Package htsjdk.samtools.cram
Class CRAIEntry
- java.lang.Object
-
- htsjdk.samtools.cram.CRAIEntry
-
- All Implemented Interfaces:
Comparable<CRAIEntry>
public class CRAIEntry extends Object implements Comparable<CRAIEntry>
A class representing CRAI index entry: file and alignment offsets for each slice. Created by vadim on 10/08/2015.
-
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description 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 offsetboolean
equals(Object o)
int
getAlignmentSpan()
int
getAlignmentStart()
long
getContainerStartByteOffset()
int
getSequenceId()
int
getSliceByteOffsetFromCompressionHeaderStart()
int
getSliceByteSize()
int
hashCode()
static boolean
intersect(CRAIEntry e0, CRAIEntry e1)
String
toString()
void
writeToStream(OutputStream os)
Serialize the entry to a CRAI index stream.
-
-
-
Constructor Detail
-
CRAIEntry
public CRAIEntry(int sequenceId, int alignmentStart, int alignmentSpan, long containerStartByteOffset, int sliceByteOffsetFromCompressionHeaderStart, int sliceByteSize)
-
CRAIEntry
public CRAIEntry(String line)
Create a CRAI Entry from a serialized CRAI index line.- Parameters:
line
- string formatted as a CRAI index entry
-
-
Method Detail
-
writeToStream
public void writeToStream(OutputStream os)
Serialize the entry to a CRAI index stream.- Parameters:
os
- stream to write to
-
compareTo
public 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- Specified by:
compareTo
in interfaceComparable<CRAIEntry>
- Parameters:
other
- the CRAIEntry to compare against- Returns:
- int representing the comparison result, suitable for ordering
-
getSequenceId
public int getSequenceId()
-
getAlignmentStart
public int getAlignmentStart()
-
getAlignmentSpan
public int getAlignmentSpan()
-
getContainerStartByteOffset
public long getContainerStartByteOffset()
-
getSliceByteOffsetFromCompressionHeaderStart
public int getSliceByteOffsetFromCompressionHeaderStart()
-
getSliceByteSize
public int getSliceByteSize()
-
-