Class AbstractRecordAndOffset

  • Direct Known Subclasses:
    EdgingRecordAndOffset, SamLocusIterator.RecordAndOffset

    public class AbstractRecordAndOffset
    extends Object
    Holds a SAMRecord plus the zero-based offset into that SAMRecord's bases and quality scores that corresponds to the base and quality at the genomic position described the containing AbstractLocusInfo. One object represents one base for SamLocusIterator.RecordAndOffset implementation or one alignment block of SAMRecord for TypedRecordAndOffset implementation.
    • Field Detail

      • record

        protected final SAMRecord record
        A SAMRecord aligned to reference position
      • offset

        protected final int offset
        Zero-based offset in the read corresponding to the current position in AbstractLocusInfo
    • Constructor Detail

      • AbstractRecordAndOffset

        public AbstractRecordAndOffset​(SAMRecord record,
                                       int offset)
        Parameters:
        record - inner SAMRecord
        offset - from the start of the read
    • Method Detail

      • getOffset

        public int getOffset()
        Returns:
        offset of aligned read base from the start of the read.
      • getRecord

        public SAMRecord getRecord()
        Returns:
        inner SAMRecord object.
      • getReadBase

        public byte getReadBase()
        Returns:
        the read base according to offset.
      • getLength

        public int getLength()
        Returns:
        the length of alignment block represented by the object.
      • getReadName

        public String getReadName()
        Returns:
        read name of inner SAMRecord.
      • getBaseQualities

        public byte[] getBaseQualities()
        Returns:
        array of base qualities of inner SAMRecord.
      • getBaseQuality

        public byte getBaseQuality()
        Returns:
        the base quality according to offset.
      • validateOffset

        protected void validateOffset​(int offset,
                                      byte[] array)