org.broadinstitute.gatk.utils.sam.GATKSAMRecord.<init>()方法的使用及代码示例

x33g5p2x  于2022-01-20 转载在 其他  
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本文整理了Java中org.broadinstitute.gatk.utils.sam.GATKSAMRecord.<init>()方法的一些代码示例，展示了GATKSAMRecord.<init>()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.<init>()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：<init>

GATKSAMRecord.<init>介绍

[英]HACK TO CREATE GATKSAMRECORD WITH ONLY A HEADER FOR TESTING PURPOSES ONLY
[中]HACK创建只有一个头的GATKSAMRECORD仅用于测试目的

代码示例

代码示例来源：origin: broadgsa/gatk

@Override public GATKSAMRecord next() {
  SAMRecord next = it.next();
  if (next instanceof GATKSAMRecord) {
    return (GATKSAMRecord)next;
  } else {
    return new GATKSAMRecord(next);
  }
}
@Override public void remove() { it.remove(); }

代码示例来源：origin: broadgsa/gatk

(refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START))
  throw new ReviewedGATKException("Invalid alignment start for artificial read, start = " + alignmentStart);
GATKSAMRecord record = new GATKSAMRecord(header);
record.setReadName(name);
record.setReferenceIndex(refIndex);

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

@Test
  public void testUnmappedReadsDoNotFail() {
    // create an unmapped read
    final GATKSAMRecord read = new GATKSAMRecord(ArtificialSAMUtils.createArtificialSamHeader());
    read.setReadName("foo");
    read.setReferenceName("*");
    read.setAlignmentStart(100);
    read.setCigarString("*");
    read.setReadUnmappedFlag(true);

    // try to add it to the manager
    final OverhangFixingManager manager = new OverhangFixingManager(null, null, null, 100, 1, 30, false);
    manager.addRead(read); // we just want to make sure that the following call does not fail
    Assert.assertTrue(true);
  }
}

代码示例来源：origin: broadgsa/gatk

@Test
public void testSecondaryAlignmentsDoNotCauseAccidentalRemovalOfMate() {
  final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 530, 1594, true, false);
  final GATKSAMRecord read1 = properReads.get(0);
  read1.setFlags(99);   // first in proper pair, mate negative strand
  final GATKSAMRecord read2Primary = properReads.get(1);
  read2Primary.setFlags(147);   // second in pair, mate unmapped, not primary alignment
  read2Primary.setAlignmentStart(1596); // move the read
  final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary);
  read2NonPrimary.setReadName("foo");
  read2NonPrimary.setFlags(393);   // second in proper pair, on reverse strand
  read2NonPrimary.setAlignmentStart(451);
  read2NonPrimary.setMateAlignmentStart(451);
  final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 10000, 200, 10000);
  manager.addRead(read2NonPrimary, false, false);
  manager.addRead(read1, false, false);
  for ( int i = 0; i < ConstrainedMateFixingManager.EMIT_FREQUENCY; i++ )
    manager.addRead(ArtificialSAMUtils.createArtificialRead(header, "foo" + i, 0, 1500, 10), false, false);
  Assert.assertTrue(manager.forMateMatching.containsKey("foo"));
}

代码示例来源：origin: broadgsa/gatk

@Test
public void testSecondaryAlignmentsDoNotInterfere() {
  final List<GATKSAMRecord> properReads = ArtificialSAMUtils.createPair(header, "foo", 1, 10, 30, true, false);
  final GATKSAMRecord read1 = properReads.get(0);
  read1.setAlignmentStart(8); // move the read
  read1.setFlags(99);   // first in proper pair, mate negative strand
  final GATKSAMRecord read2Primary = properReads.get(1);
  read2Primary.setFlags(147);   // second in pair, mate unmapped, not primary alignment
  Assert.assertEquals(read1.getInferredInsertSize(), 21);
  final GATKSAMRecord read2NonPrimary = new GATKSAMRecord(read2Primary);
  read2NonPrimary.setFlags(393);   // second in proper pair, on reverse strand
  final ConstrainedMateFixingManager manager = new ConstrainedMateFixingManager(null, genomeLocParser, 1000, 1000, 1000);
  manager.addRead(read1, true, false);
  manager.addRead(read2NonPrimary, false, false);
  manager.addRead(read2Primary, false, false);
  Assert.assertEquals(manager.getNReadsInQueue(), 3);
  for ( final SAMRecord read : manager.getReadsInQueueForTesting() ) {
    if ( read.getFirstOfPairFlag() ) {
      Assert.assertEquals(read.getFlags(), 99);
      Assert.assertEquals(read.getInferredInsertSize(), 23);
    } else if ( read.getNotPrimaryAlignmentFlag() ) {
      Assert.assertEquals(read.getFlags(), 393);
      Assert.assertEquals(read.getInferredInsertSize(), -21);
    } else {
      Assert.assertEquals(read.getFlags(), 147);
      Assert.assertEquals(read.getInferredInsertSize(), -23);
    }
  }
}

代码示例来源：origin: broadgsa/gatk

read2.setFlags(161);   // second in pair, mate negative strand
final GATKSAMRecord read2Supp = new GATKSAMRecord(read2);
read2Supp.setReadName("foo");
read2Supp.setFlags(2209);   // second in pair, mate negative strand, supplementary

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

/**
 * Creates and writes an artificial read given the appropriate data
 *
 * @param readBases   the bases
 * @param contig      the contig
 * @param start       the read start
 * @param cigar       the cigar string
 * @param sample      the sample name (used to get the right read group)
 * @param isNegStrand should this read be on the negative strand?
 */
private void writeRead(final byte[] readBases, final String contig, final int start,
      final String cigar, final String sample, final boolean isNegStrand) {
  final GATKSAMRecord read = new GATKSAMRecord(header);
  read.setBaseQualities(readQuals);
  read.setReadBases(readBases);
  read.setReadName("" + readNameCounter++);
  read.setCigarString(cigar);
  read.setReadPairedFlag(false);
  read.setAlignmentStart(start);
  read.setMappingQuality(60);
  read.setReferenceName(contig);
  read.setReadNegativeStrandFlag(isNegStrand);
  read.setAttribute("RG", sampleRG(sample).getReadGroupId());
  readWriter.addAlignment(read);
}

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

Arrays.fill(readQuals, (byte)phredScaledErrorRate);
GATKSAMRecord read = new GATKSAMRecord(header);
read.setBaseQualities(readQuals);
read.setReadBases(readBases);

代码示例来源：origin: broadgsa/gatk

final GATKSAMRecord returnRead = new GATKSAMRecord( firstRead.getHeader() );
returnRead.setIsStrandless(true);
returnRead.setAlignmentStart( firstRead.getAlignmentStart() );

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

GATKSAMRecord correctedRead = new GATKSAMRecord(inputRead);

代码示例来源：origin: broadgsa/gatk

final GATKSAMRecord emptyRead = new GATKSAMRecord(read.getHeader());
emptyRead.setReferenceIndex(read.getReferenceIndex());
emptyRead.setAlignmentStart(0);

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

/**
 * 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;
}

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