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

GATKSAMRecord.getCigarString介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

private void assertNoLowQualBases(GATKSAMRecord read, byte low_qual) {
  if (!read.isEmpty()) {
    byte[] quals = read.getBaseQualities();
    for (int i = 0; i < quals.length; i++)
      Assert.assertFalse(quals[i] <= low_qual, String.format("Found low qual (%d) base after hard clipping. Position: %d -- %s", low_qual, i, read.getCigarString()));
  }
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = true)
public void testWonkyCigars() {
  for (String cigarString : BAD_CIGAR_LIST) {
    GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigarString, 0);
    Assert.assertTrue(filter.filterOut(read), read.getCigarString());
  }
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = true)
public void testReadCigarLengthMismatch() {
  GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar("4M", 1);
  Assert.assertTrue(filter.filterOut(read), read.getCigarString());
}

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

@Test(enabled = !DEBUG)
public void testHardClipByReadCoordinates() {
  for (Cigar cigar : cigarList) {
    GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar, 0);
    int readLength = read.getReadLength();
    for (int i = 0; i < readLength; i++) {
      GATKSAMRecord clipLeft = ReadClipper.hardClipByReadCoordinates(read, 0, i);
      Assert.assertTrue(clipLeft.getReadLength() <= readLength - i, String.format("Clipped read length is greater than original read length (minus %d): %s -> %s", i, read.getCigarString(), clipLeft.getCigarString()));
      assertUnclippedLimits(read, clipLeft);
      GATKSAMRecord clipRight = ReadClipper.hardClipByReadCoordinates(read, i, readLength - 1);
      Assert.assertTrue(clipRight.getReadLength() <= i, String.format("Clipped read length is greater than original read length (minus %d): %s -> %s", i, read.getCigarString(), clipRight.getCigarString()));
      assertUnclippedLimits(read, clipRight);
    }
  }
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = true)
  public void testGoodCigars() {
    List<Cigar> cigarList = ReadClipperTestUtils.generateCigarList(10);
    for (Cigar cigar : cigarList) {
      GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar, 0);
      Assert.assertFalse(filter.filterOut(read), read.getCigarString());
    }
  }
}

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

@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

/**
   * Asserts that the two reads have the same bases, qualities and cigar strings
   *
   * @param actual the calculated read
   * @param expected the expected read
   */
  public static void assertEqualReads(GATKSAMRecord actual, GATKSAMRecord expected) {
    // If they're both not empty, test their contents
    if(!actual.isEmpty() && !expected.isEmpty()) {
      Assert.assertEquals(actual.getReadBases(), expected.getReadBases());
      Assert.assertEquals(actual.getBaseQualities(), expected.getBaseQualities());
      Assert.assertEquals(actual.getCigarString(), expected.getCigarString());
    }
    // Otherwise test if they're both empty
    else
      Assert.assertEquals(actual.isEmpty(), expected.isEmpty());
   }
}

代码示例来源：origin: broadgsa/gatk

@Test(enabled = !DEBUG)
public void testRevertSoftClippedBasesWithThreshold() {
  for (Cigar cigar : cigarList) {
    final int leadingSoftClips = leadingCigarElementLength(cigar, CigarOperator.SOFT_CLIP);
    final int tailSoftClips = leadingCigarElementLength(CigarUtils.invertCigar(cigar), CigarOperator.SOFT_CLIP);
    final GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar, 0);
    final GATKSAMRecord unclipped = ReadClipper.revertSoftClippedBases(read);
    assertUnclippedLimits(read, unclipped);                                                                     // Make sure limits haven't changed
    Assert.assertNull(read.getCigar().isValid(null, -1));
    Assert.assertNull(unclipped.getCigar().isValid(null, -1));
    if (!(leadingSoftClips > 0 || tailSoftClips > 0))
      Assert.assertEquals(read.getCigarString(), unclipped.getCigarString());
  }
}

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 testRevertSoftClippedBases() {
  for (Cigar cigar : cigarList) {
    final int leadingSoftClips = leadingCigarElementLength(cigar, CigarOperator.SOFT_CLIP);
    final int tailSoftClips = leadingCigarElementLength(CigarUtils.invertCigar(cigar), CigarOperator.SOFT_CLIP);
    final GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar, 0);
    final GATKSAMRecord unclipped = ReadClipper.revertSoftClippedBases(read);
    assertUnclippedLimits(read, unclipped);                                                                     // Make sure limits haven't changed
    if (leadingSoftClips > 0 || tailSoftClips > 0) {
      final int expectedStart = read.getAlignmentStart() - leadingSoftClips;
      final int expectedEnd = read.getAlignmentEnd() + tailSoftClips;
      Assert.assertEquals(unclipped.getAlignmentStart(), expectedStart);
      Assert.assertEquals(unclipped.getAlignmentEnd(), expectedEnd);
    } else
      Assert.assertEquals(read.getCigarString(), unclipped.getCigarString());
  }
}

代码示例来源：origin: broadgsa/gatk

throw new ReviewedGATKException(String.format("START (%d) > (%d) STOP -- this should never happen, please check read: %s (CIGAR: %s)", start, stop, read, read.getCigarString()));
throw new ReviewedGATKException(String.format("Trying to clip the middle of the read: start %d, stop %d, cigar: %s", start, stop, read.getCigarString()));

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

@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-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(enabled = false)
public void testHardClipLeadingInsertions() {
  for (Cigar cigar : cigarList) {
    if (startsWithInsertion(cigar)) {
      GATKSAMRecord read = ReadClipperTestUtils.makeReadFromCigar(cigar, 0);
      GATKSAMRecord clippedRead = ReadClipper.hardClipLeadingInsertions(read);
      assertUnclippedLimits(read, clippedRead);        // Make sure limits haven't changed
      int expectedLength = read.getReadLength() - leadingCigarElementLength(read.getCigar(), CigarOperator.INSERTION);
      if (cigarHasElementsDifferentThanInsertionsAndHardClips(read.getCigar()))
        expectedLength -= leadingCigarElementLength(CigarUtils.invertCigar(read.getCigar()), CigarOperator.INSERTION);
      if (!clippedRead.isEmpty()) {
        Assert.assertEquals(expectedLength, clippedRead.getReadLength(), String.format("%s -> %s", read.getCigarString(), clippedRead.getCigarString()));  // check that everything else is still there
        Assert.assertFalse(startsWithInsertion(clippedRead.getCigar()));                                                                                   // check that the insertions are gone
      } else
        Assert.assertTrue(expectedLength == 0, String.format("expected length: %d", expectedLength));                                                      // check that the read was expected to be fully clipped
    }
  }
}

代码示例来源：origin: broadgsa/gatk

Assert.assertEquals(actual.getCigarString(), expectedMerged.getCigarString());
Assert.assertEquals(actual.getReadBases(), expectedMerged.getReadBases());
Assert.assertEquals(actual.getReadGroup(), expectedMerged.getReadGroup());

代码示例来源：origin: broadgsa/gatk

for ( final GATKSAMRecord read : bamBuilder.makeReads() ) {
  Assert.assertTrue(readNamesInRegion.contains(read.getReadName()),
      "Region " + region + " should contain read " + read + " with cigar " + read.getCigarString() + " but it wasn't");
  nReadsExpectedInRegion++;

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

cigarSecondIndex--;
if(cigarFirstIndex > cigarSecondIndex)
  throw new UserException.BadInput("Cannot split this read (might be an empty section between Ns, for example 1N1D1N): "+read.getCigarString());