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Added optional mappability and segmental-duplication annotation to An…
…notateIntervals. (#5162) * Added optional mappability and segmental-duplication annotation to AnnotateIntervals. * Updated AnnotateIntervals task and calls in WDL (untested).
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254 changes: 220 additions & 34 deletions
254
src/main/java/org/broadinstitute/hellbender/tools/copynumber/AnnotateIntervals.java
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40 changes: 40 additions & 0 deletions
40
...n/java/org/broadinstitute/hellbender/tools/copynumber/formats/CopyNumberFormatsUtils.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,11 +1,51 @@ | ||
| package org.broadinstitute.hellbender.tools.copynumber.formats; | ||
|
|
||
| import org.broadinstitute.hellbender.exceptions.UserException; | ||
| import org.broadinstitute.hellbender.utils.io.IOUtils; | ||
| import org.broadinstitute.hellbender.utils.text.XReadLines; | ||
| import org.broadinstitute.hellbender.utils.tsv.TableColumnCollection; | ||
| import org.broadinstitute.hellbender.utils.tsv.TableUtils; | ||
|
|
||
| import java.io.File; | ||
| import java.io.IOException; | ||
| import java.util.Arrays; | ||
| import java.util.List; | ||
|
|
||
| public final class CopyNumberFormatsUtils { | ||
| public static final String COMMENT_PREFIX = "@"; //SAMTextHeaderCodec.HEADER_LINE_START; we need TableReader to treat SAM header as comment lines | ||
| public static final String DOUBLE_FORMAT = "%.6f"; | ||
|
|
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| private CopyNumberFormatsUtils() {} | ||
|
|
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| public static String formatDouble(final double value) { | ||
| return String.format(DOUBLE_FORMAT, value); | ||
| } | ||
|
|
||
| /** | ||
| * Extracts column names from a TSV file | ||
| */ | ||
| public static TableColumnCollection readColumnsFromHeader(final File inputFile) { | ||
| IOUtils.canReadFile(inputFile); | ||
| List<String> columns = null; | ||
| try (final XReadLines reader = new XReadLines(inputFile)) { | ||
| while (reader.hasNext()) { | ||
| String nextLine = reader.next(); | ||
| if (!nextLine.startsWith(COMMENT_PREFIX)) { | ||
| columns = Arrays.asList(nextLine.split(TableUtils.COLUMN_SEPARATOR_STRING)); | ||
| break; | ||
| } | ||
| } | ||
| } catch (final IOException e) { | ||
| throw new UserException.CouldNotReadInputFile(inputFile); | ||
| } | ||
| if (columns == null) { | ||
| throw new UserException.BadInput(String.format( | ||
| "The input file %s does not have a header (starting with comment character %s).", | ||
| inputFile.getAbsolutePath(), COMMENT_PREFIX)); | ||
| } | ||
| if (columns.stream().distinct().count() != columns.size()) { | ||
| throw new UserException.BadInput("Column headers must all be unique."); | ||
| } | ||
| return new TableColumnCollection(columns); | ||
| } | ||
| } |
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171 changes: 148 additions & 23 deletions
171
...nstitute/hellbender/tools/copynumber/formats/collections/AnnotatedIntervalCollection.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,56 +1,181 @@ | ||
| package org.broadinstitute.hellbender.tools.copynumber.formats.collections; | ||
|
|
||
| import org.apache.commons.collections4.ListUtils; | ||
| import org.apache.commons.lang3.tuple.Pair; | ||
| import org.broadinstitute.hellbender.exceptions.UserException; | ||
| import org.broadinstitute.hellbender.tools.copynumber.formats.CopyNumberFormatsUtils; | ||
| import org.broadinstitute.hellbender.tools.copynumber.formats.metadata.LocatableMetadata; | ||
| import org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotatedInterval; | ||
| import org.broadinstitute.hellbender.tools.copynumber.formats.records.AnnotationSet; | ||
| import org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationKey; | ||
| import org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.AnnotationMap; | ||
| import org.broadinstitute.hellbender.tools.copynumber.formats.records.annotation.CopyNumberAnnotations; | ||
| import org.broadinstitute.hellbender.utils.SimpleInterval; | ||
| import org.broadinstitute.hellbender.utils.Utils; | ||
| import org.broadinstitute.hellbender.utils.io.IOUtils; | ||
| import org.broadinstitute.hellbender.utils.tsv.DataLine; | ||
| import org.broadinstitute.hellbender.utils.tsv.TableColumnCollection; | ||
