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

GATKSAMRecord.getReadBases介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

/**
 * Given a read, outputs the read bases in a string format
 *
 * @param read the read
 * @return a string representation of the read bases
 */
public static String convertReadBasesToString(GATKSAMRecord read) {
  String bases = "";
  for (byte b : read.getReadBases()) {
    bases += (char) b;
  }
  return bases.toUpperCase();
}

代码示例来源：origin: broadgsa/gatk

/**
 * Returns the reverse complement of the read bases
 *
 * @param read the read
 * @return the reverse complement of the read bases
 */
public static String getBasesReverseComplement(GATKSAMRecord read) {
  return getBasesReverseComplement(read.getReadBases());
}

代码示例来源：origin: broadgsa/gatk

public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker tracker) {
  for(byte base: read.getReadBases()) {
    switch(base) {
      case 'A': As++; break;
      case 'C': Cs++; break;
      case 'G': Gs++; break;
      case 'T': Ts++; break;
    }
  }
  return 1;
}

代码示例来源：origin: broadgsa/gatk

/**
 * Get the base aligned to the genome at this location
 *
 * If the current element is a deletion returns DELETION_BASE
 *
 * @return a base encoded as a byte
 */
@Ensures("result != DELETION_BASE || (isDeletion() && result == DELETION_BASE)")
public byte getBase() {
  return isDeletion() ? DELETION_BASE : read.getReadBases()[offset];
}

代码示例来源：origin: broadgsa/gatk

public static String expectedContext (GATKSAMRecord read, int offset, int contextSize) {
  final String bases = stringFrom(read.getReadBases());
  String expectedContext = null;
  if (offset - contextSize + 1 >= 0) {
    String context = bases.substring(offset - contextSize + 1, offset + 1);
    if (!context.contains("N"))
      expectedContext = context;
  }
  return expectedContext;
}

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

private void performBatchAdditions(final List<GATKSAMRecord> reads, final List<Haplotype> haplotypes, Map<GATKSAMRecord,byte[]> gcp) {
  for(final GATKSAMRecord read : reads){
    final byte[] readBases = read.getReadBases();
    final byte[] readQuals = read.getBaseQualities();
    final byte[] readInsQuals = read.getBaseInsertionQualities();
    final byte[] readDelQuals = read.getBaseDeletionQualities();
    final byte[] overallGCP = gcp.get(read);
    batchAdd(haplotypes, readBases, readQuals, readInsQuals, readDelQuals, overallGCP);
  }
}

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

/**
* Main entry routine to add all kmers in a read to the read map counter
* @param read                        Read to add bases
*/
@Requires("read != null")
protected void addReadKmers(final GATKSAMRecord read) {
  if (DONT_CORRECT_IN_LONG_HOMOPOLYMERS && maxHomopolymerLengthInRegion > MAX_HOMOPOLYMER_THRESHOLD)
    return;
  final byte[] readBases = read.getReadBases();
  for (int offset = 0; offset <= readBases.length-kmerLength; offset++ )  {
    countsByKMer.addKmer(new Kmer(readBases,offset,kmerLength),1);
  }
}

代码示例来源：origin: broadgsa/gatk

/**
 * Get the bases for an insertion that immediately follows this alignment state, or null if none exists
 *
 * @see #getLengthOfImmediatelyFollowingIndel() for details on the meaning of immediately.
 *
 * If the immediately following state isn't an insertion, returns null
 *
 * @return actual sequence of inserted bases, or a null if the event is a deletion or if there is no event in the associated read.
 */
@Ensures("result == null || result.length() == getLengthOfImmediatelyFollowingIndel()")
public String getBasesOfImmediatelyFollowingInsertion() {
  final CigarElement element = getNextIndelCigarElement();
  if ( element != null && element.getOperator() == CigarOperator.I ) {
    final int getFrom = offset + 1;
    final byte[] bases = Arrays.copyOfRange(read.getReadBases(), getFrom, getFrom + element.getLength());
    return new String(bases);
  } else
    return null;
}

