org.broadinstitute.hellbender.utils

Class SimpleInterval

java.lang.Object

org.broadinstitute.hellbender.utils.SimpleInterval

All Implemented Interfaces:

htsjdk.samtools.util.Locatable, java.io.Serializable

public final class SimpleInterval
extends java.lang.Object
implements htsjdk.samtools.util.Locatable, java.io.Serializable

Minimal immutable class representing a 1-based closed ended genomic interval SimpleInterval does not allow null contig names. It cannot represent an unmapped Locatable.

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static char	CONTIG_SEPARATOR
static java.lang.String	END_OF_CONTIG
static char	START_END_SEPARATOR

Constructor Summary

Constructors

Constructor and Description
SimpleInterval(htsjdk.samtools.util.Locatable locatable) Create a new SimpleInterval from a Locatable
SimpleInterval(java.lang.String str) Makes an interval by parsing the string.
SimpleInterval(java.lang.String contig, int start, int end) Create a new immutable 1-based interval of the form [start, end]

Method Summary

Modifier and Type	Method and Description
boolean	contains(htsjdk.samtools.util.Locatable other) Determines whether this interval contains the entire region represented by other (in other words, whether it covers it).
boolean	equals(java.lang.Object o)
SimpleInterval	expandWithinContig(int padding, int contigLength) Returns a new SimpleInterval that represents this interval as expanded by the specified amount in both directions, bounded by the contig start/stop if necessary.
SimpleInterval	expandWithinContig(int padding, htsjdk.samtools.SAMSequenceDictionary sequenceDictionary) Returns a new SimpleInterval that represents this interval as expanded by the specified amount in both directions, bounded by the contig start/stop if necessary.
java.lang.String	getContig()
int	getEnd()
long	getGA4GHEnd()
long	getGA4GHStart()
int	getStart() Gets the 1-based start position of the interval on the contig.
int	hashCode()
SimpleInterval	intersect(htsjdk.samtools.util.Locatable that) Returns the intersection of the two intervals.
static boolean	isValid(java.lang.String contig, int start, int end) Test that these are valid values for constructing a SimpleInterval: contig cannot be null start must be >= 1 end must be >= start
SimpleInterval	mergeWithContiguous(htsjdk.samtools.util.Locatable that) Returns a new SimpleInterval that represents the entire span of this and that.
boolean	overlaps(htsjdk.samtools.util.Locatable other) Determines whether this interval overlaps the provided locatable.
boolean	overlapsWithMargin(htsjdk.samtools.util.Locatable other, int margin) Determines whether this interval comes within "margin" of overlapping the provided locatable.
int	size()
SimpleInterval	spanWith(htsjdk.samtools.util.Locatable other) Returns a new SimpleInterval that represents the region between the endpoints of this and other.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.util.Locatable

contigsMatch, getLengthOnReference, withinDistanceOf

Field Detail

CONTIG_SEPARATOR

public static final char CONTIG_SEPARATOR

See Also:

Constant Field Values

START_END_SEPARATOR

public static final char START_END_SEPARATOR

See Also:

Constant Field Values

END_OF_CONTIG

public static final java.lang.String END_OF_CONTIG

See Also:

Constant Field Values

Constructor Detail

SimpleInterval

public SimpleInterval(java.lang.String contig,
                      int start,
                      int end)

Create a new immutable 1-based interval of the form [start, end]

Parameters:

contig - the name of the contig, must not be null

start - 1-based inclusive start position

end - 1-based inclusive end position

SimpleInterval

public SimpleInterval(htsjdk.samtools.util.Locatable locatable)

Create a new SimpleInterval from a Locatable

Parameters:

locatable - any Locatable

Throws:

java.lang.IllegalArgumentException - if locatable violates any of the SimpleInterval constraints or is null

SimpleInterval

public SimpleInterval(java.lang.String str)

Makes an interval by parsing the string.

