本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.getReadGroup()方法的一些代码示例，展示了GATKSAMRecord.getReadGroup()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。GATKSAMRecord.getReadGroup()方法的具体详情如下：
包路径：org.broadinstitute.gatk.utils.sam.GATKSAMRecord
类名称：GATKSAMRecord
方法名：getReadGroup

GATKSAMRecord.getReadGroup介绍

[英]Get the GATKSAMReadGroupRecord of this read
[中]获取此读取的GATKSAMReadGroupRecord

代码示例

代码示例来源：origin: broadgsa/gatk

/**
 * Efficient caching accessor that returns the GATK NGSPlatform of this read
 * @return
 */
public NGSPlatform getNGSPlatform() {
  return getReadGroup().getNGSPlatform();
}

代码示例来源：origin: broadgsa/gatk

/**
 * Convenience get -- get the NGSPlatform from a GATKSAMRecord.
 *
 * Just gets the platform from the GATKReadGroupRecord associated with this read.
 *
 * @param read a non-null GATKSAMRecord
 * @return an NGSPlatform object matching the PL field of the header, of UNKNOWN if there was no match,
 *         if there is no read group for read, or there's no PL field for the read group
 */
public static NGSPlatform fromRead(final GATKSAMRecord read) {
  if ( read == null ) throw new IllegalArgumentException("read cannot be null");
  final GATKSAMReadGroupRecord rg = read.getReadGroup();
  return rg == null ? UNKNOWN : rg.getNGSPlatform();
}

代码示例来源：origin: broadgsa/gatk-protected

private boolean isReadFromNormal(final GATKSAMRecord rec) {
  return normalSampleName != null && normalSampleName.equals(rec.getReadGroup().getSample());
}

代码示例来源：origin: broadgsa/gatk

/**
 * checks if the read has a platform tag in the readgroup equal to 'name'.
 * Assumes that 'name' is upper-cased.
 *
 * @param read the read to test
 * @param name the upper-cased platform name to test
 * @return whether or not name == PL tag in the read group of read
 */
public static boolean isPlatformRead(GATKSAMRecord read, String name) {
  SAMReadGroupRecord readGroup = read.getReadGroup();
  if (readGroup != null) {
    Object readPlatformAttr = readGroup.getAttribute("PL");
    if (readPlatformAttr != null)
      return readPlatformAttr.toString().toUpperCase().contains(name);
  }
  return false;
}

代码示例来源：origin: broadgsa/gatk

public Collection<String> getSamples() {
  if (pileupElementTracker instanceof PerSamplePileupElementTracker) {
    PerSamplePileupElementTracker<PileupElement> tracker = (PerSamplePileupElementTracker<PileupElement>) pileupElementTracker;
    return new HashSet<String>(tracker.getSamples());
  } else {
    Collection<String> sampleNames = new HashSet<String>();
    for (PileupElement p : this) {
      GATKSAMRecord read = p.getRead();
      String sampleName = read.getReadGroup() != null ? read.getReadGroup().getSample() : null;
      sampleNames.add(sampleName);
    }
    return sampleNames;
  }
}

代码示例来源：origin: broadgsa/gatk

/**
 * Gets a list of the read groups represented in this pileup.
 *
 * @return
 */
@Override
public Collection<String> getReadGroups() {
  Set<String> readGroups = new HashSet<String>();
  for (PileupElement pileupElement : this)
    readGroups.add(pileupElement.getRead().getReadGroup().getReadGroupId());
  return readGroups;
}

代码示例来源：origin: broadgsa/gatk-protected

public static Map<String, List<GATKSAMRecord>> splitReadsBySample( final SampleList samplesList, final Collection<GATKSAMRecord> reads ) {
  final Map<String, List<GATKSAMRecord>> returnMap = new HashMap<>();
  final int sampleCount = samplesList.sampleCount();
  for (int i = 0; i < sampleCount; i++)
    returnMap.put(samplesList.sampleAt(i), new ArrayList<GATKSAMRecord>());
  for( final GATKSAMRecord read : reads )
    returnMap.get(read.getReadGroup().getSample()).add(read);
  return returnMap;
}

代码示例来源：origin: broadgsa/gatk

@Override
public Integer map(final ReferenceContext referenceContext,final GATKSAMRecord samRecord,final RefMetaDataTracker RefMetaDataTracker) {
  final int length = Math.abs(samRecord.getReadLength());
  final SAMReadGroupRecord rg = samRecord.getReadGroup();
  increment(table,length, rg);
  return null;
}

