Package htsjdk.samtools

Class QueryInterval

java.lang.Object

htsjdk.samtools.QueryInterval

All Implemented Interfaces:

Comparable<QueryInterval>

public class QueryInterval
extends Object
implements Comparable<QueryInterval>

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

Field Summary

Fields

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

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
static void	assertIntervalsOptimized(QueryInterval[] intervals)
int	compareTo(QueryInterval other)
boolean	endsAtStartOf(QueryInterval other)
boolean	equals(Object o)
int	hashCode()
static QueryInterval[]	optimizeIntervals(QueryInterval[] inputIntervals)
boolean	overlaps(QueryInterval other)
String	toString()

Methods inherited from class java.lang.Object

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

Field Details

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 Details

QueryInterval

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

Method Details

compareTo

public int compareTo(QueryInterval other)

Specified by:

compareTo in interface Comparable<QueryInterval>

endsAtStartOf

public boolean endsAtStartOf(QueryInterval other)

Returns:

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

overlaps

public boolean overlaps(QueryInterval other)

Returns:

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

toString

public String toString()

Overrides:

toString in class 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.

assertIntervalsOptimized

public static void assertIntervalsOptimized(QueryInterval[] intervals)

Throws:

IllegalArgumentException - if the intervals are not optimized

See Also:

• optimizeIntervals(QueryInterval[])

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object