Package htsjdk.samtools.util

Class AbstractRecordAndOffset

java.lang.Object
htsjdk.samtools.util.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 Details

  • Constructor Details

  • Method Details

    • getOffset

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

    • getRecord

      public SAMRecord getRecord()
      Returns:
      inner SAMRecord object.

    • getAlignmentType

      public AbstractRecordAndOffset.AlignmentType getAlignmentType()
      The AbstractRecordAndOffset.AlignmentType of this object, which classifies whether the given event is a match, insertion, or deletion when queried from a SamLocusIterator.

    • 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)