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

GATKSAMRecord.isEmpty介绍

[英]Checks whether if the read has any bases. Empty reads can be dangerous as it may have no cigar strings, no read names and other missing attributes.
[中]检查读取是否有任何基数。空读取可能很危险，因为它可能没有雪茄字符串、读取名称和其他缺少的属性。

代码示例

代码示例来源：origin: broadgsa/gatk

public static List<GATKSAMRecord> hardClipToRegion( final List<GATKSAMRecord> reads, final int refStart, final int refStop ) {
  final List<GATKSAMRecord> returnList = new ArrayList<GATKSAMRecord>( reads.size() );
  for( final GATKSAMRecord read : reads ) {
    final GATKSAMRecord clippedRead = hardClipToRegion( read, refStart, refStop );
    if( !clippedRead.isEmpty() ) {
      returnList.add( clippedRead );
    }
  }
  return returnList;
}

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

/**
 * 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

/**
 * Turns soft clipped bases into matches
 * @return a new read with every soft clip turned into a match
 */
private GATKSAMRecord revertSoftClippedBases() {
  if (read.isEmpty())
    return read;
  this.addOp(new ClippingOp(0, 0));
  return this.clipRead(ClippingRepresentation.REVERT_SOFTCLIPPED_BASES);
}

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

/**
   * 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-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

/**
 * Clips a read according to ops and the chosen algorithm.
 *
 * @param algorithm What mode of clipping do you want to apply for the stacked operations.
 * @return the read with the clipping applied.
 */
public GATKSAMRecord clipRead(ClippingRepresentation algorithm) {
  if (ops == null)
    return getRead();
  GATKSAMRecord clippedRead = read;
  for (ClippingOp op : getOps()) {
    final int readLength = clippedRead.getReadLength();
    //check if the clipped read can still be clipped in the range requested
    if (op.start < readLength) {
      ClippingOp fixedOperation = op;
      if (op.stop >= readLength)
        fixedOperation = new ClippingOp(op.start, readLength - 1);
      clippedRead = fixedOperation.apply(algorithm, clippedRead);
    }
  }
  wasClipped = true;
  ops.clear();
  if ( clippedRead.isEmpty() )
    return GATKSAMRecord.emptyRead(clippedRead);
  return clippedRead;
}

代码示例来源：origin: broadgsa/gatk

/**
 * Hard clips a read using read coordinates.
 *
 * @param start the first base to clip (inclusive)
 * @param stop the last base to clip (inclusive)
 * @return a new read, without the clipped bases
 */
@Requires({"start >= 0 && stop <= read.getReadLength() - 1",   // start and stop have to be within the read
      "start == 0 || stop == read.getReadLength() - 1"})  // cannot clip the middle of the read
private GATKSAMRecord hardClipByReadCoordinates(int start, int stop) {
  if (read.isEmpty() || (start == 0 && stop == read.getReadLength() - 1))
    return GATKSAMRecord.emptyRead(read);
  this.addOp(new ClippingOp(start, stop));
  return clipRead(ClippingRepresentation.HARDCLIP_BASES);
}
public static GATKSAMRecord hardClipByReadCoordinates(GATKSAMRecord read, int start, int stop) {

代码示例来源：origin: broadgsa/gatk

/**
 * Hard clips both tails of a read.
 *   Left tail goes from the beginning to the 'left' coordinate (inclusive)
 *   Right tail goes from the 'right' coordinate (inclusive) until the end of the read
 *
 * @param left the coordinate of the last base to be clipped in the left tail (inclusive)
 * @param right the coordinate of the first base to be clipped in the right tail (inclusive)
 * @return a new read, without the clipped bases
 */
@Requires({"left <= right",                    // tails cannot overlap
      "left >= read.getAlignmentStart()", // coordinate has to be within the mapped read
      "right <= read.getAlignmentEnd()"}) // coordinate has to be within the mapped read
private GATKSAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
  if (read.isEmpty() || left == right)
    return GATKSAMRecord.emptyRead(read);
  GATKSAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
  // after clipping one tail, it is possible that the consequent hard clipping of adjacent deletions
  // make the left cut index no longer part of the read. In that case, clip the read entirely.
  if (left > leftTailRead.getAlignmentEnd())
    return GATKSAMRecord.emptyRead(read);
  ReadClipper clipper = new ReadClipper(leftTailRead);
  return clipper.hardClipByReferenceCoordinatesLeftTail(left);
}
public static GATKSAMRecord hardClipBothEndsByReferenceCoordinates(GATKSAMRecord read, int left, int right) {

代码示例来源：origin: broadgsa/gatk

if (read.isEmpty())
  return read;

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

/**
 * Hard clips any leading insertions in the read. Only looks at the beginning of the read, not the end.
 *
 * @return a new read without leading insertions
 */
private GATKSAMRecord hardClipLeadingInsertions() {
  if (read.isEmpty())
    return read;
  for(CigarElement cigarElement : read.getCigar().getCigarElements()) {
    if (cigarElement.getOperator() != CigarOperator.HARD_CLIP && cigarElement.getOperator() != CigarOperator.SOFT_CLIP &&
      cigarElement.getOperator() != CigarOperator.INSERTION)
      break;
    else if (cigarElement.getOperator() == CigarOperator.INSERTION)
      this.addOp(new ClippingOp(0, cigarElement.getLength() - 1));
  }
  return clipRead(ClippingRepresentation.HARDCLIP_BASES);
}
public static GATKSAMRecord hardClipLeadingInsertions(GATKSAMRecord read) {

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 = 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

@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

if( !clippedRead.isEmpty() && clippedRead.getCigar().getReadLength() > 0 ) {
  clippedRead = ReadClipper.hardClipToRegion(clippedRead, activeRegion.getExtendedLoc().getStart(), activeRegion.getExtendedLoc().getStop());
  if( activeRegion.readOverlapsRegion(clippedRead) && clippedRead.getReadLength() > 0 ) {

代码示例来源：origin: broadgsa/gatk

if (read.isEmpty() || nLeadingSoftClips > read.getReadLength())
  return GATKSAMRecord.emptyRead(read);

代码示例来源：origin: broadgsa/gatk

if (read.isEmpty())
  return read;

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

if( read.isEmpty() ) { return 0L; } // the whole read was inside the adaptor so skip it