代码示例来源：origin: broadgsa/gatk-protected

private void removeReadsFromAllSamplesExcept(final String targetSample, final ActiveRegion activeRegion) {
  final Set<GATKSAMRecord> readsToRemove = new LinkedHashSet<>();
  for( final GATKSAMRecord rec : activeRegion.getReads() ) {
    if( !rec.getReadGroup().getSample().equals(targetSample) ) {
      readsToRemove.add(rec);
    }
  }
  activeRegion.removeAll( readsToRemove );
}

代码示例来源：origin: broadgsa/gatk

public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
  if ( ! newSampleName.equals(read.getReadGroup().getSample()) ) {
    throw new IllegalStateException(String.format("Encountered read with the wrong sample name. Expected %s found %s",
                           newSampleName, read.getReadGroup().getSample()));
  }
  return 1;
}

代码示例来源：origin: broadgsa/gatk-protected

private Set<GATKSAMRecord> filterNonPassingReads( final ActiveRegion activeRegion ) {
  final Set<GATKSAMRecord> readsToRemove = new LinkedHashSet<>();
  for( final GATKSAMRecord rec : activeRegion.getReads() ) {
    if( rec.getReadLength() < READ_LENGTH_FILTER_THRESHOLD || rec.getMappingQuality() < READ_QUALITY_FILTER_THRESHOLD || (!isBadMateFilterDisabled && BadMateFilter.hasBadMate(rec)) || (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
      readsToRemove.add(rec);
    }
  }
  activeRegion.removeAll( readsToRemove );
  return readsToRemove;
}

代码示例来源：origin: broadgsa/gatk

@Override
public ReadBackedPileup getPileupForSample(String sampleName) {
  if (pileupElementTracker instanceof PerSamplePileupElementTracker) {
    PerSamplePileupElementTracker<PileupElement> tracker = (PerSamplePileupElementTracker<PileupElement>) pileupElementTracker;
    PileupElementTracker<PileupElement> filteredElements = tracker.getElements(sampleName);
    return filteredElements != null ? createNewPileup(loc, filteredElements) : null;
  } else {
    UnifiedPileupElementTracker<PileupElement> filteredTracker = new UnifiedPileupElementTracker<PileupElement>();
    for (PileupElement p : pileupElementTracker) {
      GATKSAMRecord read = p.getRead();
      if (sampleName != null) {
        if (read.getReadGroup() != null && sampleName.equals(read.getReadGroup().getSample()))
          filteredTracker.add(p);
      } else {
        if (read.getReadGroup() == null || read.getReadGroup().getSample() == null)
          filteredTracker.add(p);
      }
    }
    return filteredTracker.size() > 0 ? createNewPileup(loc, filteredTracker) : null;
  }
}

代码示例来源：origin: broadgsa/gatk

@Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
  final String readGroupId = readGroupValueFromRG(read.getReadGroup());
  final int key = keyForReadGroup(readGroupId);
  final int l = read.getReadLength();
  for (int i = 0; i < l; i++)
    values.addCovariate(key, key, key, i);
}

代码示例来源：origin: broadgsa/gatk-protected

protected Set<GATKSAMRecord> filterNonPassingReads( final ActiveRegion activeRegion) {
  final Set<GATKSAMRecord> readsToRemove = new LinkedHashSet<>();
  for( final GATKSAMRecord rec : activeRegion.getReads() ) {
    //TODO: Takuto points out that this is questionable.  Let's think hard abut it.
    // KCIBUL: only perform read quality filtering on tumor reads...
    if (isReadFromNormal(rec)) {
      if( rec.getReadLength() < MIN_READ_LENGTH ) {
        readsToRemove.add(rec);
      }
    } else if( rec.getReadLength() < MIN_READ_LENGTH || rec.getMappingQuality() < MQthreshold || BadMateFilter.hasBadMate(rec) ||
        (keepRG != null && !rec.getReadGroup().getId().equals(keepRG)) ) {
      readsToRemove.add(rec);
    }
  }
  activeRegion.removeAll(readsToRemove);
  return readsToRemove;
}