|
|
||
| import java.io.File; | ||
| import java.util.List; | ||
| import java.util.*; | ||
| import java.util.function.BiConsumer; | ||
| import java.util.function.Function; | ||
| import java.util.stream.Collectors; | ||
|
|
||
| /** | ||
| * Represents a collection of intervals annotated with {@link CopyNumberAnnotations}. | ||
| * Supports {@link AnnotationKey}s of integer, long, double, and string type. | ||
| * Can be constructed from a TSV file that contains the standard interval column headers, | ||
| * any subset of the {@link CopyNumberAnnotations}, and additional columns (which are ignored). | ||
| * | ||
| * @author Samuel Lee <[email protected]> | ||
| */ | ||
| public final class AnnotatedIntervalCollection extends AbstractLocatableCollection<LocatableMetadata, AnnotatedInterval> { | ||
| //note to developers: repeat the column headers in Javadoc so that they are viewable when linked | ||
| /** | ||
| * CONTIG, START, END, GC_CONTENT | ||
| * CONTIG, START, END; columns headers for additional annotations can be specified | ||
| */ | ||
| enum AnnotatedIntervalTableColumn { | ||
| CONTIG, | ||
| START, | ||
| END, | ||
| GC_CONTENT; | ||
| END; | ||
|
|
||
| static final TableColumnCollection COLUMNS = new TableColumnCollection((Object[]) values()); | ||
| static final TableColumnCollection STANDARD_COLUMNS = new TableColumnCollection((Object[]) values()); | ||
| } | ||
|
|
||
| enum AnnotationValueType { | ||
| Integer, | ||
| Long, | ||
| Double, | ||
| String | ||
| } | ||
|
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||
| private static final Function<DataLine, AnnotatedInterval> ANNOTATED_INTERVAL_RECORD_FROM_DATA_LINE_DECODER = dataLine -> { | ||
| final String contig = dataLine.get(AnnotatedIntervalTableColumn.CONTIG); | ||
| final int start = dataLine.getInt(AnnotatedIntervalTableColumn.START); | ||
| final int end = dataLine.getInt(AnnotatedIntervalTableColumn.END); | ||
| final double gcContent = dataLine.getDouble(AnnotatedIntervalTableColumn.GC_CONTENT); | ||
| final SimpleInterval interval = new SimpleInterval(contig, start, end); | ||
| final AnnotationSet annotationSet = new AnnotationSet(gcContent); | ||
| return new AnnotatedInterval(interval, annotationSet); | ||
| private static final BiConsumer<AnnotatedInterval, DataLine> ANNOTATED_INTERVAL_RECORD_TO_DATA_LINE_ENCODER = (annotatedInterval, dataLine) -> { | ||
| dataLine.append(annotatedInterval.getInterval().getContig()) | ||
| .append(annotatedInterval.getInterval().getStart()) | ||
| .append(annotatedInterval.getInterval().getEnd()); | ||
| final AnnotationMap annotations = annotatedInterval.getAnnotationMap(); | ||
| for (final AnnotationKey<?> key : annotations.getKeys()) { | ||
| final AnnotationValueType type = AnnotationValueType.valueOf(key.getType().getSimpleName()); | ||
| switch (type) { | ||
| case Integer: | ||
| dataLine.append((Integer) annotations.getValue(key)); | ||
| break; | ||
| case Long: | ||
| dataLine.append((Long) annotations.getValue(key)); | ||
| break; | ||
| case Double: | ||
| dataLine.append(formatDouble((Double) annotations.getValue(key))); | ||
| break; | ||
| case String: | ||
| dataLine.append((String) annotations.getValue(key)); | ||
| break; | ||
| default: | ||
| throw new UserException.BadInput(String.format("Unsupported annotation type: %s", type)); | ||
| } | ||
| } | ||
| }; | ||
|
|
||
| private static final BiConsumer<AnnotatedInterval, DataLine> ANNOTATED_INTERVAL_RECORD_TO_DATA_LINE_ENCODER = (annotatedInterval, dataLine) -> | ||
| dataLine.append(annotatedInterval.getInterval().getContig()) | ||
| .append(annotatedInterval.getInterval().getStart()) | ||
| .append(annotatedInterval.getInterval().getEnd()) | ||
| .append(formatDouble(annotatedInterval.getAnnotationSet().getGCContent())); | ||
|
|
||
| public AnnotatedIntervalCollection(final File inputFile) { | ||
| super(inputFile, AnnotatedIntervalCollection.AnnotatedIntervalTableColumn.COLUMNS, ANNOTATED_INTERVAL_RECORD_FROM_DATA_LINE_DECODER, ANNOTATED_INTERVAL_RECORD_TO_DATA_LINE_ENCODER); | ||
| this(inputFile, getAnnotationKeys(CopyNumberFormatsUtils.readColumnsFromHeader(inputFile))); | ||
| } | ||
|
|
||
| private AnnotatedIntervalCollection(final File inputFile, | ||
| final List<AnnotationKey<?>> annotationKeys) { | ||
| super( | ||
| inputFile, | ||
| getColumns(annotationKeys), | ||
| getAnnotatedIntervalRecordFromDataLineDecoder(annotationKeys), | ||
