Constructor and Description |
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CRAIEntry(int sequenceId,
int alignmentStart,
int alignmentSpan,
long containerStartByteOffset,
int sliceByteOffsetFromCompressionHeaderStart,
int sliceByteSize) |
CRAIEntry(java.lang.String line)
Create a CRAI Entry from a serialized CRAI index line.
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Modifier and Type | Method and Description |
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int |
compareTo(CRAIEntry other)
Sort by numerical order of reference sequence ID, except that unmapped-unplaced reads come last
For valid reference sequence ID (placed reads):
- sort by alignment start
- if alignment start is equal, sort by container offset
- if alignment start and container offset are equal, sort by slice offset
For unmapped-unplaced reads:
- ignore (invalid) alignment start value
- sort by container offset
- if container offset is equal, sort by slice offset
|
boolean |
equals(java.lang.Object o) |
int |
getAlignmentSpan() |
int |
getAlignmentStart() |
long |
getContainerStartByteOffset() |
int |
getSequenceId() |
int |
getSliceByteOffsetFromCompressionHeaderStart() |
int |
getSliceByteSize() |
int |
hashCode() |
static boolean |
intersect(CRAIEntry e0,
CRAIEntry e1) |
java.lang.String |
toString() |
void |
writeToStream(java.io.OutputStream os)
Serialize the entry to a CRAI index stream.
|
public CRAIEntry(int sequenceId, int alignmentStart, int alignmentSpan, long containerStartByteOffset, int sliceByteOffsetFromCompressionHeaderStart, int sliceByteSize)
public CRAIEntry(java.lang.String line)
line
- string formatted as a CRAI index entryCRAIIndex.CRAIIndexException
public void writeToStream(java.io.OutputStream os)
os
- stream to write topublic java.lang.String toString()
toString
in class java.lang.Object
public int compareTo(CRAIEntry other)
compareTo
in interface java.lang.Comparable<CRAIEntry>
other
- the CRAIEntry to compare againstpublic int getSequenceId()
public int getAlignmentStart()
public int getAlignmentSpan()
public long getContainerStartByteOffset()
public int getSliceByteOffsetFromCompressionHeaderStart()
public int getSliceByteSize()
public boolean equals(java.lang.Object o)
equals
in class java.lang.Object
public int hashCode()
hashCode
in class java.lang.Object