代码示例来源：origin: broadgsa/gatk

@Override
public Integer map(ReferenceContext referenceContext, GATKSAMRecord read, RefMetaDataTracker RefMetaDataTracker) {
  final String rgID = read.getReadGroup().getId();
  final PerReadGroupInfo info = readGroupInfo.get(rgID);
  if ( info.needsMoreData() ) {
    info.readLength.add(read.getReadLength());
    info.nReadsSeen++;
    if ( read.getReadPairedFlag() ) {
      info.nReadsPaired++;
      if ( read.getInferredInsertSize() != 0) {
        info.insertSize.add(Math.abs(read.getInferredInsertSize()));
      }
    }
  }
  return null;
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = !DEBUG, dataProvider = "MergeFragmentsTest")
public void testMergingTwoReads(final String name, final GATKSAMRecord read1, final GATKSAMRecord read2, final GATKSAMRecord expectedMerged) {
  final GATKSAMRecord actual = FragmentUtils.mergeOverlappingPairedFragments(read1, read2);
  if ( expectedMerged == null ) {
    Assert.assertNull(actual, "Expected reads not to merge, but got non-null result from merging");
  } else {
    Assert.assertTrue(actual.isStrandless(), "Merged reads should be strandless");
    Assert.assertNotNull(actual, "Expected reads to merge, but got null result from merging");
    // I really care about the bases, the quals, the CIGAR, and the read group tag
    Assert.assertEquals(actual.getCigarString(), expectedMerged.getCigarString());
    Assert.assertEquals(actual.getReadBases(), expectedMerged.getReadBases());
    Assert.assertEquals(actual.getReadGroup(), expectedMerged.getReadGroup());
    Assert.assertEquals(actual.getMappingQuality(), expectedMerged.getMappingQuality());
    for ( final EventType type : EventType.values() )
      Assert.assertEquals(actual.getBaseQualities(type), expectedMerged.getBaseQualities(type), "Failed base qualities for event type " + type);
  }
}

代码示例来源：origin: broadgsa/gatk

/**
 * Clears all attributes except ReadGroup of the read.
 */
public GATKSAMRecord simplify () {
  GATKSAMReadGroupRecord rg = getReadGroup(); // save the read group information
  byte[] insQuals = (this.getAttribute(BQSR_BASE_INSERTION_QUALITIES) == null) ? null : getBaseInsertionQualities();
  byte[] delQuals = (this.getAttribute(BQSR_BASE_DELETION_QUALITIES)  == null) ? null : getBaseDeletionQualities();
  this.clearAttributes(); // clear all attributes from the read
  this.setReadGroup(rg); // restore read group
  if (insQuals != null)
    this.setBaseQualities(insQuals, EventType.BASE_INSERTION); // restore base insertion if we had any
  if (delQuals != null)
    this.setBaseQualities(delQuals, EventType.BASE_DELETION); // restore base deletion if we had any
  return this;
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = true)
  public void testMaxCyclePasses() {
    int readLength = RAC.MAXIMUM_CYCLE_VALUE;
    GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
    read.setReadPairedFlag(true);
    read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
    read.getReadGroup().setPlatform("illumina");

    ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
    covariate.recordValues(read, readCovariates);
  }
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = true, expectedExceptions={UserException.class})
public void testMoreThanMaxCycleFails() {
  int readLength = RAC.MAXIMUM_CYCLE_VALUE + 1;
  GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
  read.setReadPairedFlag(true);
  read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
  read.getReadGroup().setPlatform("illumina");
  ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
  covariate.recordValues(read, readCovariates);
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = true)
public void testSimpleCycles() {
  short readLength = 10;
  GATKSAMRecord read = ReadUtils.createRandomRead(readLength);
  read.setReadPairedFlag(true);
  read.setReadGroup(new GATKSAMReadGroupRecord("MY.ID"));
  read.getReadGroup().setPlatform("illumina");
  ReadCovariates readCovariates = new ReadCovariates(read.getReadLength(), 1);
  covariate.recordValues(read, readCovariates);
  verifyCovariateArray(readCovariates.getMismatchesKeySet(), 1, (short) 1);
  read.setReadNegativeStrandFlag(true);
  covariate.recordValues(read, readCovariates);
  verifyCovariateArray(readCovariates.getMismatchesKeySet(), readLength, -1);
  read.setSecondOfPairFlag(true);
  covariate.recordValues(read, readCovariates);
  verifyCovariateArray(readCovariates.getMismatchesKeySet(), -readLength, 1);
  read.setReadNegativeStrandFlag(false);
  covariate.recordValues(read, readCovariates);
  verifyCovariateArray(readCovariates.getMismatchesKeySet(), -1, -1);
}