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

GATKSAMRecord.getBaseInsertionQualities介绍

[英]Default utility to query the base insertion quality of a read. If the read doesn't have one, it creates an array of default qualities (currently Q45) and assigns it to the read.
[中]用于查询读取的基本插入质量的默认实用程序。如果读取没有，它将创建一个默认质量数组（当前为Q45）并将其分配给读取。

代码示例

代码示例来源：origin: broadgsa/gatk

/**
 * Get the Base Insertion quality at this pileup position
 * @return a phred-scaled quality score as a byte
 */
public byte getBaseInsertionQual() {
  return isDeletion() ? DELETION_QUAL : read.getBaseInsertionQualities()[offset];
}

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

@Override
public void recordValues(final GATKSAMRecord read, final ReadCovariates values) {
  final byte[] baseQualities = read.getBaseQualities();
  final byte[] baseInsertionQualities = read.getBaseInsertionQualities();
  final byte[] baseDeletionQualities = read.getBaseDeletionQualities();
  for (int i = 0; i < baseQualities.length; i++) {
    values.addCovariate((int)baseQualities[i], (int)baseInsertionQualities[i], (int)baseDeletionQualities[i], i);
  }
}

代码示例来源：origin: broadgsa/gatk

public byte[] getBaseQualities( final EventType errorModel ) {
  switch( errorModel ) {
    case BASE_SUBSTITUTION:
      return getBaseQualities();
    case BASE_INSERTION:
      return getBaseInsertionQualities();
    case BASE_DELETION:
      return getBaseDeletionQualities();
    default:
      throw new ReviewedGATKException("Unrecognized Base Recalibration type: " + errorModel );
  }
}

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

readDataArray[idx].readBases = read.getReadBases();
readDataArray[idx].readQuals = read.getBaseQualities();
readDataArray[idx].insertionGOP = read.getBaseInsertionQualities();
readDataArray[idx].deletionGOP = read.getBaseDeletionQualities();
readDataArray[idx].overallGCP = gcp.get(read);

代码示例来源：origin: broadgsa/gatk

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);

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

/**
 * Pre-processing of the reads to be evaluated at the current location from the current sample.
 * We apply the PCR Error Model, and cap the minimum base, insertion, and deletion qualities of each read.
 * Modified copies of reads are packed into a new list, while original reads are retained for downstream use
 *
 * @param reads The original list of unmodified reads
 * @return processedReads. A new list of reads, in the same order, whose qualities have been altered by PCR error model and minimal quality thresholding
 */
private List<GATKSAMRecord> modifyReadQualities(final List<GATKSAMRecord> reads) {
  final List<GATKSAMRecord> result = new ArrayList<>(reads.size());
  for (final GATKSAMRecord read : reads) {
    final byte[] readBases = read.getReadBases();
    // NOTE -- must clone anything that gets modified here so we don't screw up future uses of the read
    final byte[] readQuals = read.getBaseQualities().clone();
    final byte[] readInsQuals = read.getBaseInsertionQualities().clone();
    final byte[] readDelQuals = read.getBaseDeletionQualities().clone();
    applyPCRErrorModel(readBases, readInsQuals, readDelQuals);
    capMinimumReadQualities(read, readQuals, readInsQuals, readDelQuals);
    // Create a new copy of the read and sets its base qualities to the modified versions.
    // Pack this into a new list for return
    result.add(GATKSAMRecord.createQualityModifiedRead(read, readBases, readQuals, readInsQuals, readDelQuals));
  }
  return result;
}

代码示例来源：origin: broadgsa/gatk

/**
 * Clears all attributes except ReadGroup of the read.
 */
public GATKSAMRecord simplify () {
  GATKSAMReadGroupRecord rg = getReadGroup(); // save the read group information
  byte[] insQuals = (this.getAttribute(BQSR_BASE_INSERTION_QUALITIES) == null) ? null : getBaseInsertionQualities();
  byte[] delQuals = (this.getAttribute(BQSR_BASE_DELETION_QUALITIES)  == null) ? null : getBaseDeletionQualities();
  this.clearAttributes(); // clear all attributes from the read
  this.setReadGroup(rg); // restore read group
  if (insQuals != null)
    this.setBaseQualities(insQuals, EventType.BASE_INSERTION); // restore base insertion if we had any
  if (delQuals != null)
    this.setBaseQualities(delQuals, EventType.BASE_DELETION); // restore base deletion if we had any
  return this;
}