| ANNOTATED_INTERVAL_RECORD_TO_DATA_LINE_ENCODER); | ||
| } | ||
|
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| public AnnotatedIntervalCollection(final LocatableMetadata metadata, | ||
| final List<AnnotatedInterval> annotatedIntervals) { | ||
| super(metadata, annotatedIntervals, AnnotatedIntervalCollection.AnnotatedIntervalTableColumn.COLUMNS, ANNOTATED_INTERVAL_RECORD_FROM_DATA_LINE_DECODER, ANNOTATED_INTERVAL_RECORD_TO_DATA_LINE_ENCODER); | ||
| super( | ||
| metadata, | ||
| annotatedIntervals, | ||
| getColumns(getAnnotationKeys(annotatedIntervals)), | ||
| getAnnotatedIntervalRecordFromDataLineDecoder(getAnnotationKeys(annotatedIntervals)), | ||
| ANNOTATED_INTERVAL_RECORD_TO_DATA_LINE_ENCODER); | ||
| } | ||
|
|
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| private static TableColumnCollection getColumns(final List<AnnotationKey<?>> annotationKeys) { | ||
| return new TableColumnCollection( | ||
| ListUtils.union( | ||
| AnnotatedIntervalTableColumn.STANDARD_COLUMNS.names(), | ||
| annotationKeys.stream().map(AnnotationKey::getName).collect(Collectors.toList()))); | ||
| } | ||
|
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| private static List<AnnotationKey<?>> getAnnotationKeys(final TableColumnCollection columns) { | ||
| Utils.nonNull(columns); | ||
| Utils.validateArg(columns.columnCount() != 0, "TableColumnCollection cannot be empty."); | ||
| Utils.validateArg(columns.containsAll(AnnotatedIntervalTableColumn.STANDARD_COLUMNS.names()), | ||
| String.format("TableColumnCollection must contain standard columns: %s.", | ||
| AnnotatedIntervalTableColumn.STANDARD_COLUMNS.names())); | ||
| return CopyNumberAnnotations.ANNOTATIONS.stream() | ||
| .filter(a -> columns.contains(a.getName())) | ||
| .collect(Collectors.toList()); | ||
| } | ||
|
|
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| private static List<AnnotationKey<?>> getAnnotationKeys(final List<AnnotatedInterval> annotatedIntervals) { | ||
| return annotatedIntervals.isEmpty() ? new ArrayList<>() : annotatedIntervals.get(0).getAnnotationMap().getKeys(); | ||
| } | ||
|
|
||
| private static Function<DataLine, AnnotatedInterval> getAnnotatedIntervalRecordFromDataLineDecoder( | ||
| final List<AnnotationKey<?>> annotationKeys) { | ||
| return dataLine -> { | ||
| final String contig = dataLine.get(AnnotatedIntervalTableColumn.CONTIG); | ||
| final int start = dataLine.getInt(AnnotatedIntervalTableColumn.START); | ||
| final int end = dataLine.getInt(AnnotatedIntervalTableColumn.END); | ||
| final SimpleInterval interval = new SimpleInterval(contig, start, end); | ||
| final List<Pair<AnnotationKey<?>, Object>> annotations = new ArrayList<>(annotationKeys.size()); | ||
| for (final AnnotationKey<?> key : annotationKeys) { | ||
| final AnnotationValueType type = AnnotationValueType.valueOf(key.getType().getSimpleName()); | ||
| switch (type) { | ||
| case Integer: | ||
| annotations.add(Pair.of(key, dataLine.getInt(key.getName()))); | ||
| break; | ||
| case Long: | ||
| annotations.add(Pair.of(key, dataLine.getLong(key.getName()))); | ||
| break; | ||
| case Double: | ||
| annotations.add(Pair.of(key, dataLine.getDouble(key.getName()))); | ||
| break; | ||
| case String: | ||
| annotations.add(Pair.of(key, dataLine.get(key.getName()))); | ||
| break; | ||
| default: | ||
| throw new UserException.BadInput(String.format("Unsupported annotation type: %s", type)); | ||
| } | ||
| } | ||
| final AnnotationMap annotationMap = new AnnotationMap(annotations); | ||
| return new AnnotatedInterval(interval, annotationMap); | ||
| }; | ||
| } | ||
|
|
||
| /** | ||
| * Columns, encoder, and decoder are not used. | ||
| */ | ||
| @Override | ||
| public boolean equals(Object o) { | ||
| if (this == o) { | ||
| return true; | ||
| } | ||
| if (o == null || getClass() != o.getClass()) { | ||
| return false; | ||
| } | ||
|
|
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| final AbstractRecordCollection<?, ?> that = (AbstractRecordCollection<?, ?>) o; | ||
| return getMetadata().equals(that.getMetadata()) && | ||
| getRecords().equals(that.getRecords()); | ||
| } | ||
|
|
||
| /** | ||
| * Columns, encoder, and decoder are not used. | ||
| */ | ||
| @Override | ||
| public int hashCode() { | ||
| int result = getMetadata().hashCode(); | ||
| result = 31 * result + getRecords().hashCode(); | ||
| return result; | ||
| } | ||
| } | ||
| } |
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