Package htsjdk.samtools.util

Class IntervalUtil

java.lang.Object

htsjdk.samtools.util.IntervalUtil

public class IntervalUtil
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	IntervalUtil.IntervalCombiner

Constructor Summary

Constructors

Constructor	Description
IntervalUtil()

Method Summary

Modifier and Type	Method	Description
static void	assertOrderedNonOverlapping(Iterator<Interval> intervals, SAMSequenceDictionary sequenceDictionary)	Throws RuntimeException if the given intervals are not locus ordered and non-overlapping
static boolean	contains(IntervalList intervalList, String sequenceName, long position)	Return true if the sequence/position lie in the provided interval list.
static boolean	contains(Interval interval, String sequenceName, long position)	Return true if the sequence/position lie in the provided interval.

Methods inherited from class java.lang.Object

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

Constructor Details

IntervalUtil

public IntervalUtil()

Method Details

contains

public static boolean contains(Interval interval,
 String sequenceName,
 long position)

Return true if the sequence/position lie in the provided interval.

contains

public static boolean contains(IntervalList intervalList,
 String sequenceName,
 long position)

Return true if the sequence/position lie in the provided interval list.

assertOrderedNonOverlapping

public static void assertOrderedNonOverlapping(Iterator<Interval> intervals,
 SAMSequenceDictionary sequenceDictionary)

Throws RuntimeException if the given intervals are not locus ordered and non-overlapping

Parameters:

intervals -

sequenceDictionary - used to determine order of sequences