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

private void writeDebugLikelihoods(final GATKSAMRecord processedRead, final Haplotype haplotype, final double log10l){
  likelihoodsStream.printf("%s %s %s %s %s %s %f%n",
        haplotype.getBaseString(),
        new String(processedRead.getReadBases() ),
        SAMUtils.phredToFastq(processedRead.getBaseQualities()),
        SAMUtils.phredToFastq(processedRead.getBaseInsertionQualities() ),
        SAMUtils.phredToFastq(processedRead.getBaseDeletionQualities() ),
        SAMUtils.phredToFastq(constantGCP),
        log10l);
}

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

/**
 * Loads the read that is going to be evaluated in following calls to {@link #calculateLocalLikelihoods}.
 *
 * @param read the target read.
 * @throws NullPointerException if {@code read} is null.
 */
@Override
public void loadRead(final GATKSAMRecord read) {
  loadRead(read.getReadBases(),read.getBaseQualities(),read.getBaseInsertionQualities(),read.getBaseDeletionQualities(),read.getMappingQuality());
}

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

protected boolean[] calculateSkipArray( final GATKSAMRecord read, final RefMetaDataTracker metaDataTracker ) {
  final byte[] bases = read.getReadBases();
  final boolean[] skip = new boolean[bases.length];
  final boolean[] knownSites = calculateKnownSites(read, metaDataTracker.getValues(RAC.knownSites));
  for( int iii = 0; iii < bases.length; iii++ ) {
    skip[iii] = !BaseUtils.isRegularBase(bases[iii]) || isLowQualityBase(read, iii) || knownSites[iii] || badSolidOffset(read, iii);
  }
  return skip;
}

代码示例来源：origin: broadgsa/gatk

public static GATKSAMRecord combineDuplicates(GenomeLocParser genomeLocParser,List<GATKSAMRecord> duplicates, int maxQScore) {
  if ( duplicates.size() == 0 )
    return null;
  // make the combined read by copying the first read and setting the
  // bases and quals to new arrays
  GATKSAMRecord comb = tmpCopyRead(duplicates.get(0));
  //GATKSAMRecord comb = tmpCopyRead(duplicates.get(0));
  comb.setDuplicateReadFlag(false);
  int readLen = comb.getReadBases().length;
  byte[] bases = new byte[readLen];
  byte[] quals = new byte[readLen];
  for ( int i = 0; i < readLen; i++ ) {
    //System.out.printf("I is %d%n", i);
    //for ( GATKSAMRecord read : duplicates ) {
    //    System.out.printf("dup base %c %d%n", (char)read.getReadBases()[i], read.getBaseQualities()[i]);
    //}
    Pair<Byte, Byte> baseAndQual = combineBaseProbs(genomeLocParser,duplicates, i, maxQScore);
    bases[i] = baseAndQual.getFirst();
    quals[i] = baseAndQual.getSecond();            
  }
  comb.setBaseQualities(quals);
  comb.setReadBases(bases);
  return comb;
}

代码示例来源：origin: broadgsa/gatk

@Test (enabled = true)
public void testGetBasesReverseComplement() {
  int iterations = 1000;
  Random random = Utils.getRandomGenerator();
  while(iterations-- > 0) {
    final int l = random.nextInt(1000);
    GATKSAMRecord read = GATKSAMRecord.createRandomRead(l);
    byte [] original = read.getReadBases();
    byte [] reconverted = new byte[l];
    String revComp = ReadUtils.getBasesReverseComplement(read);
    for (int i=0; i<l; i++) {
      reconverted[l-1-i] = BaseUtils.getComplement((byte) revComp.charAt(i));
    }
    Assert.assertEquals(reconverted, original);
  }
}

代码示例来源：origin: broadgsa/gatk

@Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
  // store the original bases and then write Ns over low quality ones
  final byte[] originalBases = read.getReadBases().clone();
  final boolean negativeStrand = read.getReadNegativeStrandFlag();
  byte[] bases = read.getReadBases();
  if (negativeStrand)
    bases = BaseUtils.simpleReverseComplement(bases);
  // don't record reads with N's
  if (!BaseUtils.isAllRegularBases(bases))
    return;
  for (int i = 0; i < bases.length; i++) {
    final Pair<byte[], Integer> res = findTandemRepeatUnits(bases, i);
    // to merge repeat unit and repeat length to get covariate value:
    final String repeatID =  getCovariateValueFromUnitAndLength(res.first,  res.second);
    final int key = keyForRepeat(repeatID);
    final int readOffset = (negativeStrand ? bases.length - i - 1 : i);
    values.addCovariate(key, key, key, readOffset);
  }
  // put the original bases back in
  read.setReadBases(originalBases);
}

