htsjdk.samtools.cram

Class BAIEntry

java.lang.Object

htsjdk.samtools.cram.BAIEntry

All Implemented Interfaces:

java.lang.Comparable<BAIEntry>

public class BAIEntry
extends java.lang.Object
implements java.lang.Comparable<BAIEntry>

Class used to construct a BAI index for a CRAM file. Each BAIEntry represents a Slice or a subset of a Slice (since MULTI_REF slices can contain records for more than one reference context), as these need to be separated for BAI index creation).

Constructor Summary

Constructors

Constructor and Description
BAIEntry(CRAIEntry craiEntry) Create a BAIEntry from a CRAIEntry (used to read a .crai as a .bai).
BAIEntry(ReferenceContext referenceContext, AlignmentSpan alignmentSpan, long containerStartByteOffset, long sliceHeaderBlockByteOffset, int landmarkIndex)

Method Summary

Modifier and Type	Method and Description
int	compareTo(BAIEntry 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
int	getAlignmentSpan()
int	getAlignmentStart()
long	getContainerStartByteOffset()
int	getLandmarkIndex()
int	getMappedReadsCount()
ReferenceContext	getReferenceContext()
long	getSliceByteOffsetFromCompressionHeaderStart()
int	getUnmappedReadsCount()
int	getUnmappedUnplacedReadsCount()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BAIEntry

public BAIEntry(ReferenceContext referenceContext,
                AlignmentSpan alignmentSpan,
                long containerStartByteOffset,
                long sliceHeaderBlockByteOffset,
                int landmarkIndex)

BAIEntry

public BAIEntry(CRAIEntry craiEntry)

Create a BAIEntry from a CRAIEntry (used to read a .crai as a .bai). Note that there are no mapped/unmapped/unplaced counts present in the crai, which makes BAIEntries created this way less full featured (i.e., wrong), but that is inherent in the idea of converting a CRAi to a BAI to satisfy an index query). HTSJDK needs a native implementation satisfying queries using a CRAI directly. see https://github.com/samtools/htsjdk/issues/851

Parameters:

craiEntry -

Method Detail

compareTo

public int compareTo(BAIEntry 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 interface java.lang.Comparable<BAIEntry>

Parameters:

other - the CRAIEntry to compare against

Returns:

int representing the comparison result, suitable for ordering

getReferenceContext

public ReferenceContext getReferenceContext()

getAlignmentStart

public int getAlignmentStart()

getAlignmentSpan

public int getAlignmentSpan()

getMappedReadsCount

public int getMappedReadsCount()

getUnmappedReadsCount

public int getUnmappedReadsCount()

getUnmappedUnplacedReadsCount

public int getUnmappedUnplacedReadsCount()

getContainerStartByteOffset

public long getContainerStartByteOffset()

getSliceByteOffsetFromCompressionHeaderStart

public long getSliceByteOffsetFromCompressionHeaderStart()

getLandmarkIndex

public int getLandmarkIndex()