Package htsjdk.samtools.util

Class AbstractLocusInfo<E extends AbstractRecordAndOffset>

  • All Implemented Interfaces:
    Locatable, Locus
    Direct Known Subclasses:
    SamLocusIterator.LocusInfo
    public class AbstractLocusInfo<E extends AbstractRecordAndOffset>
extends Object
implements Locus, Locatable
    The unit of iteration for AbstractLocusIterator. Holds information about the locus (the SAMSequenceRecord and 1-based position on the reference), plus list of AbstractRecordAndOffset objects, If RecordAndOffset class is used, one object represents one aligned read that overlaps the locus. If TypedRecordAndOffset class is used, one object represents one aligned read, that starts or ends at the locus.

    • Constructor Detail

      • AbstractLocusInfo

        public AbstractLocusInfo​(SAMSequenceRecord referenceSequence,
                         int position)
        Parameters:
        referenceSequence - reference sequence to which the reads are aligned
        position - position in the sequence to which the reads are aligned

    • Method Detail

      • add

        public void add​(E recordAndOffset)
        Accumulates info for one read aligned to the locus. Method doesn't check, that recordAndOffset is really aligned to current reference position, so it must have valid reference sequence and position or further processing can go wrong.
        Parameters:
        recordAndOffset - object to add to current locus

      • getSequenceIndex

        public int getSequenceIndex()
        Specified by:
        getSequenceIndex in interface Locus
        Returns:
        the index of reference sequence

      • getPosition

        public int getPosition()
        Specified by:
        getPosition in interface Locus
        Returns:
        1-based reference position

      • getRecordAndPositions

        @Deprecated
public List<E> getRecordAndPositions()
        Deprecated.
        since name of the method can be confusing, new implementation should be used getRecordAndOffsets()
        Returns:
        unmodifiable list of aligned to the reference position recordsAndOffsets

      • getRecordAndOffsets

        public List<E> getRecordAndOffsets()
        Returns:
        unmodifiable list of aligned to the reference position recordsAndOffsets

      • getSequenceName

        public String getSequenceName()
        Returns:
        the name of reference sequence

      • getSequenceLength

        public int getSequenceLength()
        Returns:
        the length of reference sequence

      • size

        public int size()
        Returns:
        the number of records overlapping the position

      • isEmpty

        public boolean isEmpty()
        Returns:
        true if RecordAndOffset list is empty;

      • getContig

        public String getContig()
        Description copied from interface: Locatable
        Gets the contig name for the contig this is mapped to. May return null if there is no unique mapping.
        Specified by:
        getContig in interface Locatable
        Returns:
        name of the contig this is mapped to, potentially null

      • getStart

        public int getStart()
        Specified by:
        getStart in interface Locatable
        Returns:
        1-based start position, undefined if getContig() == null

      • getEnd

        public int getEnd()
        Specified by:
        getEnd in interface Locatable
        Returns:
        1-based closed-ended position, undefined if getContig() == null