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

GATKSAMRecord.getReferenceIndex介绍

暂无

代码示例

代码示例来源：origin: broadgsa/gatk

/**
 * Does read start at the same position as described by currentContextIndex and currentAlignmentStart?
 *
 * @param read the read we want to test
 * @param currentContigIndex the contig index (from the read's getReferenceIndex) of the reads in this state manager
 * @param currentAlignmentStart the alignment start of the of the left-most position on the
 *                           genome of the reads in this read state manager
 * @return true if read has contig index and start equal to the current ones
 */
private boolean readStartsAtCurrentPosition(final GATKSAMRecord read, final int currentContigIndex, final int currentAlignmentStart) {
  return read.getAlignmentStart() == currentAlignmentStart && read.getReferenceIndex() == currentContigIndex;
}

代码示例来源：origin: broadgsa/gatk

/**
 * Get the reference index of the underlying read
 *
 * @return the reference index of the read
 */
@Ensures("result == getRead().getReferenceIndex()")
public int getReferenceIndex() {
  return getRead().getReferenceIndex();
}

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

/**
 * Add a read to the manager
 *
 * @param read  the read to add
 */
public void addRead(final GATKSAMRecord read) {
  if ( read == null ) throw new IllegalArgumentException("read added to manager is null, which is not allowed");
  // if the new read is on a different contig or we have too many reads, then we need to flush the queue and clear the map
  final boolean tooManyReads = getNReadsInQueue() >= MAX_RECORDS_IN_MEMORY;
  final boolean encounteredNewContig = getNReadsInQueue() > 0 && !waitingReads.peek().read.getReferenceIndex().equals(read.getReferenceIndex());
  if ( tooManyReads || encounteredNewContig ) {
    if ( DEBUG ) logger.warn("Flushing queue on " + (tooManyReads ? "too many reads" : ("move to new contig: " + read.getReferenceName() + " from " + waitingReads.peek().read.getReferenceName())) + " at " + read.getAlignmentStart());
    final int targetQueueSize = encounteredNewContig ? 0 : MAX_RECORDS_IN_MEMORY / 2;
    // write the required number of waiting reads to disk
    while ( getNReadsInQueue() > targetQueueSize )
      writer.addAlignment(waitingReads.poll().read);
  }
  final SplitRead splitRead = new SplitRead(read);
  // fix overhangs, as needed
  for ( final Splice splice : splices)
    fixSplit(splitRead, splice);
  // add the new read to the queue
  waitingReads.add(splitRead);
}

代码示例来源：origin: broadgsa/gatk

/**
 * Add read to this active region
 *
 * Read must have alignment start >= than the last read currently in this active region.
 *
 * @throws IllegalArgumentException if read doesn't overlap the extended region of this active region
 *
 * @param read a non-null GATKSAMRecord
 */
@Ensures("reads.size() == old(reads.size()) + 1")
public void add( final GATKSAMRecord read ) {
  if ( read == null ) throw new IllegalArgumentException("Read cannot be null");
  final GenomeLoc readLoc = genomeLocParser.createGenomeLoc( read );
  if ( ! readOverlapsRegion(read) )
    throw new IllegalArgumentException("Read location " + readLoc + " doesn't overlap with active region extended span " + extendedLoc);
  spanIncludingReads = spanIncludingReads.union( readLoc );
  if ( ! reads.isEmpty() ) {
    final GATKSAMRecord lastRead = reads.get(size() - 1);
    if ( ! lastRead.getReferenceIndex().equals(read.getReferenceIndex()) )
      throw new IllegalArgumentException("Attempting to add a read to ActiveRegion not on the same contig as other reads: lastRead " + lastRead + " attempting to add " + read);
    if ( read.getAlignmentStart() < lastRead.getAlignmentStart() )
      throw new IllegalArgumentException("Attempting to add a read to ActiveRegion out of order w.r.t. other reads: lastRead " + lastRead + " at " + lastRead.getAlignmentStart() + " attempting to add " + read + " at " + read.getAlignmentStart());
  }
  reads.add( read );
}

代码示例来源：origin: broadgsa/gatk

private static boolean unclippedReadOverlapsRegion(final GATKSAMRecord sampleRead, final int referenceIndex, final int start, final int end) {
  final int readReference = sampleRead.getReferenceIndex();
  if (readReference != referenceIndex)
    return false;
  final int readStart = sampleRead.getUnclippedStart();
  if (readStart > end)
    return false;
  final int readEnd = sampleRead.getReadUnmappedFlag() ? sampleRead.getUnclippedEnd()
      : Math.max(sampleRead.getUnclippedEnd(), sampleRead.getUnclippedStart());
  return readEnd >= start;
}

