] { 1.1, -2.2, Double.POSITIVE_INFINITY, Double.NEGATIVE_INFINITY, 0.0111e10 - 10 };
final double[] testValues2 = new double[] { 11.1, -22.2, Double.POSITIVE_INFINITY, Double.NEGATIVE_INFINITY, 1.0111e10 - 10 };
Assert.assertTrue(file.makeDoubleArray("test-group/double-group/my-double", testValues1));
System.err.println(testFile);
file.close();
final long time = System.currentTimeMillis();
Assert.assertTrue(testFile.length() > 0);
Assert.assertTrue(testFile.lastModified() <= time);
file = new HDF5File(testFile, HDF5File.OpenMode.READ_WRITE);
final double[] theDoubles1 = file.readDoubleArray("test-group/double-group/my-double");
Assert.assertEquals(theDoubles1, testValues1.clone());
Assert.assertFalse(file.makeDoubleArray("test-group/double-group/my-double", testValues2));
final double[] theDoubles2 = file.readDoubleArray("test-group/double-group/my-double");
Assert.assertEquals(theDoubles2, testValues2.clone());
file.close();
}
use of org.broadinstitute.hdf5.HDF5File in project gatk-protected by broadinstitute.
the class HDF5LibraryUnitTest method testIsPresent.
@Test(dependsOnMethods = { "testCreateGroup", "testMakeDouble" })
public void testIsPresent() {
final File testFile = BaseTest.createTempFile("hdf5", ".hd5");
final HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE);
Assert.assertFalse(file.isPresent("test-group"));
Assert.assertFalse(file.isPresent("test-group/lola-run"));
Assert.assertFalse(file.isPresent("test-group/lola-run/bernie-follows"));
Assert.assertFalse(file.isPresent("test-group/lola-run/jill-follows"));
file.makeGroup("test-group/lola-run");
Assert.assertTrue(file.isPresent("test-group"));
Assert.assertTrue(file.isPresent("test-group/lola-run"));
Assert.assertFalse(file.isPresent("test-group/lola-run/bernie-follows"));
Assert.assertFalse(file.isPresent("test-group/lola-run/jill-follows"));
file.makeDouble("test-group/lola-run/bernie-follows", 0.1);
Assert.assertTrue(file.isPresent("test-group"));
Assert.assertTrue(file.isPresent("test-group/lola-run"));
Assert.assertTrue(file.isPresent("test-group/lola-run/bernie-follows"));
Assert.assertFalse(file.isPresent("test-group/lola-run/jill-follows"));
Assert.assertFalse(file.isPresent("test-group/lola-run/bernie-follows/and-so-does-jill"));
file.close();
final HDF5File file2 = new HDF5File(testFile, HDF5File.OpenMode.READ_ONLY);
Assert.assertTrue(file2.isPresent("test-group"));
Assert.assertTrue(file2.isPresent("test-group/lola-run"));
Assert.assertTrue(file2.isPresent("test-group/lola-run/bernie-follows"));
Assert.assertFalse(file2.isPresent("test-group/lola-run/jill-follows"));
Assert.assertFalse(file2.isPresent("test-group/lola-run/bernie-follows/and-so-does-jill"));
file2.close();
}
use of org.broadinstitute.hdf5.HDF5File in project gatk-protected by broadinstitute.
the class HDF5LibraryUnitTest method testMakeDoubleMatrix.
@Test()
public void testMakeDoubleMatrix() throws IOException {
final File testFile = File.createTempFile("hdf5", ".hd5");
HDF5File file = new HDF5File(testFile, HDF5File.OpenMode.CREATE);
file.makeGroup("test-group/double-group");
final double[][] testValues = new double[][] { new double[] { 1.1, -2.2, Double.POSITIVE_INFINITY, Double.NEGATIVE_INFINITY, 0.0111e10 - 10 }, new double[] { -1.1, 2.2, Double.NEGATIVE_INFINITY, Double.POSITIVE_INFINITY, -0.01111e10 - 10 } };
Assert.assertTrue(file.makeDoubleMatrix("test-group/double-group/my-double", testValues));
System.err.println(testFile);
file.close();
final long time = System.currentTimeMillis();
Assert.assertTrue(testFile.length() > 0);
Assert.assertTrue(testFile.lastModified() <= time);
file = new HDF5File(testFile, HDF5File.OpenMode.READ_ONLY);
final double[][] theDoubles = file.readDoubleMatrix("test-group/double-group/my-double");
Assert.assertTrue(Arrays.deepEquals(theDoubles, testValues.clone()));
file.close();
}
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