Parameters:

str - non-empty string to be parsed

Method Detail

isValid

public static boolean isValid(java.lang.String contig,
                              int start,
                              int end)

Test that these are valid values for constructing a SimpleInterval: contig cannot be null start must be >= 1 end must be >= start

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

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

getContig

public java.lang.String getContig()

Specified by:

getContig in interface htsjdk.samtools.util.Locatable

Returns:

name of the contig this is mapped to

getStart

public int getStart()

Gets the 1-based start position of the interval on the contig.

Specified by:

getStart in interface htsjdk.samtools.util.Locatable

getGA4GHStart

public long getGA4GHStart()

Returns:

the 0-based start position (from the GA4GH spec).

getEnd

public int getEnd()

Specified by:

getEnd in interface htsjdk.samtools.util.Locatable

Returns:

the 1-based closed-ended end position of the interval on the contig.

getGA4GHEnd

public long getGA4GHEnd()

Returns:

the typical end spans are [zero-start,end) (from the GA4GH spec).

size

public int size()

Returns:

number of bases covered by this interval (will always be > 0)

overlaps

public boolean overlaps(htsjdk.samtools.util.Locatable other)

Determines whether this interval overlaps the provided locatable.

Specified by:

overlaps in interface htsjdk.samtools.util.Locatable

Parameters:

other - interval to check

Returns:

true if this interval overlaps other, otherwise false

overlapsWithMargin

public boolean overlapsWithMargin(htsjdk.samtools.util.Locatable other,
                                  int margin)

Determines whether this interval comes within "margin" of overlapping the provided locatable. This is the same as plain overlaps if margin=0.

Parameters:

other - interval to check

margin - how many bases may be between the two interval for us to still consider them overlapping; must be non-negative

Returns:

true if this interval overlaps other, otherwise false

Throws:

java.lang.IllegalArgumentException - if margin is negative

contains

public boolean contains(htsjdk.samtools.util.Locatable other)

Determines whether this interval contains the entire region represented by other (in other words, whether it covers it).

Specified by:

contains in interface htsjdk.samtools.util.Locatable

Parameters:

other - interval to check

Returns:

true if this interval contains all of the bases spanned by other, otherwise false

intersect

public SimpleInterval intersect(htsjdk.samtools.util.Locatable that)

Returns the intersection of the two intervals. The intervals must overlap or IllegalArgumentException will be thrown.

mergeWithContiguous

public SimpleInterval mergeWithContiguous(htsjdk.samtools.util.Locatable that)

Returns a new SimpleInterval that represents the entire span of this and that. Requires that this and that SimpleInterval are contiguous.

spanWith

public SimpleInterval spanWith(htsjdk.samtools.util.Locatable other)

Returns a new SimpleInterval that represents the region between the endpoints of this and other. Unlike mergeWithContiguous(htsjdk.samtools.util.Locatable), the two intervals do not need to be contiguous

Parameters:

other - the other interval with which to calculate the span

Returns:

a new SimpleInterval that represents the region between the endpoints of this and other.

expandWithinContig

public SimpleInterval expandWithinContig(int padding,
                                         int contigLength)

Returns a new SimpleInterval that represents this interval as expanded by the specified amount in both directions, bounded by the contig start/stop if necessary.

Parameters:

padding - amount to expand this interval

contigLength - length of this interval's contig

Returns:

a new SimpleInterval that represents this interval as expanded by the specified amount in both directions, bounded by the contig start/stop if necessary.

expandWithinContig

public SimpleInterval expandWithinContig(int padding,
                                         htsjdk.samtools.SAMSequenceDictionary sequenceDictionary)

Returns a new SimpleInterval that represents this interval as expanded by the specified amount in both directions, bounded by the contig start/stop if necessary.

Parameters:

padding - amount to expand this interval

sequenceDictionary - dictionary to use to determine the length of this interval's contig

Returns:

a new SimpleInterval that represents this interval as expanded by the specified amount in both directions, bounded by the contig start/stop if necessary.