Java SAMRecord.getReferenceIndex方法代码示例

import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
public BAQCalculationResult calcBAQFromHMM(SAMRecord read, RefContentProvider refContentProvider) {
    // start is alignment start - band width / 2 - size of first I element, if there is one.  Stop is similar
    int offset = getBandWidth() / 2;
    long readStart = includeClippedBases ? read.getUnclippedStart() : read.getAlignmentStart();
    long start = Math.max(readStart - offset - ReadUtils.getFirstInsertionOffset(read), 0);
    long stop = (includeClippedBases ? read.getUnclippedEnd() : read.getAlignmentEnd()) + offset + ReadUtils.getLastInsertionOffset(read);

    if ( stop > refContentProvider.getSamSequenceDictionary().getSequence(read.getReferenceName()).getSequenceLength() ) {
        return null;
    } else {
        // now that we have the start and stop, get the reference sequence covering it
        GenomeLoc locus = new GenomeLoc(read.getReferenceName(), read.getReferenceIndex(), (int)start, (int)stop);
        byte[] refSeq = refContentProvider.getReferenceContext(locus).getBases();
        return calcBAQFromHMM(read, refSeq, (int)(start - readStart));
    }
}
 

import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
/**
 * Write the record.
 *
 * @param alignment SAMRecord.
 */
public BasicSamRecord transfer(final SAMRecord alignment) {
    String readName = alignment.getReadName();
    int flags = alignment.getFlags();
    int contigId = alignment.getReferenceIndex();
    if (contigId == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
        contigId = FAKE_CONTIG_ID;
    }
    String contigName = alignment.getReferenceName();
    int position = alignment.getAlignmentStart();
    int mapQ = alignment.getMappingQuality();
    String cigar = alignment.getCigarString();
    int mateContigId = alignment.getMateReferenceIndex();
    if (mateContigId == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX) {
        mateContigId = FAKE_CONTIG_ID;
    }
    String mateContigName = alignment.getMateReferenceName();
    int matePosition = alignment.getMateAlignmentStart();
    int inferredSize = alignment.getInferredInsertSize();
    byte[] sequence = alignment.getReadString().getBytes();
    byte[] quality = alignment.getBaseQualityString().getBytes();
    List<SAMRecord.SAMTagAndValue> attributes = alignment.getAttributes();
    List<String> encodedTags = new ArrayList<>(attributes.size());
    for (SAMRecord.SAMTagAndValue attribute : attributes) {
        encodedTags.add(tagCodec.encode(attribute.tag, attribute.value));
    }

    // 在这里统一不压缩，压缩操作是由scala代码中的执行引擎统一调配的。
    return BasicSamRecord.apply(false, readName, flags, contigId, contigName, position, mapQ,
            cigar, mateContigId, mateContigName, matePosition, inferredSize,
            sequence, quality, encodedTags);
}
 

import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
/**
 * Create a genome loc, given a read. If the read is unmapped, *and* yet the read has a contig and start position,
 * then a GenomeLoc is returned for contig:start-start, otherwise an UNMAPPED GenomeLoc is returned.
 *
 * @param read the read from which to create a genome loc
 * @return the GenomeLoc that was created
 */
public GenomeLoc createGenomeLoc(final SAMRecord read) {
    if (read.getReadUnmappedFlag() && read.getReferenceIndex() == -1)
        // read is unmapped and not placed anywhere on the genome
        return GenomeLoc.UNMAPPED;
    else {
        // Use Math.max to ensure that end >= start (Picard assigns the end to reads that are entirely within an insertion as start-1)
        final int end = read.getReadUnmappedFlag() ? read.getAlignmentStart() : Math.max(read.getAlignmentEnd(), read.getAlignmentStart());
        return createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getAlignmentStart(), end, false);
    }
}
 

import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
/**
 * Create a genome loc, given a read using its unclipped alignment. If the read is unmapped, *and* yet the read has a contig and start position,
 * then a GenomeLoc is returned for contig:start-start, otherwise an UNMAPPED GenomeLoc is returned.
 *
 * @param read the read from which to create a genome loc
 * @return the GenomeLoc that was created
 */
public GenomeLoc createGenomeLocUnclipped(final SAMRecord read) {
    if (read.getReadUnmappedFlag() && read.getReferenceIndex() == -1)
        // read is unmapped and not placed anywhere on the genome
        return GenomeLoc.UNMAPPED;
    else {
        // Use Math.max to ensure that end >= start (Picard assigns the end to reads that are entirely within an insertion as start-1)
        final int end = read.getReadUnmappedFlag() ? read.getUnclippedEnd() : Math.max(read.getUnclippedEnd(), read.getUnclippedStart());
        return createGenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getUnclippedStart(), end, false);
    }
}
 

import htsjdk.samtools.SAMRecord; //导入方法依赖的package包/类
/**
 * Due to (unfortunate) multiple ways to indicate that read is unmapped allowed by SAM format
 * specification, one may need this convenience shortcut. Checks both 'read unmapped' flag and
 * alignment reference index/start.
 *
 * Our life would be so much easier if all sam files followed the specs. In reality,
 * sam files (including those generated by maq or bwa) miss headers altogether. When
 * reading such a SAM file, reference name is set, but since there is no sequence dictionary,
 * null is always returned for referenceIndex. Let's be paranoid here, and make sure that
 * we do not call the read "unmapped" when it has only reference name set with ref. index missing
 * or vice versa.
 *
 * @param r a non-null record
 * @return true if read is unmapped
 */
public static boolean isReadUnmapped(final SAMRecord r) {
    if ( r == null )
        throw new IllegalArgumentException("Read cannot be null");

    return r.getReadUnmappedFlag() ||
            !((r.getReferenceIndex() != null && r.getReferenceIndex() != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX ||
                    r.getReferenceName() != null && !r.getReferenceName().equals(SAMRecord.NO_ALIGNMENT_REFERENCE_NAME)) &&
                    r.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START);

}