Examples with DataLine org.broadinstitute.hellbender.utils.tsv.DataLine used on opensource projects

Example 11 with DataLine

use of org.broadinstitute.hellbender.utils.tsv.DataLine in project gatk-protected by broadinstitute.

the class ReadCountRecordUnitTest method testAppendCountsTo.

@Test(dataProvider = "testData", dependsOnMethods = "testCreation")
public void testAppendCountsTo(@SuppressWarnings("unused") final String testName, final BiFunction<Target, double[], ? extends ReadCountRecord> constructor, final int size) {
    final double[] counts = generateCounts(size);
    final boolean round = testName.equals("long[]");
    final ReadCountRecord record = constructor.apply(TEST_TARGET, counts);
    final List<String> columnNames = Stream.concat(Stream.concat(IntStream.range(0, 10).mapToObj(i -> "pre-padding_" + i), IntStream.range(0, counts.length).mapToObj(i -> "column_" + i)), IntStream.range(0, 10).mapToObj(i -> "post-padding_" + i)).collect(Collectors.toList());
    final TableColumnCollection columns = new TableColumnCollection(columnNames);
    final DataLine dataLine = new DataLine(columns, RuntimeException::new);
    final double[] copiedCounts = new double[counts.length + 20];
    Arrays.fill(copiedCounts, -11);
    for (int i = 0; i < 10 + 10 + counts.length; i++) {
        dataLine.append("-11");
    }
    dataLine.seek(10);
    record.appendCountsTo(dataLine);
    // Check the copied values.
    if (!round) {
        for (int i = 0; i < counts.length; i++) {
            Assert.assertEquals(dataLine.getDouble(10 + i), counts[i], 0.0);
        }
    } else {
        for (int i = 0; i < counts.length; i++) {
            Assert.assertEquals(dataLine.getDouble(10 + i), Math.round(counts[i]), 0.00001);
        }
    }
    // Check that the padding remains intact:
    for (int i = 0; i < 10; i++) {
        Assert.assertEquals(dataLine.get(i), "-11");
    }
    for (int i = counts.length + 10; i < copiedCounts.length; i++) {
        Assert.assertEquals(dataLine.get(i), "-11");
    }
}

Example 12 with DataLine

use of org.broadinstitute.hellbender.utils.tsv.DataLine in project gatk-protected by broadinstitute.

the class ReadCountRecordUnitTest method testAppendCountsToBeyondEnd.

@Test(dataProvider = "testNonZeroCountsData", dependsOnMethods = "testAppendCountsTo", expectedExceptions = IllegalStateException.class)
public void testAppendCountsToBeyondEnd(@SuppressWarnings("unused") final String testName, final BiFunction<Target, double[], ? extends ReadCountRecord> constructor, final int size) {
    final double[] counts = generateCounts(size);
    final ReadCountRecord record = constructor.apply(TEST_TARGET, counts);
    final List<String> columnNames = Stream.concat(Stream.concat(IntStream.range(0, 10).mapToObj(i -> "pre-padding_" + i), IntStream.range(0, counts.length).mapToObj(i -> "column_" + i)), IntStream.range(0, 10).mapToObj(i -> "post-padding_" + i)).collect(Collectors.toList());
    final TableColumnCollection columns = new TableColumnCollection(columnNames);
    final DataLine dataLine = new DataLine(columns, RuntimeException::new);
    final double[] copiedCounts = new double[counts.length + 20];
    Arrays.fill(copiedCounts, -11);
    dataLine.seek(columnNames.size());
    record.appendCountsTo(dataLine);
}