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

GATKSAMRecord.setReadString介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

@Test(enabled = true)
public void testCheckSeqStored () {
  final GATKSAMRecord goodRead = ArtificialSAMUtils.createArtificialRead(new byte[]{(byte)'A'}, new byte[]{(byte)'A'}, "1M");
  final GATKSAMRecord badRead = ArtificialSAMUtils.createArtificialRead(new byte[]{}, new byte[]{}, "1M");
  badRead.setReadString("*");
  Assert.assertTrue(MalformedReadFilter.checkSeqStored(goodRead, true));
  Assert.assertFalse(MalformedReadFilter.checkSeqStored(badRead, true));
  try {
    MalformedReadFilter.checkSeqStored(badRead, false);
    Assert.assertTrue(false, "We should have exceptioned out in the previous line");
  } catch (UserException e) { }
}

代码示例来源：origin: broadgsa/gatk

protected GATKSAMRecord buildSAMRecord(final String readName, final String contig, final int alignmentStart) {
  GATKSAMRecord record = new GATKSAMRecord(header);
  record.setReadName(readName);
  record.setReferenceIndex(dictionary.getSequenceIndex(contig));
  record.setAlignmentStart(alignmentStart);
  record.setCigarString("1M");
  record.setReadString("A");
  record.setBaseQualityString("A");
  record.setReadGroup(readGroup);
  return record;
}

代码示例来源：origin: broadgsa/gatk

protected GATKSAMRecord buildSAMRecord(String readName, String contig, int alignmentStart, int alignmentEnd) {
  SAMFileHeader header = ArtificialSAMUtils.createDefaultReadGroup(new SAMFileHeader(), "test", "test");
  header.setSequenceDictionary(dictionary);
  header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
  GATKSAMRecord record = new GATKSAMRecord(header);
  record.setReadName(readName);
  record.setReferenceIndex(dictionary.getSequenceIndex(contig));
  record.setAlignmentStart(alignmentStart);
  Cigar cigar = new Cigar();
  int len = alignmentEnd - alignmentStart + 1;
  cigar.add(new CigarElement(len, CigarOperator.M));
  record.setCigar(cigar);
  record.setReadString(new String(new char[len]).replace("\0", "A"));
  record.setBaseQualities(new byte[len]);
  record.setReadGroup(new GATKSAMReadGroupRecord(header.getReadGroup("test")));
  return record;
}

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

correctedRead.setIsStrandless(inputRead.isStrandless());
correctedRead.setReadBases(inputRead.getReadBases());
correctedRead.setReadString(inputRead.getReadString());
correctedRead.setReadGroup(inputRead.getReadGroup());
return correctedRead;