Class SamLocusIterator.LocusInfo
java.lang.Object
htsjdk.samtools.util.AbstractLocusInfo<SamLocusIterator.RecordAndOffset>
htsjdk.samtools.util.SamLocusIterator.LocusInfo
- Enclosing class:
SamLocusIterator
public static final class SamLocusIterator.LocusInfo
extends AbstractLocusInfo<SamLocusIterator.RecordAndOffset>
The unit of iteration. Holds information about the locus (the SAMSequenceRecord and 1-based position
on the reference), plus List of ReadAndOffset objects, one for each read that overlaps the locus;
two more List_s_ of ReadAndOffset objects include reads that overlap the locus with insertions and deletions
respectively
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoidaddDeleted(SAMRecord read, int previousPosition) Accumulate info for one read with a deletionvoidaddInserted(SAMRecord read, int firstPosition) Accumulate info for one read with an insertion.booleanisEmpty()intsize()Methods inherited from class AbstractLocusInfo
add, getContig, getEnd, getPosition, getRecordAndOffsets, getRecordAndPositions, getSequenceIndex, getSequenceLength, getSequenceName, getStart, toStringMethods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, waitMethods inherited from interface Locatable
contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf
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Constructor Details
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LocusInfo
- Parameters:
referenceSequence- reference sequence at which the reads are alignedposition- position in the sequence at which the reads are aligned
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Method Details
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addDeleted
Accumulate info for one read with a deletion -
addInserted
Accumulate info for one read with an insertion. For this locus, the reads in the insertion are included also in recordAndOffsets -
getDeletedInRecord
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getInsertedInRecord
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size
public int size()- Overrides:
sizein classAbstractLocusInfo<SamLocusIterator.RecordAndOffset>- Returns:
- the number of records overlapping the position, with deletions included if they are being tracked.
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isEmpty
public boolean isEmpty()- Overrides:
isEmptyin classAbstractLocusInfo<SamLocusIterator.RecordAndOffset>- Returns:
trueif all the RecordAndOffset lists are empty;falseif at least one have records
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