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

Example 1 with TableWriter

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

the class ReadCountCollectionUtils method createReadCountRecordTableWriterWithoutIntervals.

private static TableWriter<ReadCountRecord> createReadCountRecordTableWriterWithoutIntervals(final Writer writer, List<String> columnNames) throws IOException {
    final TableColumnCollection columns = new TableColumnCollection(columnNames);
    return new TableWriter<ReadCountRecord>(writer, columns) {

        @Override
        protected void composeLine(final ReadCountRecord record, final DataLine dataLine) {
            dataLine.append(record.getTarget().getName());
            record.appendCountsTo(dataLine);
        }
    };
}

Example 2 with TableWriter

use of org.broadinstitute.hellbender.utils.tsv.TableWriter in project gatk-protected 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 3 with TableWriter

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

the class ReadCountCollectionUtils method createReadCountRecordTableWriterWithoutIntervals.

private static TableWriter<ReadCountRecord> createReadCountRecordTableWriterWithoutIntervals(final Writer writer, List<String> columnNames) throws IOException {
    final TableColumnCollection columns = new TableColumnCollection(columnNames);
    return new TableWriter<ReadCountRecord>(writer, columns) {

        @Override
        protected void composeLine(final ReadCountRecord record, final DataLine dataLine) {
            dataLine.append(record.getTarget().getName());
            record.appendCountsTo(dataLine);
        }
    };
}

Example 4 with TableWriter

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

the class XHMMSegmentCallerBaseIntegrationTest method writeChainInTempFile.

public static File writeChainInTempFile(final XHMMData chain) {
    final File result = createTempFile("chain-", ".tab");
    //final File result = new File("/tmp/input");
    final List<String> sampleNames = IntStream.range(0, chain.data.size()).mapToObj(a -> "SAMPLE_" + a).collect(Collectors.toList());
    final List<String> columnNames = new ArrayList<>(sampleNames.size() + 4);
    columnNames.addAll(Arrays.asList(TargetTableColumn.CONTIG.toString(), TargetTableColumn.START.toString(), TargetTableColumn.END.toString(), TargetTableColumn.NAME.toString()));
    columnNames.addAll(sampleNames);
    try (final TableWriter<Integer> writer = new TableWriter<Integer>(result, new TableColumnCollection(columnNames)) {

        @Override
        protected void composeLine(final Integer record, final DataLine dataLine) {
            dataLine.append(chain.targets.get(record).getContig()).append(chain.targets.get(record).getStart()).append(chain.targets.get(record).getEnd()).append(chain.targets.get(record).getName());
            for (final List<Double> sampleData : chain.data) {
                dataLine.append(sampleData.get(record));
            }
        }
    }) {
        writer.writeAllRecords(IntStream.range(0, chain.targets.size()).boxed().collect(Collectors.toList()));
    } catch (final IOException ex) {
        throw new UncheckedIOException(ex);
    }
    return result;
}

Example 5 with TableWriter

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

the class XHMMSegmentCallerBaseIntegrationTest method writeChainInTempFile.

public static File writeChainInTempFile(final XHMMData chain) {
    final File result = createTempFile("chain-", ".tab");
    //final File result = new File("/tmp/input");
    final List<String> sampleNames = IntStream.range(0, chain.data.size()).mapToObj(a -> "SAMPLE_" + a).collect(Collectors.toList());
    final List<String> columnNames = new ArrayList<>(sampleNames.size() + 4);
    columnNames.addAll(Arrays.asList(TargetTableColumn.CONTIG.toString(), TargetTableColumn.START.toString(), TargetTableColumn.END.toString(), TargetTableColumn.NAME.toString()));
    columnNames.addAll(sampleNames);
    try (final TableWriter<Integer> writer = new TableWriter<Integer>(result, new TableColumnCollection(columnNames)) {

        @Override
        protected void composeLine(final Integer record, final DataLine dataLine) {
            dataLine.append(chain.targets.get(record).getContig()).append(chain.targets.get(record).getStart()).append(chain.targets.get(record).getEnd()).append(chain.targets.get(record).getName());
            for (final List<Double> sampleData : chain.data) {
                dataLine.append(sampleData.get(record));
            }
        }
    }) {
        writer.writeAllRecords(IntStream.range(0, chain.targets.size()).boxed().collect(Collectors.toList()));
    } catch (final IOException ex) {
        throw new UncheckedIOException(ex);
    }
    return result;
}