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-protected

@Test(dataProvider = "ReadAlignedToRefData", enabled = true)
public void testReadAlignedToRef(final GATKSAMRecord read, final Haplotype haplotype, final int refStart, final int expectedReadStart, final String expectedReadCigar) throws Exception {
  final HaplotypeBAMWriter writer = new CalledHaplotypeBAMWriter(new MockDestination());
  final GATKSAMRecord originalReadCopy = (GATKSAMRecord)read.clone();
  if ( expectedReadCigar == null ) {
    Assert.assertNull(AlignmentUtils.createReadAlignedToRef(read, haplotype, haplotype, refStart, true));
  } else {
    final Cigar expectedCigar = TextCigarCodec.decode(expectedReadCigar);
    final GATKSAMRecord alignedRead = AlignmentUtils.createReadAlignedToRef(read, haplotype, haplotype, refStart, true);
    Assert.assertEquals(alignedRead.getReadName(), originalReadCopy.getReadName());
    Assert.assertEquals(alignedRead.getAlignmentStart(), expectedReadStart);
    Assert.assertEquals(alignedRead.getReadBases(), originalReadCopy.getReadBases());
    Assert.assertEquals(alignedRead.getBaseQualities(), originalReadCopy.getBaseQualities());
    Assert.assertEquals(alignedRead.getAlignmentStart(), expectedReadStart);
    Assert.assertEquals(alignedRead.getCigar(), expectedCigar);
    Assert.assertNotNull(alignedRead.getAttribute("HC"));
  }
  Assert.assertEquals(read, originalReadCopy, "createReadAlignedToRef seems be modifying the original read!");
}

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-protected

/**
 * Try to fix the given read using the given split
 *
 * @param read        the read to fix
 * @param splice      the split (bad region to clip out)
 */
private void fixSplit(final SplitRead read, final Splice splice) {
  // if the read doesn't even overlap the split position then we can just exit
  if ( read.loc == null || !splice.loc.overlapsP(read.loc) )
    return;
  if ( isLeftOverhang(read.loc, splice.loc) ) {
    final int overhang = splice.loc.getStop() - read.loc.getStart() + 1;
    if ( overhangingBasesMismatch(read.read.getReadBases(), 0, splice.reference, splice.reference.length - overhang, overhang) ) {
      final GATKSAMRecord clippedRead = ReadClipper.hardClipByReadCoordinates(read.read, 0, overhang - 1);
      read.setRead(clippedRead);
    }
  }
  else if ( isRightOverhang(read.loc, splice.loc) ) {
    final int overhang = read.loc.getStop() - splice.loc.getStart() + 1;
    if ( overhangingBasesMismatch(read.read.getReadBases(), read.read.getReadLength() - overhang, splice.reference, 0, overhang) ) {
      final GATKSAMRecord clippedRead = ReadClipper.hardClipByReadCoordinates(read.read, read.read.getReadLength() - overhang, read.read.getReadLength() - 1);
      read.setRead(clippedRead);
    }
  }
}

代码示例来源：origin: broadgsa/gatk

public Integer map(ReferenceContext ref, GATKSAMRecord read, RefMetaDataTracker metaDataTracker) {
  // we can not deal with screwy records
  if ( read.getReadUnmappedFlag() || read.getCigar().numCigarElements() == 0 ) {
    emit(read);
    return 0;
  }
  // move existing indels (for 1 indel reads only) to leftmost position within identical sequence
  int numBlocks = AlignmentUtils.getNumAlignmentBlocks(read);
  if ( numBlocks == 2 ) {
    Cigar newCigar = AlignmentUtils.leftAlignIndel(IndelRealigner.unclipCigar(read.getCigar()), ref.getBases(), read.getReadBases(), 0, 0, true);
    newCigar = IndelRealigner.reclipCigar(newCigar, read);
    read.setCigar(newCigar);
  }
  emit(read);
  return 1;
}