Package htsjdk.samtools.cram.ref
Class ReferenceTracks
- java.lang.Object
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- htsjdk.samtools.cram.ref.ReferenceTracks
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public class ReferenceTracks extends Object
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Field Summary
Fields Modifier and Type Field Description static int
DEFAULT_WINDOW_SIZE
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Constructor Summary
Constructors Constructor Description ReferenceTracks(int sequenceId, String sequenceName, byte[] reference)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addCoverage(int pos, int amount)
void
addMismatches(int pos, int amount)
byte
baseAt(int pos)
short
coverageAt(int pos)
void
ensure(int start, int end)
void
ensureRange(int start, int length)
int
getReferenceLength()
int
getSequenceId()
String
getSequenceName()
int
getWindowLength()
int
getWindowPosition()
short
mismatchesAt(int pos)
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Field Detail
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DEFAULT_WINDOW_SIZE
public static final int DEFAULT_WINDOW_SIZE
- See Also:
- Constant Field Values
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Constructor Detail
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ReferenceTracks
public ReferenceTracks(int sequenceId, String sequenceName, byte[] reference)
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Method Detail
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getSequenceId
public int getSequenceId()
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getSequenceName
public String getSequenceName()
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getWindowPosition
public int getWindowPosition()
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getWindowLength
public int getWindowLength()
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getReferenceLength
public int getReferenceLength()
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ensure
public void ensure(int start, int end)
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ensureRange
public void ensureRange(int start, int length)
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baseAt
public final byte baseAt(int pos)
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coverageAt
public final short coverageAt(int pos)
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mismatchesAt
public final short mismatchesAt(int pos)
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addCoverage
public final void addCoverage(int pos, int amount)
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addMismatches
public final void addMismatches(int pos, int amount)
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