htsjdk.samtools.cram.structure

Class AlignmentSpan

java.lang.Object

htsjdk.samtools.cram.structure.AlignmentSpan

public class AlignmentSpan
extends java.lang.Object

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

Field Summary

Fields

Modifier and Type	Field and Description
static AlignmentSpan	UNPLACED_SPAN A constant to represent a span of unmapped-unplaced reads.

Constructor Summary

Constructors

Constructor and Description
AlignmentSpan(int start, int span, int mappedCount, int unmappedCount) 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	getMappedCount()
int	getSpan()
int	getStart()
int	getUnmappedCount()
int	hashCode()

Methods inherited from class java.lang.Object

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

Field Detail

UNPLACED_SPAN

public static final AlignmentSpan UNPLACED_SPAN

A constant to represent a span of unmapped-unplaced reads.

Constructor Detail

AlignmentSpan

public AlignmentSpan(int start,
                     int span,
                     int mappedCount,
                     int unmappedCount)

Create a new span with a multiple reads in it.

Parameters:

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

span - 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

getStart

public int getStart()

getSpan

public int getSpan()

getMappedCount

public int getMappedCount()

getUnmappedCount

public int getUnmappedCount()

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