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

GATKSAMRecord.getSoftStart介绍

[英]Calculates the reference coordinate for the beginning of the read taking into account soft clips but not hard clips. Note: getUnclippedStart() adds soft and hard clips, this function only adds soft clips.
[中]计算读取开始时的参考坐标，考虑软剪辑，但不考虑硬剪辑。注意：getUnclippedStart（）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

/**
 * Should we clip a downstream portion of a read because it spans off the end of a haplotype?
 *
 * @param read               the read in question
 * @param refWindowStop      the end of the reference window
 * @return true if the read needs to be clipped, false otherwise
 */
protected static boolean mustClipDownstream(final GATKSAMRecord read, final int refWindowStop) {
  return ( !read.isEmpty() && read.getSoftStart() < refWindowStop && read.getSoftStart() + read.getReadLength() - 1 > refWindowStop );
}

代码示例来源：origin: broadgsa/gatk

public static int getReadCoordinateForReferenceCoordinateUpToEndOfRead(GATKSAMRecord read, int refCoord, ClippingTail tail) {
  final int leftmostSafeVariantPosition = Math.max(read.getSoftStart(), refCoord);
  return getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), leftmostSafeVariantPosition, tail, false);
}

代码示例来源：origin: broadgsa/gatk

public static void adjustQualsOfOverlappingPairedFragments( 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);
  if ( secondRead.getSoftStart() < firstRead.getSoftStart() ) {
    adjustQualsOfOverlappingPairedFragments(secondRead, firstRead);
  } else {
    adjustQualsOfOverlappingPairedFragments(firstRead, secondRead);
  }
}

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-protected

@Override
  protected boolean isUsableRead(final GATKSAMRecord read, final int refLoc) {
    return super.isUsableRead(read, refLoc) && read.getSoftStart() + read.getCigar().getReadLength() > refLoc;
  }
}

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

/**
 * The function assumes that read contains the variant allele.
 *
 * @param read
 * @param variantStartPosition the location of the variant in the reference
 * @return
 */
protected Pair<OptionalInt, OptionalInt> getVariantPositionInRead(final GATKSAMRecord read, final int variantStartPosition) {
  final Pair<Integer, Boolean> refPositionAndDeletionFlag = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), variantStartPosition, true);
  // the +1 is needed there because getReadCoordinateForReferenceCoordinate() returns the number of read bases from the left end to the variant - 1
  int numReadBasesFromLeftEndToVariant = refPositionAndDeletionFlag.getFirst() + 1;
  // we don't take advantage of fallsInsideOrJustBeforeDeletionOrSkippedRegion flag now, but we might want to, so I will leave it here in comments.
  // boolean fallsInsideOrJustBeforeDeletionOrSkippedRegion = refPositionAndDeletionFlag.getSecond();
  if ( numReadBasesFromLeftEndToVariant == ReadUtils.CLIPPING_GOAL_NOT_REACHED ) {
    return new Pair(OptionalInt.empty(), OptionalInt.empty());
  } else {
    int leftOffset = numReadBasesFromLeftEndToVariant - 1;
    int rightOffset = read.getReadLength() - numReadBasesFromLeftEndToVariant;
    return new Pair(OptionalInt.of(leftOffset), OptionalInt.of(rightOffset));
  }
}

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

@Test(dataProvider = "ClipDownstreamProvider", enabled = true)
public void clipDownstreamTest(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.mustClipDownstream(read, refWindowEnd);
  Assert.assertEquals(result, read.getSoftStart() < refWindowEnd && read.getSoftStart() + readLength > refWindowEnd);
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = !DEBUG)
public void testRevertEntirelySoftclippedReads() {
  GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar("2H1S3H", 0);
  GATKSAMRecord clippedRead = ReadClipper.revertSoftClippedBases(read);
  Assert.assertEquals(clippedRead.getAlignmentStart(), read.getSoftStart());
}

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

/**
 * Pre-processes the results of getReadCoordinateForReferenceCoordinate(GATKSAMRecord, int) to take care of
 * two corner cases:
 * 
 * 1. If clipping the right tail (end of the read) getReadCoordinateForReferenceCoordinate and fall inside
 * a deletion return the base after the deletion. If clipping the left tail (beginning of the read) it
 * doesn't matter because it already returns the previous base by default.
 * 
 * 2. If clipping the left tail (beginning of the read) getReadCoordinateForReferenceCoordinate and the
 * read starts with an insertion, and you're requesting the first read based coordinate, it will skip
 * the leading insertion (because it has the same reference coordinate as the following base).
 *
 * @param read
 * @param refCoord
 * @param tail
 * @return the read coordinate corresponding to the requested reference coordinate for clipping.
 */
@Requires({"refCoord >= read.getUnclippedStart()", "refCoord <= read.getUnclippedEnd() || (read.getUnclippedEnd() < read.getUnclippedStart())"})
@Ensures({"result >= 0", "result < read.getReadLength()"})
public static int getReadCoordinateForReferenceCoordinate(GATKSAMRecord read, int refCoord, ClippingTail tail) {
  return getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refCoord, tail, false);
}

