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

GATKSAMRecord.hasBaseIndelQualities介绍

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代码示例

代码示例来源：origin: broadgsa/gatk

hardClippedRead.setAlignmentStart(read.getAlignmentStart() + calculateAlignmentStartShift(read.getCigar(), cigarShift.cigar));
if (read.hasBaseIndelQualities()) {
  final byte[] newBaseInsertionQuals = new byte[newLength];
  final byte[] newBaseDeletionQuals = new byte[newLength];

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

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

代码示例来源：origin: broadgsa/gatk

returnRead.setMappingQuality( firstRead.getMappingQuality() );
if( firstRead.hasBaseIndelQualities() || secondRead.hasBaseIndelQualities() ) {
  final byte[] firstReadInsertionQuals = firstRead.getBaseInsertionQualities();
  final byte[] firstReadDeletionQuals = firstRead.getBaseDeletionQualities();