代码示例来源：origin: broadgsa/gatk

/**
 * Is the read dead?  That is, can it no longer be in any future active region, and therefore can be discarded?
 *
 * read: start |--------> stop ------ stop + extension
 * region:                      start |-----------------| end
 *
 * Since the regions are coming in order, read could potentially be contained in a future interval if
 * stop + activeRegionExtension >= end.  If, on the other hand, stop + extension is < the end
 * of this region, then we can discard it, since any future region could only include reads
 * up to end + 1 - extension.
 *
 * Note that this function doesn't care about the dead zone.  We're assuming that by
 * actually calling this function with an active region that region is already in the dead zone,
 * so checking that the read is in the dead zone doesn't make sense.
 *
 * @param read the read we're testing
 * @param activeRegion the current active region
 * @return true if the read is dead, false other
 */
@Requires({"read != null", "activeRegion != null"})
private boolean readCannotOccurInAnyMoreActiveRegions(final GATKSAMRecord read, final ActiveRegion activeRegion) {
  return read.getReferenceIndex() < activeRegion.getLocation().getContigIndex() ||
      ( read.getReferenceIndex() == activeRegion.getLocation().getContigIndex()
          && read.getAlignmentEnd() + getActiveRegionExtension() < activeRegion.getLocation().getStop() );
}

代码示例来源：origin: broadgsa/gatk

/**
 * Did read appear in the last shard?
 *
 * When we transition across shard boundaries we see duplicate reads because
 * each shard contains the reads that *overlap* the shard.  So if we just finished
 * shard 1-1000 and are now in 1001-2000 we'll see duplicate reads from 1001
 * that overlapped 1-1000.  This function tests read to determine if we would have
 * seen it before by asking if read.getAlignmentStart() is less than the
 * stop position of the last seen read at the start of the traversal.  The reason
 * we need to use the location of the last read at the start of the traversal
 * is that we update the lastRead during the traversal, and we only want to filter
 * out reads whose start is before the last read of the previous shard, not the
 * current shard.
 *
 * @param locOfLastReadAtTraversalStart the location of the last read seen at the start of the traversal
 * @param read the read we want to test if it's already been seen in the last shard
 * @return true if read would have appeared in the last shard, false otherwise
 */
@Requires({"read != null"})
private boolean appearedInLastShard(final GenomeLoc locOfLastReadAtTraversalStart, final GATKSAMRecord read) {
  if ( locOfLastReadAtTraversalStart == null )
    // we're in the first shard, so obviously the answer is no
    return false;
  else {
    // otherwise check to see if the alignment occurred in the previous shard
    return read.getAlignmentStart() <= locOfLastReadAtTraversalStart.getStart()
        // we're on the same contig
        && read.getReferenceIndex() == locOfLastReadAtTraversalStart.getContigIndex();
  }
}

代码示例来源：origin: broadgsa/gatk

if ( clippedFirstRead.getAlignmentEnd() < clippedSecondRead.getAlignmentStart() || !clippedFirstRead.getReferenceIndex().equals(clippedSecondRead.getReferenceIndex()) )
  return;

代码示例来源：origin: broadgsa/gatk

@Test( )
public void testCreationFromSAMRecord() {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 5);
  final GenomeLoc loc = genomeLocParser.createGenomeLoc(read);
  Assert.assertEquals(loc.getContig(), read.getReferenceName());
  Assert.assertEquals(loc.getContigIndex(), (int)read.getReferenceIndex());
  Assert.assertEquals(loc.getStart(), read.getAlignmentStart());
  Assert.assertEquals(loc.getStop(), read.getAlignmentEnd());
}

代码示例来源：origin: broadgsa/gatk

@Test( )
public void testCreationFromSAMRecordUnmappedButOnGenome() {
  final GATKSAMRecord read = ArtificialSAMUtils.createArtificialRead(header, "foo", 0, 1, 5);
  read.setReadUnmappedFlag(true);
  read.setCigarString("*");
  final GenomeLoc loc = genomeLocParser.createGenomeLoc(read);
  Assert.assertEquals(loc.getContig(), read.getReferenceName());
  Assert.assertEquals(loc.getContigIndex(), (int)read.getReferenceIndex());
  Assert.assertEquals(loc.getStart(), read.getAlignmentStart());
  Assert.assertEquals(loc.getStop(), read.getAlignmentStart());
}

代码示例来源：origin: broadgsa/gatk

/**
 * Tests the GenomeLoc variable in the ReadBin after adding arbitrary reads
 *
 * @param cigarString    the read's cigar string
 * @param alignmentStart the read's alignment start
 */
@Test(enabled = true, dataProvider = "reads")
public void testAddingReads(String cigarString, int alignmentStart) {
  final GATKSAMRecord read = createReadAndAddToBin(cigarString, alignmentStart);
  final GenomeLoc readLoc = parser.createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getSoftStart(), Math.max(read.getSoftStart(), read.getSoftEnd()));
  Assert.assertEquals(readBin.getLocation(), readLoc);
  readBin.clear();
}

代码示例来源：origin: broadgsa/gatk

if ( read.getReferenceIndex() == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX ) {
  cleanAndCallMap(ref, read, metaDataTracker, null);
  return 0;

代码示例来源：origin: broadgsa/gatk

this.with_itself_and_mate_mapped++;
if (!read.getReferenceIndex().equals(read.getMateReferenceIndex())) {
  this.with_mate_mapped_to_a_different_chr++;

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

if ( isEmpty() ) {
  firstContigIndex = iterator.peek().getReferenceIndex();
  firstAlignmentStart = iterator.peek().getAlignmentStart();
} else {

代码示例来源：origin: broadgsa/gatk

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