htsjdk.samtools.cram.structure

Class AlignmentSpan

java.lang.Object

htsjdk.samtools.cram.structure.AlignmentSpan

public class AlignmentSpan
extends java.lang.Object

A span of over a single reference. Immutable. Holds alignment start and span values as well as counts of how many are mapped vs. unmapped vs unmapped-unplaced.

Constructor Summary

Constructors

Constructor and Description
AlignmentSpan(AlignmentContext alignmentContext, int mappedCount, int unmappedCount, int unmappedUnplacedCount) This does not retain the alignmentContext referenceContext state (its just a shorthand for passing the rest of the alignmentContext values in).
AlignmentSpan(int alignmentStart, int alignmentSpan, int mappedCount, int unmappedCount, int unmappedUnplacedCount) Create a new span with a multiple reads in it.

Method Summary

Modifier and Type	Method and Description
static AlignmentSpan	combine(AlignmentSpan a, AlignmentSpan b) Combine two AlignmentSpans
boolean	equals(java.lang.Object o)
int	getAlignmentSpan()
int	getAlignmentStart()
int	getMappedCount()
int	getUnmappedCount()
int	getUnmappedUnplacedCount()
int	hashCode()

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentSpan

public AlignmentSpan(AlignmentContext alignmentContext,
                     int mappedCount,
                     int unmappedCount,
                     int unmappedUnplacedCount)

This does not retain the alignmentContext referenceContext state (its just a shorthand for passing the rest of the alignmentContext values in).

Parameters:

alignmentContext -

mappedCount -

unmappedCount -

unmappedUnplacedCount -

AlignmentSpan

public AlignmentSpan(int alignmentStart,
                     int alignmentSpan,
                     int mappedCount,
                     int unmappedCount,
                     int unmappedUnplacedCount)

Create a new span with a multiple reads in it.

Parameters:

alignmentStart - minimum alignment start of the reads represented by this span, using a 1-based coordinate system

alignmentSpan - span from minimum alignment start to maximum alignment end of the reads represented by this span span = max(end) - min(start) + 1

mappedCount - number of mapped reads in the span

unmappedCount - number of unmapped reads in the span

Method Detail

combine

public static AlignmentSpan combine(AlignmentSpan a,
                                    AlignmentSpan b)

Combine two AlignmentSpans

Parameters:

a - the first AlignmentSpan to combine

b - the second AlignmentSpan to combine

Returns:

the new combined AlignmentSpan

getAlignmentStart

public int getAlignmentStart()

getAlignmentSpan

public int getAlignmentSpan()

getMappedCount

public int getMappedCount()

getUnmappedCount

public int getUnmappedCount()

getUnmappedUnplacedCount

public int getUnmappedUnplacedCount()

equals

public boolean equals(java.lang.Object o)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object