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

Example 16 with TableColumnCollection

use of org.broadinstitute.hellbender.utils.tsv.TableColumnCollection in project gatk by broadinstitute.

the class PCATangentNormalizationResult method writeTangentBetaHats.

/**
     * Write the beta-hats.
     * If the output file is null, we do not write a file.
     */
private void writeTangentBetaHats(final File file, final String commandLine) {
    if (file == null) {
        return;
    }
    final List<String> countColumnNames = targetFactorNormalizedCounts.columnNames();
    final List<String> columnNames = new ArrayList<>(countColumnNames.size() + 1);
    columnNames.add(PON_SAMPLE_BETA_HAT_COLUMN_NAME);
    columnNames.addAll(countColumnNames);
    final TableColumnCollection columns = new TableColumnCollection(columnNames);
    try (final TableWriter<Integer> writer = TableUtils.writer(file, columns, (i, dataLine) -> dataLine.append(Integer.toString(i)).append(tangentBetaHats.getRow(i)))) {
        writer.writeComment("fileFormat  = tsv");
        writer.writeComment("commandLine = " + commandLine);
        writer.writeComment("title = Tangent normalization Beta Hats");
        for (int i = 0; i < tangentBetaHats.getRowDimension(); i++) {
            writer.writeRecord(i);
        }
    } catch (final IOException ex) {
        throw new UserException.CouldNotCreateOutputFile(file, ex.getMessage());
    }
}

Example 17 with TableColumnCollection

use of org.broadinstitute.hellbender.utils.tsv.TableColumnCollection in project gatk 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);
}

Example 18 with TableColumnCollection

use of org.broadinstitute.hellbender.utils.tsv.TableColumnCollection in project gatk 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 19 with TableColumnCollection

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

the class PCATangentNormalizationResult method writeTangentBetaHats.

/**
     * Write the beta-hats.
     * If the output file is null, we do not write a file.
     */
private void writeTangentBetaHats(final File file, final String commandLine) {
    if (file == null) {
        return;
    }
    final List<String> countColumnNames = targetFactorNormalizedCounts.columnNames();
    final List<String> columnNames = new ArrayList<>(countColumnNames.size() + 1);
    columnNames.add(PON_SAMPLE_BETA_HAT_COLUMN_NAME);
    columnNames.addAll(countColumnNames);
    final TableColumnCollection columns = new TableColumnCollection(columnNames);
    try (final TableWriter<Integer> writer = TableUtils.writer(file, columns, (i, dataLine) -> dataLine.append(Integer.toString(i)).append(tangentBetaHats.getRow(i)))) {
        writer.writeComment("fileFormat  = tsv");
        writer.writeComment("commandLine = " + commandLine);
        writer.writeComment("title = Tangent normalization Beta Hats");
        for (int i = 0; i < tangentBetaHats.getRowDimension(); i++) {
            writer.writeRecord(i);
        }
    } catch (final IOException ex) {
        throw new UserException.CouldNotCreateOutputFile(file, ex.getMessage());
    }
}

Example 20 with TableColumnCollection

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

the class SexGenotypeDataCollection method write.

/**
     * Write the collection to a writer. If extended genotyping inference data is available, they will
     * be also written as optional columns.
     *
     * @param dataWriter an instance of {@link Writer}
     */
public void write(@Nonnull final Writer dataWriter) {
    if (sexGenotypeDataList.isEmpty()) {
        throw new IllegalStateException("The sex genotype data collection is empty");
    }
    /* check if extended genotyping information is available; first, check for nulls */
    boolean extended = true;
    if (sexGenotypeDataList.stream().filter(dat -> !dat.hasExtendedGenotypingInfo()).count() > 0) {
        extended = false;
    }
    Set<String> commonGenotypes = new HashSet<>();
    /* check if there is a non-empty intersection */
    if (extended) {
        /* pool all genotypes */
        commonGenotypes = new HashSet<>(sexGenotypeDataList.get(0).getSexGenotypesSet());
        for (final SexGenotypeData dat : sexGenotypeDataList) {
            commonGenotypes = Sets.intersection(commonGenotypes, dat.getSexGenotypesSet());
        }
        if (commonGenotypes.isEmpty()) {
            extended = false;
        }
    }
    final TableColumnCollection columns;
    if (extended) {
        final List<String> columnNames = new ArrayList<>();
        columnNames.addAll(SexGenotypeTableColumn.MANDATORY_SEX_GENOTYPE_COLUMNS.names());
        columnNames.addAll(commonGenotypes);
        columns = new TableColumnCollection(columnNames);
    } else {
        columns = new TableColumnCollection(SexGenotypeTableColumn.MANDATORY_SEX_GENOTYPE_COLUMNS.names());
    }
    try (final SexGenotypeTableWriter writer = new SexGenotypeTableWriter(dataWriter, columns)) {
        writer.writeAllRecords(sexGenotypeDataList);
    } catch (final IOException e) {
        throw new UserException.CouldNotCreateOutputFile("Could not write sex genotype data", e);
    }
}