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2,513
src/main/java/org/broadinstitute/hellbender/tools/LocalAssembler.java
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src/main/java/org/broadinstitute/hellbender/tools/PrintDistantMates.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,115 @@ | ||
| package org.broadinstitute.hellbender.tools; | ||
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| import htsjdk.samtools.SAMRecord; | ||
| import htsjdk.samtools.SAMTag; | ||
| import org.broadinstitute.barclay.argparser.Argument; | ||
| import org.broadinstitute.barclay.argparser.CommandLineProgramProperties; | ||
| import org.broadinstitute.barclay.help.DocumentedFeature; | ||
| import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions; | ||
| import org.broadinstitute.hellbender.engine.FeatureContext; | ||
| import org.broadinstitute.hellbender.engine.GATKPath; | ||
| import org.broadinstitute.hellbender.engine.ReadWalker; | ||
| import org.broadinstitute.hellbender.engine.ReferenceContext; | ||
| import org.broadinstitute.hellbender.engine.filters.ReadFilter; | ||
| import org.broadinstitute.hellbender.engine.filters.ReadFilterLibrary; | ||
| import org.broadinstitute.hellbender.exceptions.UserException; | ||
| import org.broadinstitute.hellbender.utils.read.GATKRead; | ||
| import org.broadinstitute.hellbender.utils.read.SAMFileGATKReadWriter; | ||
| import picard.cmdline.programgroups.ReadDataManipulationProgramGroup; | ||
|
|
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| import java.util.*; | ||
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| @CommandLineProgramProperties( | ||
| summary = "Unmaps reads that have distant mates. "+ | ||
| "This ensures that a PairWalker will always see both mates, "+ | ||
| "even when one of them is mapped far away, when given the output "+ | ||
| "of this tool along with the original inputs.", | ||
| oneLineSummary = "Unmaps reads with distant mates.", | ||
| programGroup = ReadDataManipulationProgramGroup.class | ||
| ) | ||
| @DocumentedFeature | ||
| public class PrintDistantMates extends ReadWalker { | ||
| @Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, | ||
| shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, | ||
| doc="Write output to this file") | ||
| public GATKPath output; | ||
| public static String DISTANT_MATE_TAG = "DM"; | ||
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| private SAMFileGATKReadWriter outputWriter; | ||
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| @Override public List<ReadFilter> getDefaultReadFilters() { | ||
| final List<ReadFilter> readFilters = new ArrayList<>(super.getDefaultReadFilters()); | ||
| readFilters.add(ReadFilterLibrary.PAIRED); | ||
| readFilters.add(ReadFilterLibrary.PRIMARY_LINE); | ||
| readFilters.add(ReadFilterLibrary.NOT_DUPLICATE); | ||
| readFilters.add(ReadFilterLibrary.MATE_DISTANT); | ||
| return readFilters; | ||
| } | ||
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| @Override | ||
| public boolean requiresReads() { return true; } | ||
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| @Override | ||
| public void onTraversalStart() { | ||
| outputWriter = createSAMWriter(output, false); | ||
| } | ||
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| @Override | ||
| public void apply( final GATKRead read, | ||
| final ReferenceContext referenceContext, | ||
| final FeatureContext featureContext ) { | ||
| final GATKRead copy = doDistantMateAlterations(read); | ||
| outputWriter.addRead(copy); | ||
| } | ||
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| @Override | ||
| public void closeTool() { | ||
| if ( outputWriter != null ) { | ||
| outputWriter.close(); | ||
| } | ||
| } | ||
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| public static boolean isDistantMate( final GATKRead read ) { | ||
| return read.hasAttribute(DISTANT_MATE_TAG); | ||
| } | ||
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| public static GATKRead doDistantMateAlterations( final GATKRead read ) { | ||
| final GATKRead copy = read.copy(); | ||
| final Integer nmValue = read.getAttributeAsInteger(SAMTag.NM.name()); | ||
| final String oaValue = read.getContig() + "," + read.getStart() + "," + | ||
| (read.isReverseStrand() ? "-," : "+,") + read.getCigar() + "," + | ||
| read.getMappingQuality() + "," + (nmValue == null ? "" : nmValue) + ";"; | ||
| copy.clearAttribute(SAMTag.NM.name()); | ||
| copy.setAttribute(SAMTag.OA.name(), oaValue); | ||
| copy.setAttribute(DISTANT_MATE_TAG, ""); | ||
| copy.setPosition(read.getMateContig(), read.getMateStart()); | ||
| copy.setCigar(SAMRecord.NO_ALIGNMENT_CIGAR); | ||
| copy.setMappingQuality(0); | ||
| copy.setIsUnmapped(); | ||
| return copy; | ||
| } | ||
|
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| public static GATKRead undoDistantMateAlterations( final GATKRead read ) { | ||
| final String oaValue = read.getAttributeAsString(SAMTag.OA.name()); | ||
| if ( oaValue == null ) { | ||
| return read; | ||
| } | ||
| final GATKRead copy = read.copy(); | ||
| copy.clearAttribute(DISTANT_MATE_TAG); | ||
| copy.clearAttribute(SAMTag.OA.name()); | ||
| try { | ||
| final String[] tokens = oaValue.split(","); | ||
| copy.setPosition(tokens[0], Integer.parseInt(tokens[1])); | ||
| copy.setIsReverseStrand("-".equals(tokens[2])); | ||
| copy.setCigar(tokens[3]); | ||
| copy.setMappingQuality(Integer.parseInt(tokens[4])); | ||
| if ( tokens[5].length() > 1 ) { | ||
| final String nmValue = tokens[5].substring(0, tokens[5].length() - 1); | ||
| copy.setAttribute(SAMTag.NM.name(), Integer.parseInt(nmValue)); | ||
| } | ||
| } catch ( final Exception exc ) { | ||
| throw new UserException("can't recover alignment from OA tag: " + oaValue, exc); | ||
| } | ||
| return copy; | ||
| } | ||
| } |
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