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

GATKSAMRecord.setReferenceIndex介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

@Test( )
public void testCreationFromSAMRecordUnmapped() {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 5);
  read.setReadUnmappedFlag(true);
  read.setReferenceIndex(-1);
  final GenomeLoc loc = genomeLocParser.createGenomeLoc(read);
  Assert.assertTrue(loc.isUnmapped());
}

代码示例来源：origin: broadgsa/gatk

GATKSAMRecord record = new GATKSAMRecord(header);
record.setReadName(name);
record.setReferenceIndex(refIndex);
record.setAlignmentStart(alignmentStart);
List<CigarElement> elements = new ArrayList<CigarElement>();

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

/**
 * Write out a representation of this haplotype as a read
 *
 * @param haplotype a haplotype to write out.  Cannot be null
 * @param paddedRefLoc the reference location.  Cannot be null
 * @param isAmongBestHaplotypes true if among the best haplotypes, false if it was just one possible but not so good
 */
private void writeHaplotype(final Haplotype haplotype,
              final GenomeLoc paddedRefLoc,
              final boolean isAmongBestHaplotypes) {
  final GATKSAMRecord record = new GATKSAMRecord(output.getHeader());
  record.setReadBases(haplotype.getBases());
  record.setAlignmentStart(paddedRefLoc.getStart() + haplotype.getAlignmentStartHapwrtRef());
  record.setBaseQualities(Utils.dupBytes((byte) '!', haplotype.getBases().length));
  record.setCigar(AlignmentUtils.consolidateCigar(haplotype.getCigar()));
  record.setMappingQuality(isAmongBestHaplotypes ? 60 : 0);
  record.setReadName("HC" + uniqueNameCounter++);
  record.setAttribute(AlignmentUtils.HAPLOTYPE_TAG,haplotype.hashCode());
  record.setReadUnmappedFlag(false);
  record.setReferenceIndex(paddedRefLoc.getContigIndex());
  record.setAttribute(SAMTag.RG.toString(), READ_GROUP_ID);
  record.setFlags(16);
  output.add(record);
}

代码示例来源：origin: broadgsa/gatk

emptyRead.setReferenceIndex(read.getReferenceIndex());
emptyRead.setAlignmentStart(0);
emptyRead.setMappingQuality(0);

代码示例来源：origin: broadgsa/gatk

/**
 * Build a SAM record featuring the absolute minimum required dataset.
 *
 * @param contig         Contig to populate.
 * @param alignmentStart start of alignment
 * @param alignmentEnd   end of alignment
 *
 * @return New SAM Record
 */
protected GATKSAMRecord buildSAMRecord(String readName, String contig, int alignmentStart, int alignmentEnd) {
  SAMFileHeader header = new SAMFileHeader();
  header.setSequenceDictionary(sequenceSourceFile.getSequenceDictionary());
  GATKSAMRecord record = new GATKSAMRecord(header);
  record.setReadName(readName);
  record.setReferenceIndex(sequenceSourceFile.getSequenceDictionary().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.setReadBases(new byte[len]);
  record.setBaseQualities(new byte[len]);
  return record;
}