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

GATKSAMRecord.getAlignmentStart介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

@Override
public int compareTo(final PileupElement pileupElement) {
  if (offset < pileupElement.offset)
    return -1;
  else if (offset > pileupElement.offset)
    return 1;
  else if (read.getAlignmentStart() < pileupElement.read.getAlignmentStart())
    return -1;
  else if (read.getAlignmentStart() > pileupElement.read.getAlignmentStart())
    return 1;
  else
    return 0;
}

代码示例来源：origin: broadgsa/gatk

public int getAlignmentStart() {
  return (newStart != -1 ? newStart : read.getAlignmentStart());
}

代码示例来源：origin: broadgsa/gatk

public int getOriginalAlignmentStart() {
  return read.getAlignmentStart();
}

代码示例来源：origin: broadgsa/gatk

/**
 * Does read start at the same position as described by currentContextIndex and currentAlignmentStart?
 *
 * @param read the read we want to test
 * @param currentContigIndex the contig index (from the read's getReferenceIndex) of the reads in this state manager
 * @param currentAlignmentStart the alignment start of the of the left-most position on the
 *                           genome of the reads in this read state manager
 * @return true if read has contig index and start equal to the current ones
 */
private boolean readStartsAtCurrentPosition(final GATKSAMRecord read, final int currentContigIndex, final int currentAlignmentStart) {
  return read.getAlignmentStart() == currentAlignmentStart && read.getReferenceIndex() == currentContigIndex;
}

代码示例来源：origin: broadgsa/gatk

/**
 * Is a base inside a read?
 *
 * @param read                the read to evaluate
 * @param referenceCoordinate the reference coordinate of the base to test
 * @return true if it is inside the read, false otherwise.
 */
public static boolean isInsideRead(final GATKSAMRecord read, final int referenceCoordinate) {
  return referenceCoordinate >= read.getAlignmentStart() && referenceCoordinate <= read.getAlignmentEnd();
}

代码示例来源：origin: broadgsa/gatk

/**
 * Test that the reads are ordered by their alignment starts
 * @return true if well ordered, false otherwise
 */
private boolean readStartsAreWellOrdered() {
  int lastStart = -1;
  for ( final AlignmentStateMachine machine : readStatesByAlignmentStart ) {
    if ( lastStart > machine.getRead().getAlignmentStart() )
      return false;
    lastStart = machine.getRead().getAlignmentStart();
  }
  return true;
}

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

private boolean useSoftClippedBases(GATKSAMRecord read, long eventStartPos, int eventLength) {
  return !((read.getAlignmentStart() >= eventStartPos-eventLength && read.getAlignmentStart() <= eventStartPos+1) || (read.getAlignmentEnd() >= eventStartPos && read.getAlignmentEnd() <= eventStartPos + eventLength));
}

代码示例来源：origin: broadgsa/gatk

private void verifySortednessOfReads( final List<GATKSAMRecord> reads) {
    int lastStart = -1;
    for ( GATKSAMRecord read : reads ) {
      Assert.assertTrue(lastStart <= read.getAlignmentStart(), "Reads should be sorted but weren't.  Found read with start " + read.getAlignmentStart() + " while last was " + lastStart);
      lastStart = read.getAlignmentStart();
    }
  }
}

代码示例来源：origin: broadgsa/gatk

/**
 * Get the position (1-based as standard) of the current alignment on the genome w.r.t. the read's alignment start
 * @return the position on the genome of the current state in absolute coordinates
 */
@Ensures("result > 0")
public int getGenomePosition() {
  return read.getAlignmentStart() + getGenomeOffset();
}

代码示例来源：origin: broadgsa/gatk

/**
 * Hard clip the read to the variable region (from refStart to refStop)
 *
 * @param read     the read to be clipped
 * @param refStart the beginning of the variant region (inclusive)
 * @param refStop  the end of the variant region (inclusive)
 * @return the read hard clipped to the variant region
 */
public static GATKSAMRecord hardClipToRegion( final GATKSAMRecord read, final int refStart, final int refStop ) {
  final int start = read.getAlignmentStart();
  final int stop = read.getAlignmentEnd();
  return hardClipToRegion(read, refStart, refStop,start,stop);
}

代码示例来源：origin: broadgsa/gatk

@Override
  public int compare(PileupElement element1, PileupElement element2) {
    final int difference = element1.getRead().getAlignmentStart() - element2.getRead().getAlignmentStart();
    return difference != 0 ? difference : element1.getRead().getReadName().compareTo(element2.getRead().getReadName());
  }
});

