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 forSamLocusIterator.RecordAndOffset
implementation or one alignment block ofSAMRecord
forTypedRecordAndOffset
implementation.
-
-
Constructor Summary
Constructors Constructor Description AbstractRecordAndOffset(SAMRecord record, int offset)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description byte[]
getBaseQualities()
byte
getBaseQuality()
int
getLength()
int
getOffset()
byte
getReadBase()
String
getReadName()
SAMRecord
getRecord()
protected void
validateOffset(int offset, byte[] array)
-
-
-
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 SAMRecordoffset
- 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)
-
-