代码示例来源：origin: broadgsa/gatk

/**
 * Returns the read coordinate corresponding to the requested reference coordinate.
 *
 * WARNING: if the requested reference coordinate happens to fall inside or just before a deletion (or skipped region) in the read, this function
 * will return the last read base before the deletion (or skipped region). This function returns a
 * Pair(int readCoord, boolean fallsInsideOrJustBeforeDeletionOrSkippedRegion) so you can choose which readCoordinate to use when faced with
 * a deletion (or skipped region).
 *
 * SUGGESTION: Use getReadCoordinateForReferenceCoordinate(GATKSAMRecord, int, ClippingTail) instead to get a
 * pre-processed result according to normal clipping needs. Or you can use this function and tailor the
 * behavior to your needs.
 *
 * @param read
 * @param refCoord the requested reference coordinate
 * @return the read coordinate corresponding to the requested reference coordinate. (see warning!)
 */
@Requires({"refCoord >= read.getSoftStart()", "refCoord <= read.getSoftEnd()"})
@Ensures({"result.getFirst() >= 0", "result.getFirst() < read.getReadLength()"})
//TODO since we do not have contracts any more, should we check for the requirements in the method code?
public static Pair<Integer, Boolean> getReadCoordinateForReferenceCoordinate(GATKSAMRecord read, int refCoord) {
  return getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refCoord, false);
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = true, dataProvider = "RevertSoftClipsBeforeContig")
public void testRevertSoftClippedBasesBeforeStartOfContig(final int softStart, final int alignmentStart) {
  final int nMatches = 10;
  final int nSoft = -1 * (softStart - alignmentStart);
  final String cigar = nSoft + "S" + nMatches + "M";
  final GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar, 0);
  read.setAlignmentStart(alignmentStart);
  Assert.assertEquals(read.getSoftStart(), softStart);
  Assert.assertEquals(read.getAlignmentStart(), alignmentStart);
  Assert.assertEquals(read.getCigarString(), cigar);
  final GATKSAMRecord reverted = ReadClipper.revertSoftClippedBases(read);
  final int expectedAlignmentStart = 1;
  final String expectedCigar = (1 - softStart) + "H" + read.getAlignmentEnd() + "M";
  Assert.assertEquals(reverted.getSoftStart(), expectedAlignmentStart);
  Assert.assertEquals(reverted.getAlignmentStart(), expectedAlignmentStart);
  Assert.assertEquals(reverted.getCigarString(), expectedCigar);
}

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

@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-protected

@Override
protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) {
  final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate( read.getSoftStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true );
  if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED )
    return null;
  // If the offset inside a deletion, it does not lie on a read.
  if ( AlignmentUtils.isInsideDeletion(read.getCigar(), offset) ) {
    return INVALID_ELEMENT_FROM_READ;
  }
  int readPos = AlignmentUtils.calcAlignmentByteArrayOffset( read.getCigar(), offset, false, 0, 0 );
  final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read );
  if (readPos > numAlignedBases / 2)
    readPos = numAlignedBases - (readPos + 1);
  return (double)readPos;
}

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

@Override
protected Double getElementForRead(final GATKSAMRecord read, final int refLoc) {
  final int offset = ReadUtils.getReadCoordinateForReferenceCoordinate(read.getSoftStart(), read.getCigar(), refLoc, ReadUtils.ClippingTail.RIGHT_TAIL, true);
  if ( offset == ReadUtils.CLIPPING_GOAL_NOT_REACHED )
    return null;
  // If the offset inside a deletion, it does not lie on a read.
  if ( AlignmentUtils.isInsideDeletion(read.getCigar(), offset) ) {
    return INVALID_ELEMENT_FROM_READ;
  }
  int readPos = AlignmentUtils.calcAlignmentByteArrayOffset(read.getCigar(), offset, false, 0, 0);
  final int numAlignedBases = AlignmentUtils.getNumAlignedBasesCountingSoftClips( read );
  if (readPos > numAlignedBases / 2)
    readPos = numAlignedBases - (readPos + 1);
  return (double)readPos;
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = !DEBUG)
public void testHardClipByReferenceCoordinatesLeftTail() {
  for (Cigar cigar : cigarList) {
    GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar, 0);
    int alnStart = read.getAlignmentStart();
    int alnEnd = read.getAlignmentEnd();
    if (read.getSoftStart() == alnStart) {                                                                      // we can't test left clipping if the read has hanging soft clips on the left side
      for (int i = alnStart; i <= alnEnd; i++) {
        GATKSAMRecord clipLeft = ReadClipper.hardClipByReferenceCoordinatesLeftTail(read, i);
        if (!clipLeft.isEmpty()) {
          Assert.assertTrue(clipLeft.getAlignmentStart() >= 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);
        }
      }
    }
  }
}

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);
      }
    }
  }
}