htsjdk.samtools

Class QueryInterval

java.lang.Object

htsjdk.samtools.QueryInterval

All Implemented Interfaces:

java.lang.Comparable<QueryInterval>

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

Interval relative to a reference, for querying a BAM file.

Field Summary

Fields

Modifier and Type	Field and Description
int	end 1-based, inclusive.
int	referenceIndex Index of reference sequence, based on the sequence dictionary of the BAM file being queried.
int	start 1-based, inclusive

Constructor Summary

Constructors

Constructor and Description
QueryInterval(int referenceIndex, int start, int end)

Method Summary

Methods

Modifier and Type	Method and Description
boolean	abuts(QueryInterval other)
int	compareTo(QueryInterval other)
static QueryInterval[]	optimizeIntervals(QueryInterval[] inputIntervals)
boolean	overlaps(QueryInterval other)
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

referenceIndex

public final int referenceIndex

Index of reference sequence, based on the sequence dictionary of the BAM file being queried.

start

public final int start

1-based, inclusive

end

public final int end

1-based, inclusive. If <= 0, implies that the interval goes to the end of the reference sequence

Constructor Detail

QueryInterval

public QueryInterval(int referenceIndex,
             int start,
             int end)

Method Detail

compareTo

public int compareTo(QueryInterval other)

Specified by:

compareTo in interface java.lang.Comparable<QueryInterval>

abuts

public boolean abuts(QueryInterval other)

Returns:

true if both are on same reference, and other starts exactly where this ends.

overlaps

public boolean overlaps(QueryInterval other)

Returns:

true if both are on same reference, and the overlap.

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

optimizeIntervals

public static QueryInterval[] optimizeIntervals(QueryInterval[] inputIntervals)

Parameters:

inputIntervals - WARNING: This list is modified (sorted) by this method.

Returns:

Ordered list of intervals in which abutting and overlapping intervals are merged.