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

debugDump("reads_java.txt",String.format("%d\n",(int)read.getBaseInsertionQualities()[i]),true);
debugDump("reads_java.txt",String.format("%d\n",(int)read.getBaseDeletionQualities()[i]),true);
debugDump("reads_java.txt",String.format("%d\n",(int)overallGCP[i]),true);
  debugDump("debug_dump.txt",new String(tmpByteArray)+" ",true);
  for(int k=0;k<read.getReadBases().length;++k)
    tmpByteArray[k] = (byte)((int)((read.getBaseInsertionQualities())[k]) + 33);
  debugDump("debug_dump.txt",new String(tmpByteArray)+" ",true);
  for(int k=0;k<read.getReadBases().length;++k)

代码示例来源：origin: broadgsa/gatk

final byte[] newBaseInsertionQuals = new byte[newLength];
final byte[] newBaseDeletionQuals = new byte[newLength];
System.arraycopy(read.getBaseInsertionQualities(), copyStart, newBaseInsertionQuals, 0, newLength);
System.arraycopy(read.getBaseDeletionQualities(), copyStart, newBaseDeletionQuals, 0, newLength);
hardClippedRead.setBaseQualities(newBaseInsertionQuals, EventType.BASE_INSERTION);

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

/**
 * Creates a hard-clipped view on a existing read record.
 * @param read the underlying unclipped read.
 * @param start inclusive first position in {@code read} included in the clipped view.
 * @param end inclusive last position in {@code read} included in the clipped view.
 */
public ClippedGATKSAMRecord(final GATKSAMRecord read, int start, int end) {
  super(read.getHeader());
  this.setReferenceIndex(read.getReferenceIndex());
  this.setAlignmentStart(read.getAlignmentStart() + start);
  this.setMappingQuality(100);
  // setting read indexing bin below
  this.setFlags(read.getFlags());
  this.setMateReferenceIndex(read.getMateReferenceIndex());
  this.setMateAlignmentStart(read.getMateAlignmentStart());
  this.setInferredInsertSize(read.getInferredInsertSize());
  this.setReadBases(Arrays.copyOfRange(read.getReadBases(), start, end));
  this.setBaseQualities(Arrays.copyOfRange(read.getBaseQualities(),start,end));
  this.setReadName(read.getReadName());
  insertionQuals = Arrays.copyOfRange(read.getBaseInsertionQualities(),start,end);
  deletionQuals = Arrays.copyOfRange(read.getBaseDeletionQualities(),start,end);
  // Set these to null in order to mark them as being candidates for lazy initialization.
  // If this is not done, they will have non-null defaults.
  super.setReadName(null);
  super.setCigarString(null);
  super.setReadBases(null);
  super.setBaseQualities(null);
  // Do this after the above because setCigarString will clear it.
  GATKBin.setReadIndexingBin(this, -1);
}

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

baseInsertionQualities = Arrays.copyOfRange(read.getBaseInsertionQualities(), numStartSoftClippedBases, endOfCopy);
  baseDeletionQualities = Arrays.copyOfRange(read.getBaseDeletionQualities(), numStartSoftClippedBases, endOfCopy);
} else {

代码示例来源：origin: broadgsa/gatk

final byte[] firstReadInsertionQuals = firstRead.getBaseInsertionQualities();
final byte[] firstReadDeletionQuals = firstRead.getBaseDeletionQualities();
final byte[] secondReadInsertionQuals = secondRead.getBaseInsertionQualities();
final byte[] secondReadDeletionQuals = secondRead.getBaseDeletionQualities();
for(int iii = 0; iii < firstReadStop; iii++) {

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

final byte[] iq = r.getBaseInsertionQualities();
final byte[] dq = r.getBaseDeletionQualities();
int refOffset = r.getAlignmentStart() - 1;