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Added Called Legacy Segment code (#5115)
- Added functionality to generate legacy format (IGV-compatible) seg files automatically when calling copy ratio segments. Closes #5114 - Updates the WDL as well to expose the new output files.
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102 changes: 102 additions & 0 deletions
102
...titute/hellbender/tools/copynumber/formats/collections/CalledLegacySegmentCollection.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,102 @@ | ||
| package org.broadinstitute.hellbender.tools.copynumber.formats.collections; | ||
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| import org.apache.commons.lang3.StringUtils; | ||
| import org.broadinstitute.hellbender.exceptions.UserException; | ||
| import org.broadinstitute.hellbender.tools.copynumber.formats.metadata.SampleLocatableMetadata; | ||
| import org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledCopyRatioSegment; | ||
| import org.broadinstitute.hellbender.tools.copynumber.formats.records.CalledLegacySegment; | ||
| import org.broadinstitute.hellbender.utils.SimpleInterval; | ||
| import org.broadinstitute.hellbender.utils.tsv.DataLine; | ||
| import org.broadinstitute.hellbender.utils.tsv.TableColumnCollection; | ||
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| import java.io.File; | ||
| import java.io.FileWriter; | ||
| import java.io.IOException; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
| import java.util.function.BiConsumer; | ||
| import java.util.function.Function; | ||
| import java.util.stream.Stream; | ||
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| /** | ||
| * Represents a CBS-style segmentation to enable IGV-compatible plotting. | ||
| * | ||
| * IGV ignores column headers and requires that no other headers are present. | ||
| * We use the conventional CBS-style column headers (which includes the sample name) | ||
| * and suppress the SAM-style metadata header (which breaks the contract for construction from input files). | ||
| * See <a href="http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#CBS"> | ||
| * http://software.broadinstitute.org/cancer/software/genepattern/file-formats-guide#CBS</a> | ||
| * and <a href="https://software.broadinstitute.org/software/igv/SEG"> | ||
| * https://software.broadinstitute.org/software/igv/SEG</a>. | ||
| */ | ||
| public final class CalledLegacySegmentCollection extends AbstractSampleLocatableCollection<CalledLegacySegment> { | ||
| //note to developers: repeat the column headers in Javadoc so that they are viewable when linked | ||
| /** | ||
| * Sample, Chromosome, Start, End, Num_Probes, Call, Segment_Mean | ||
| */ | ||
| enum CalledLegacySegmentTableColumn { | ||
| SAMPLE("Sample"), | ||
| CHROMOSOME("Chromosome"), | ||
| START("Start"), | ||
| END("End"), | ||
| NUM_PROBES("Num_Probes"), | ||
| CALL("Call"), | ||
| SEGMENT_MEAN("Segment_Mean"); | ||
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| private final String columnName; | ||
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| CalledLegacySegmentTableColumn(final String columnName) { | ||
| this.columnName = columnName; | ||
| } | ||
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| static final TableColumnCollection COLUMNS = new TableColumnCollection( | ||
| Stream.of(values()).map(c -> c.columnName).toArray()); | ||
| } | ||
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| private static final Function<DataLine, CalledLegacySegment> CALLED_LEGACY_SEGMENT_DATA_LINE_TO_RECORD_FUNCTION = dataLine -> { | ||
| final String sampleName = dataLine.get(CalledLegacySegmentTableColumn.SAMPLE.columnName); | ||
| final String contig = dataLine.get(CalledLegacySegmentTableColumn.CHROMOSOME.columnName); | ||
| final int start = dataLine.getInt(CalledLegacySegmentTableColumn.START.columnName); | ||
| final int end = dataLine.getInt(CalledLegacySegmentTableColumn.END.columnName); | ||
| final int numProbes = dataLine.getInt(CalledLegacySegmentTableColumn.NUM_PROBES.columnName); | ||
| final double segmentMean = dataLine.getDouble(CalledLegacySegmentTableColumn.SEGMENT_MEAN.columnName); | ||
| final String callOutputString = dataLine.get(CalledCopyRatioSegmentCollection.CalledCopyRatioSegmentTableColumn.CALL); | ||
| final CalledCopyRatioSegment.Call call = Arrays.stream(CalledCopyRatioSegment.Call.values()) | ||
| .filter(c -> c.getOutputString().equals(callOutputString)).findFirst().orElseThrow( | ||
