本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.getSoftEnd()方法的一些代码示例，展示了GATKSAMRecord.getSoftEnd()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.getSoftEnd()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：getSoftEnd

GATKSAMRecord.getSoftEnd介绍

[英]Calculates the reference coordinate for the end of the read taking into account soft clips but not hard clips. Note: getUnclippedEnd() adds soft and hard clips, this function only adds soft clips.
[中]计算读取结束时的参考坐标，同时考虑软剪辑而非硬剪辑。注意：getUnclippend（）添加软剪辑和硬剪辑，此函数仅添加软剪辑。

代码示例

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

@Override
protected boolean isUsableRead(final GATKSAMRecord read, final int refLoc) {
  return super.isUsableRead(read, refLoc) && read.getSoftEnd() >= refLoc;
}

代码示例来源：origin: broadgsa/gatk

public static List<GATKSAMRecord> mergeOverlappingPairedFragments( final List<GATKSAMRecord> overlappingPair ) {
  if( overlappingPair.size() != 2 ) { throw new ReviewedGATKException("Found overlapping pair with " + overlappingPair.size() + " reads, but expecting exactly 2."); }
  final GATKSAMRecord firstRead = overlappingPair.get(0);
  final GATKSAMRecord secondRead = overlappingPair.get(1);
  final GATKSAMRecord merged;
  if( !(secondRead.getSoftStart() <= firstRead.getSoftEnd() && secondRead.getSoftStart() >= firstRead.getSoftStart() && secondRead.getSoftEnd() >= firstRead.getSoftEnd()) ) {
    merged = mergeOverlappingPairedFragments(secondRead, firstRead);
  } else {
    merged = mergeOverlappingPairedFragments(firstRead, secondRead);
  }
  return merged == null ? overlappingPair : Collections.singletonList(merged);
}

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

/**
 * Should we clip a upstream portion of a read because it spans off the end of a haplotype?
 *
 * @param read               the read in question
 * @param refWindowStart     the start of the reference window
 * @return true if the read needs to be clipped, false otherwise
 */
protected static boolean mustClipUpstream(final GATKSAMRecord read, final int refWindowStart) {
  return ( !read.isEmpty() && read.getSoftStart() < refWindowStart && read.getSoftEnd() > refWindowStart );
}

代码示例来源：origin: broadgsa/gatk

public void add(GATKSAMRecord read) {
  final int readStart = read.getSoftStart();
  final int readStop = read.getSoftEnd();
  if ( loc == null )
    loc = parser.createGenomeLoc(read.getReferenceName(), readStart, Math.max(readStop, readStart)); // in case it's all an insertion
  else if ( readStop > loc.getStop() )
    loc = parser.createGenomeLoc(loc.getContig(), loc.getStart(), readStop);
  reads.add(read);
}

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

public void setRead(final GATKSAMRecord read) {
    if ( !read.isEmpty() ) {
      this.read = read;
      if ( ! read.getReadUnmappedFlag() )
        loc = genomeLocParser.createGenomeLoc(read.getReferenceName(), read.getSoftStart(), read.getSoftEnd());
    }
  }
}

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

protected static boolean[] calculateKnownSites( final GATKSAMRecord read, final List<Feature> features ) {
  final int readLength = read.getReadBases().length;
  final boolean[] knownSites = new boolean[readLength];
  Arrays.fill(knownSites, false);
  for( final Feature f : features ) {
    if ((f.getStart() < read.getSoftStart() && f.getEnd() < read.getSoftStart()) ||
      (f.getStart() > read.getSoftEnd() && f.getEnd() > read.getSoftEnd())) {
      // feature is outside clipping window for the read, ignore
      continue;
    }
    int featureStartOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), f.getStart(), ReadUtils.ClippingTail.LEFT_TAIL, true); // BUGBUG: should I use LEFT_TAIL here?
    if( featureStartOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) {
      featureStartOnRead = 0;
    }
    int featureEndOnRead = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), f.getEnd(), ReadUtils.ClippingTail.LEFT_TAIL, true);
    if( featureEndOnRead == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) {
      featureEndOnRead = readLength;
    }
    if( featureStartOnRead > readLength ) {
      featureStartOnRead = featureEndOnRead = readLength;
    }
    Arrays.fill(knownSites, Math.max(0, featureStartOnRead), Math.min(readLength, featureEndOnRead + 1), true);
  }
  return knownSites;
}

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

@Test(dataProvider = "ClipUpstreamProvider", enabled = true)
public void clipUpstreamTest(final int readStart, final int readLength, final int delLength) {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "basicRead", 0, readStart, readLength);
  if ( delLength == 0 )
    read.setCigarString(readLength + "M");
  else
    read.setCigarString((readLength / 2) + "M" + delLength + "D" + (readLength / 2) + "M");
  final boolean result = PairHMMIndelErrorModel.mustClipUpstream(read, refWindowStart);
  Assert.assertEquals(result, read.getSoftStart() < refWindowStart && read.getSoftEnd() > refWindowStart);
}

