Package htsjdk.samtools.util
Class EdgingRecordAndOffset
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- htsjdk.samtools.util.AbstractRecordAndOffset
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- htsjdk.samtools.util.EdgingRecordAndOffset
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public abstract class EdgingRecordAndOffset extends AbstractRecordAndOffset
Holds a SAMRecord plus the zero-based offset into that SAMRecord's bases and quality scores that corresponds to the base and quality for the start of alignment block at the genomic position described by the AbstractLocusInfo. This is implementation for EdgeReadIterator, fieldtype
added to indicate whether object represents the start or the end of an alignment block.Subclasses StartEdgingRecordAndOffset and EndEdgingRecordAndOffset are used in EdgeReadIterator to distinguish starting and ending of the alignment block as for each alignment block two objects of
EdgingRecordAndOffset
are created with two different types. The main idea of using EdgeReadIterator is to process alignment block starting from locus where BEGIN type occurs, aggregate information per locus and keep it until END type occurs, then remove alignment block from consideration.
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
EdgingRecordAndOffset.Type
Describes the type ofTypedRecordAndOffset
, whether it represents the start or the end of an alignment block.-
Nested classes/interfaces inherited from class htsjdk.samtools.util.AbstractRecordAndOffset
AbstractRecordAndOffset.AlignmentType
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Field Summary
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Fields inherited from class htsjdk.samtools.util.AbstractRecordAndOffset
alignmentType, offset, record
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Method Summary
All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description static EdgingRecordAndOffset
createBeginRecord(SAMRecord record, int offset, int length, int refPos)
static EdgingRecordAndOffset
createEndRecord(EdgingRecordAndOffset startRecord)
abstract byte
getBaseQuality(int position)
abstract int
getRefPos()
abstract EdgingRecordAndOffset
getStart()
abstract EdgingRecordAndOffset.Type
getType()
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Methods inherited from class htsjdk.samtools.util.AbstractRecordAndOffset
getAlignmentType, getBaseQualities, getBaseQuality, getLength, getOffset, getReadBase, getReadName, getRecord, validateOffset
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Method Detail
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getStart
public abstract EdgingRecordAndOffset getStart()
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getType
public abstract EdgingRecordAndOffset.Type getType()
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getBaseQuality
public abstract byte getBaseQuality(int position)
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getRefPos
public abstract int getRefPos()
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createBeginRecord
public static EdgingRecordAndOffset createBeginRecord(SAMRecord record, int offset, int length, int refPos)
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createEndRecord
public static EdgingRecordAndOffset createEndRecord(EdgingRecordAndOffset startRecord)
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