| () -> new UserException("Attempting to read an invalid value for " + | ||
| CalledLegacySegmentTableColumn.CALL +": " + callOutputString + | ||
| ". Valid values are " + StringUtils.join(CalledCopyRatioSegment.Call.values(), ", ") | ||
| )); | ||
| final SimpleInterval interval = new SimpleInterval(contig, start, end); | ||
| return new CalledLegacySegment(sampleName, interval, numProbes, segmentMean, call); | ||
| }; | ||
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| private static final BiConsumer<CalledLegacySegment, DataLine> CALLED_LEGACY_SEGMENT_RECORD_AND_DATA_LINE_BI_CONSUMER = (calledLegacySegment, dataLine) -> | ||
| dataLine.append(calledLegacySegment.getSampleName()) | ||
| .append(calledLegacySegment.getContig()) | ||
| .append(calledLegacySegment.getStart()) | ||
| .append(calledLegacySegment.getEnd()) | ||
| .append(calledLegacySegment.getNumProbes()) | ||
| .append(calledLegacySegment.getCall().getOutputString()) | ||
| .append(formatDouble(calledLegacySegment.getSegmentMean())); | ||
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| public CalledLegacySegmentCollection(final SampleLocatableMetadata metadata, | ||
| final List<CalledLegacySegment> calledLegacySegments) { | ||
| super(metadata, calledLegacySegments, CalledLegacySegmentTableColumn.COLUMNS, CALLED_LEGACY_SEGMENT_DATA_LINE_TO_RECORD_FUNCTION, CALLED_LEGACY_SEGMENT_RECORD_AND_DATA_LINE_BI_CONSUMER); | ||
| } | ||
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| public CalledLegacySegmentCollection(final File inputFile) { | ||
| super(inputFile, CopyRatioSegmentCollection.CopyRatioSegmentTableColumn.COLUMNS, CALLED_LEGACY_SEGMENT_DATA_LINE_TO_RECORD_FUNCTION, CALLED_LEGACY_SEGMENT_RECORD_AND_DATA_LINE_BI_CONSUMER); | ||
| } | ||
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| // output of SAM-style header is suppressed | ||
| @Override | ||
| public void write(final File outputFile) { | ||
| try (final RecordWriter recordWriter = new RecordWriter(new FileWriter(outputFile, true))) { | ||
| recordWriter.writeAllRecords(getRecords()); | ||
| } catch (final IOException e) { | ||
| throw new UserException.CouldNotCreateOutputFile(outputFile, e); | ||
| } | ||
| } | ||
| } |
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53 changes: 53 additions & 0 deletions
53
...a/org/broadinstitute/hellbender/tools/copynumber/formats/records/CalledLegacySegment.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| package org.broadinstitute.hellbender.tools.copynumber.formats.records; | ||
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| import org.broadinstitute.hellbender.utils.SimpleInterval; | ||
| import org.broadinstitute.hellbender.utils.Utils; | ||
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| public class CalledLegacySegment extends LegacySegment { | ||
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| private final CalledCopyRatioSegment.Call call; | ||
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| public CalledLegacySegment(final String sampleName, final SimpleInterval interval, final int numProbes, | ||
| final double segmentMean, | ||
| final CalledCopyRatioSegment.Call call) { | ||
| super(sampleName, interval, numProbes, segmentMean); | ||
| Utils.nonNull(call, "Cannot initialize a called legacy segment with a null call."); | ||
| this.call = call; | ||
| } | ||
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| public CalledCopyRatioSegment.Call getCall() { | ||
| return call; | ||
| } | ||
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| @Override | ||
| public final boolean equals(final Object o) { | ||
| if (this == o) { | ||
| return true; | ||
| } | ||
| if (o == null || getClass() != o.getClass()) { | ||
| return false; | ||
| } | ||
| if (!super.equals(o)) { | ||
| return false; | ||
| } | ||
| final CalledLegacySegment that = (CalledLegacySegment) o; | ||
| return call == that.call; | ||
| } | ||
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| @Override | ||
| public final int hashCode() { | ||
| int result = super.hashCode(); | ||
| result = 31 * result + call.hashCode(); | ||
| return result; | ||
| } | ||
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| @Override | ||
| public final String toString() { | ||
| return "CalledLegacySegment{" + | ||
| "interval=" + getInterval() + | ||
| ", numPoints=" + getNumProbes() + | ||
| ", meanLog2CopyRatio=" + getSegmentMean() + | ||
| ", call=" + call + | ||
| '}'; | ||
| } | ||
| } |
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