public class ReferenceTracks
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static int |
DEFAULT_WINDOW_SIZE |
Constructor and Description |
---|
ReferenceTracks(int sequenceId,
java.lang.String sequenceName,
byte[] reference) |
Modifier and Type | Method and 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() |
java.lang.String |
getSequenceName() |
int |
getWindowLength() |
int |
getWindowPosition() |
short |
mismatchesAt(int pos) |
public static final int DEFAULT_WINDOW_SIZE
public ReferenceTracks(int sequenceId, java.lang.String sequenceName, byte[] reference)
public int getSequenceId()
public java.lang.String getSequenceName()
public int getWindowPosition()
public int getWindowLength()
public int getReferenceLength()
public void ensure(int start, int end)
public void ensureRange(int start, int length)
public final byte baseAt(int pos)
public final short coverageAt(int pos)
public final short mismatchesAt(int pos)
public final void addCoverage(int pos, int amount)
public final void addMismatches(int pos, int amount)