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

Example 11 with TableColumnCollection

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

the class ReadCountCollectionUtils method writerWithIntervals.

/**
     * Creates a new table writer that will output the target intervals.
     * @param writer where to output the table formatted content.
     * @param countColumnNames list of count column names.
     * @return never {@code null}.
     * @throws IOException if there is some low level IO problem creating the writer.
     * @throws IllegalArgumentException if {@code countColumnNames} is {@code null}, contains
     *  {@code null} or a non valid count column name (e.g. a reserved word).
     */
public static TableWriter<ReadCountRecord> writerWithIntervals(final Writer writer, final List<String> countColumnNames) throws IOException {
    final List<String> columnNames = new ArrayList<>();
    columnNames.add(TargetTableColumn.CONTIG.toString());
    columnNames.add(TargetTableColumn.START.toString());
    columnNames.add(TargetTableColumn.END.toString());
    columnNames.add(TargetTableColumn.NAME.toString());
    columnNames.addAll(Utils.nonNull(countColumnNames));
    final TableColumnCollection columns = new TableColumnCollection(columnNames);
    return new TableWriter<ReadCountRecord>(writer, columns) {

        @Override
        protected void composeLine(final ReadCountRecord record, final DataLine dataLine) {
            final SimpleInterval interval = record.getTarget().getInterval();
            if (interval == null) {
                throw new IllegalStateException("invalid combination of targets with and without intervals defined");
            }
            dataLine.append(interval.getContig()).append(interval.getStart()).append(interval.getEnd()).append(record.getTarget().getName());
            record.appendCountsTo(dataLine);
        }
    };
}

Example 12 with TableColumnCollection

use of org.broadinstitute.hellbender.utils.tsv.TableColumnCollection 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 13 with TableColumnCollection

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

Example 14 with TableColumnCollection

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

the class CombineReadCountsIntegrationTest method createTargetFile.

private File createTargetFile(final List<Target> targets) throws IOException {
    final File result = BaseTest.createTempFile("targets", ".tab");
    final TableWriter<Target> writer = TableUtils.writer(result, new TableColumnCollection(TargetTableColumn.CONTIG, TargetTableColumn.START, TargetTableColumn.END, TargetTableColumn.NAME), (t, dataLine) -> {
        final SimpleInterval interval = t.getInterval();
        dataLine.append(interval.getContig()).append(interval.getStart()).append(interval.getEnd()).append(t.getName());
    });
    for (final Target target : targets) writer.writeRecord(target);
    writer.close();
    return result;
}

Example 15 with TableColumnCollection

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

the class CombineReadCountsIntegrationTest method createCountFile.

private void createCountFile(final File output, List<Target> targets, final String sample, final double[] count, final boolean useName, final boolean useCoordinates) throws IOException {
    final List<String> columnNames = new ArrayList<>();
    if (useCoordinates) {
        columnNames.add(TargetTableColumn.CONTIG.toString());
        columnNames.add(TargetTableColumn.START.toString());
        columnNames.add(TargetTableColumn.END.toString());
    }
    if (useName) {
        columnNames.add(TargetTableColumn.NAME.toString());
    }
    columnNames.add(sample);
    final TableColumnCollection columns = new TableColumnCollection(columnNames);
    final TableWriter<Integer> writer = TableUtils.writer(output, columns, (i, d) -> {
        final Target target = targets.get(i);
        final SimpleInterval interval = target.getInterval();
        if (useCoordinates)
            d.append(interval.getContig()).append(interval.getStart()).append(interval.getEnd());
        if (useName)
            d.append(target.getName());
        d.append(count[i]);
    });
    for (int i = 0; i < targets.size(); i++) writer.writeRecord(i);
    writer.close();
}