代码示例来源：origin: broadgsa/gatk

/**
 * Tests the GenomeLoc variable in the ReadBin after adding arbitrary reads
 *
 * @param cigarString    the read's cigar string
 * @param alignmentStart the read's alignment start
 */
@Test(enabled = true, dataProvider = "reads")
public void testAddingReads(String cigarString, int alignmentStart) {
  final GATKSAMRecord read = createReadAndAddToBin(cigarString, alignmentStart);
  final GenomeLoc readLoc = parser.createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getSoftStart(), Math.max(read.getSoftStart(), read.getSoftEnd()));
  Assert.assertEquals(readBin.getLocation(), readLoc);
  readBin.clear();
}

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

final long readEnd = read.getSoftEnd();
final int numEndSoftClippedBases = softClips ? read.getSoftEnd()- read.getAlignmentEnd() : 0 ;
final byte [] unclippedReadBases = read.getReadBases();
final byte [] unclippedReadQuals = read.getBaseQualities();

代码示例来源：origin: broadgsa/gatk

@Test(enabled = !DEBUG)
public void testHardClipByReferenceCoordinatesRightTail() {
  for (Cigar cigar : cigarList) {
    GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar, 0);
    int alnStart = read.getAlignmentStart();
    int alnEnd = read.getAlignmentEnd();
    if (read.getSoftEnd() == alnEnd) {                                                                          // we can't test right clipping if the read has hanging soft clips on the right side
      for (int i = alnStart; i <= alnEnd; i++) {
        GATKSAMRecord clipRight = ReadClipper.hardClipByReferenceCoordinatesRightTail(read, i);
        if (!clipRight.isEmpty() && clipRight.getAlignmentStart() <= clipRight.getAlignmentEnd()) {         // alnStart > alnEnd if the entire read is a soft clip now. We can't test those.
          Assert.assertTrue(clipRight.getAlignmentEnd() <= i - 1, String.format("Clipped alignment end (%d) is greater than expected (%d): %s -> %s", clipRight.getAlignmentEnd(), i - 1, read.getCigarString(), clipRight.getCigarString()));
          assertUnclippedLimits(read, clipRight);
        }
      }
    }
  }
}

代码示例来源：origin: broadgsa/gatk

int sStop = read.getSoftEnd();
int uStart = read.getUnclippedStart();
int uStop = read.getUnclippedEnd();

代码示例来源：origin: broadgsa/gatk

final GATKSAMRecord secondRead = ReadClipper.hardClipAdaptorSequence(ReadClipper.revertSoftClippedBases(unclippedSecondRead));
if( !(secondRead.getSoftStart() <= firstRead.getSoftEnd() && secondRead.getSoftStart() >= firstRead.getSoftStart() && secondRead.getSoftEnd() >= firstRead.getSoftEnd()) ) {
  return null; // can't merge them, yet:  AAAAAAAAAAA-BBBBBBBBBBB-AAAAAAAAAAAAAA, B is contained entirely inside A

代码示例来源：origin: broadgsa/gatk

@Test(enabled = !DEBUG)
public void testHardClipByReferenceCoordinates() {
  for (Cigar cigar : cigarList) {
    GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar, 0);
    int start = read.getSoftStart();
    int stop = read.getSoftEnd();
    for (int i = start; i <= stop; i++) {
      GATKSAMRecord clipLeft = (new ReadClipper(read)).hardClipByReferenceCoordinates(-1, i);
      if (!clipLeft.isEmpty()) {
        Assert.assertTrue(clipLeft.getAlignmentStart() >= Math.min(read.getAlignmentEnd(), i + 1), String.format("Clipped alignment start (%d) is less the expected (%d): %s -> %s", clipLeft.getAlignmentStart(), i + 1, read.getCigarString(), clipLeft.getCigarString()));
        assertUnclippedLimits(read, clipLeft);
      }
      GATKSAMRecord clipRight = (new ReadClipper(read)).hardClipByReferenceCoordinates(i, -1);
      if (!clipRight.isEmpty() && clipRight.getAlignmentStart() <= clipRight.getAlignmentEnd()) {             // alnStart > alnEnd if the entire read is a soft clip now. We can't test those.
        Assert.assertTrue(clipRight.getAlignmentEnd() <= Math.max(read.getAlignmentStart(), i - 1), String.format("Clipped alignment end (%d) is greater than expected (%d): %s -> %s", clipRight.getAlignmentEnd(), i - 1, read.getCigarString(), clipRight.getCigarString()));
        assertUnclippedLimits(read, clipRight);
      }
    }
  }
}

代码示例来源：origin: broadgsa/gatk

int nTailingSoftClips = read.getSoftEnd() - read.getAlignmentEnd();
if (nTailingSoftClips > 0) {
  for (int i = read.getReadLength() - nTailingSoftClips; i < read.getReadLength() ; i++) {