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

private void AssertWellOrderedPileup(final ReadBackedPileup pileup) {
  if ( ! pileup.isEmpty() ) {
    int leftMostPos = -1;
    for ( final PileupElement pe : pileup ) {
      Assert.assertTrue(pileup.getLocation().getContig().equals(pe.getRead().getReferenceName()), "ReadBackedPileup contains an element " + pe + " that's on a different contig than the pileup itself");
      Assert.assertTrue(pe.getRead().getAlignmentStart() >= leftMostPos,
          "ReadBackedPileup contains an element " + pe + " whose read's alignment start " + pe.getRead().getAlignmentStart()
              + " occurs before the leftmost position we've seen previously " + leftMostPos);
    }
  }
}

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( )
public void testCreationFromSAMRecordUnmappedButOnGenome() {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 5);
  read.setReadUnmappedFlag(true);
  read.setCigarString("*");
  final GenomeLoc loc = genomeLocParser.createGenomeLoc(read);
  Assert.assertEquals(loc.getContig(), read.getReferenceName());
  Assert.assertEquals(loc.getContigIndex(), (int)read.getReferenceIndex());
  Assert.assertEquals(loc.getStart(), read.getAlignmentStart());
  Assert.assertEquals(loc.getStop(), read.getAlignmentStart());
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = !DEBUG)
public void testHardClipBothEndsByReferenceCoordinates() {
  for (Cigar cigar : cigarList) {
    GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar, 0);
    int alnStart = read.getAlignmentStart();
    int alnEnd = read.getAlignmentEnd();
    int readLength = alnStart - alnEnd;
    for (int i = 0; i < readLength / 2; i++) {
      GATKSAMRecord clippedRead = ReadClipper.hardClipBothEndsByReferenceCoordinates(read, alnStart + i, alnEnd - i);
      Assert.assertTrue(clippedRead.getAlignmentStart() >= alnStart + i, String.format("Clipped alignment start is less than original read (minus %d): %s -> %s", i, read.getCigarString(), clippedRead.getCigarString()));
      Assert.assertTrue(clippedRead.getAlignmentEnd() <= alnEnd + i, String.format("Clipped alignment end is greater than original read (minus %d): %s -> %s", i, read.getCigarString(), clippedRead.getCigarString()));
      assertUnclippedLimits(read, clippedRead);
    }
  }
}

代码示例来源：origin: broadgsa/gatk

private boolean doNotTryToClean(GATKSAMRecord read) {
  return read.getReadUnmappedFlag() ||
      read.getNotPrimaryAlignmentFlag() ||
      read.getReadFailsVendorQualityCheckFlag() ||
      read.getMappingQuality() == 0 ||
      read.getAlignmentStart() == SAMRecord.NO_ALIGNMENT_START ||
      ConstrainedMateFixingManager.iSizeTooBigToMove(read, MAX_ISIZE_FOR_MOVEMENT) ||
      ReadUtils.is454Read(read) ||
      ReadUtils.isIonRead(read);
  // TODO -- it would be nice if we could use indels from 454/Ion reads as alternate consenses
}

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

@Test(dataProvider = "ComplexReadAlignedToRef", enabled = !DEBUG)
  public void testReadAlignedToRefComplexAlignment(final int testIndex, final GATKSAMRecord read, final String reference, final Haplotype haplotype, final int expectedMaxMismatches) throws Exception {
    final HaplotypeBAMWriter writer = new CalledHaplotypeBAMWriter(new MockDestination());
    final GATKSAMRecord alignedRead = AlignmentUtils.createReadAlignedToRef(read, haplotype, new Haplotype(reference.getBytes(),true), 1, true);
    if ( alignedRead != null ) {
      final int mismatches = AlignmentUtils.getMismatchCount(alignedRead, reference.getBytes(), alignedRead.getAlignmentStart() - 1).numMismatches;
      Assert.assertTrue(mismatches <= expectedMaxMismatches,
          "Alignment of read to ref looks broken.  Expected at most " + expectedMaxMismatches + " but saw " + mismatches
              + " for readBases " + new String(read.getReadBases()) + " with cigar " + read.getCigar() + " reference " + reference + " haplotype "
              + haplotype + " with cigar " + haplotype.getCigar() + " aligned read cigar " + alignedRead.getCigarString() + " @ " + alignedRead.getAlignmentStart());
    }
  }
}

代码示例来源：origin: broadgsa/gatk

@Test( )
public void testCreationFromSAMRecord() {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 5);
  final GenomeLoc loc = genomeLocParser.createGenomeLoc(read);
  Assert.assertEquals(loc.getContig(), read.getReferenceName());
  Assert.assertEquals(loc.getContigIndex(), (int)read.getReferenceIndex());
  Assert.assertEquals(loc.getStart(), read.getAlignmentStart());
  Assert.assertEquals(loc.getStop(), read.getAlignmentEnd());
}

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);
        }
      }
    }
  }
}