Package org.broadinstitute.hellbender.utils.haplotype

Class EventMap

java.lang.Object

java.util.AbstractMap<K,V>

java.util.TreeMap<Integer,htsjdk.variant.variantcontext.VariantContext>

org.broadinstitute.hellbender.utils.haplotype.EventMap

All Implemented Interfaces:

Serializable, Cloneable, Map<Integer,htsjdk.variant.variantcontext.VariantContext>, NavigableMap<Integer,htsjdk.variant.variantcontext.VariantContext>, SortedMap<Integer,htsjdk.variant.variantcontext.VariantContext>

public final class EventMap
extends TreeMap<Integer,htsjdk.variant.variantcontext.VariantContext>

Extract simple VariantContext events from a single haplotype

See Also:

• Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from class java.util.AbstractMap

AbstractMap.SimpleEntry<K extends Object,V extends Object>, AbstractMap.SimpleImmutableEntry<K extends Object,V extends Object>

Field Summary

Fields

Modifier and Type	Field	Description
protected static final int	MIN_NUMBER_OF_EVENTS_TO_COMBINE_INTO_BLOCK_SUBSTITUTION
static final htsjdk.variant.variantcontext.Allele	SYMBOLIC_UNASSEMBLED_EVENT_ALLELE

Constructor Summary

Constructors

Constructor	Description
EventMap(Collection<htsjdk.variant.variantcontext.VariantContext> stateForTesting)	For testing.
EventMap(Haplotype haplotype, byte[] ref, htsjdk.samtools.util.Locatable refLoc, String sourceNameToAdd, int maxMnpDistance)

Method Summary

Modifier and Type	Method	Description
void	addVC(htsjdk.variant.variantcontext.VariantContext vc)	Add VariantContext vc to this map, merging events with the same start sites if necessary
void	addVC(htsjdk.variant.variantcontext.VariantContext vc, boolean merge)	Add VariantContext vc to this map
static TreeSet<Integer>	buildEventMapsForHaplotypes(List<Haplotype> haplotypes, byte[] ref, htsjdk.samtools.util.Locatable refLoc, boolean debug, int maxMnpDistance)	Build event maps for each haplotype, returning the sorted set of all of the starting positions of all events across all haplotypes
int	getNumberOfEvents()	How many events do we have?
List<htsjdk.variant.variantcontext.VariantContext>	getOverlappingEvents(int loc)	Returns any events in the map that overlap loc, including spanning deletions and events that start at loc.
Set<Integer>	getStartPositions()	Get the starting positions of events in this event map
Collection<htsjdk.variant.variantcontext.VariantContext>	getVariantContexts()	Get the variant contexts in order of start position in this event map
protected htsjdk.variant.variantcontext.VariantContext	makeBlock(htsjdk.variant.variantcontext.VariantContext vc1, htsjdk.variant.variantcontext.VariantContext vc2)	Create a block substitution out of two variant contexts that start at the same position vc1 can be SNP, and vc2 can then be either a insertion or deletion.
protected void	processCigarForInitialEvents(int maxMnpDistance)
String	toString()

Methods inherited from class java.util.TreeMap

ceilingEntry, ceilingKey, clear, clone, comparator, compute, computeIfAbsent, computeIfPresent, containsKey, containsValue, descendingKeySet, descendingMap, entrySet, firstEntry, firstKey, floorEntry, floorKey, forEach, get, headMap, headMap, higherEntry, higherKey, keySet, lastEntry, lastKey, lowerEntry, lowerKey, merge, navigableKeySet, pollFirstEntry, pollLastEntry, put, putAll, putIfAbsent, remove, replace, replace, replaceAll, size, subMap, subMap, tailMap, tailMap, values

Methods inherited from class java.util.AbstractMap

equals, hashCode, isEmpty

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Map

equals, getOrDefault, hashCode, isEmpty, remove

Field Details

MIN_NUMBER_OF_EVENTS_TO_COMBINE_INTO_BLOCK_SUBSTITUTION

protected static final int MIN_NUMBER_OF_EVENTS_TO_COMBINE_INTO_BLOCK_SUBSTITUTION

See Also:

• Constant Field Values

SYMBOLIC_UNASSEMBLED_EVENT_ALLELE

public static final htsjdk.variant.variantcontext.Allele SYMBOLIC_UNASSEMBLED_EVENT_ALLELE

Constructor Details

EventMap

public EventMap(Haplotype haplotype,
 byte[] ref,
 htsjdk.samtools.util.Locatable refLoc,
 String sourceNameToAdd,
 int maxMnpDistance)

EventMap

public EventMap(Collection<htsjdk.variant.variantcontext.VariantContext> stateForTesting)

For testing. Let's you set up a explicit configuration without having to process a haplotype and reference

Parameters:

stateForTesting -

Method Details

processCigarForInitialEvents

protected void processCigarForInitialEvents(int maxMnpDistance)

Parameters:

maxMnpDistance - Phased substitutions separated by this distance or less are merged into MNPs. More than two substitutions occurring in the same alignment block (ie the same M/X/EQ CIGAR element) are merged until a substitution is separated from the previous one by a greater distance. That is, if maxMnpDistance = 1, substitutions at 10,11,12,14,15,17 are partitioned into a MNP at 10-12, a MNP at 14-15, and a SNP at 17. May not be negative.

addVC

public void addVC(htsjdk.variant.variantcontext.VariantContext vc)

Add VariantContext vc to this map, merging events with the same start sites if necessary

Parameters:

vc - the variant context to add

addVC

public void addVC(htsjdk.variant.variantcontext.VariantContext vc,
 boolean merge)

Add VariantContext vc to this map

Parameters:

vc - the variant context to add

merge - should we attempt to merge it with an already existing element, or should we throw an error in that case?

makeBlock

protected htsjdk.variant.variantcontext.VariantContext makeBlock(htsjdk.variant.variantcontext.VariantContext vc1,
 htsjdk.variant.variantcontext.VariantContext vc2)

Create a block substitution out of two variant contexts that start at the same position vc1 can be SNP, and vc2 can then be either a insertion or deletion. If vc1 is an indel, then vc2 must be the opposite type (vc1 deletion => vc2 must be an insertion)

Parameters:

vc1 - the first variant context we want to merge

vc2 - the second

Returns:

a block substitution that represents the composite substitution implied by vc1 and vc2

getStartPositions

public Set<Integer> getStartPositions()

Get the starting positions of events in this event map

Returns:

getVariantContexts

public Collection<htsjdk.variant.variantcontext.VariantContext> getVariantContexts()

Get the variant contexts in order of start position in this event map

Returns:

getNumberOfEvents

public int getNumberOfEvents()

How many events do we have?

Returns:

toString

public String toString()

Overrides:

toString in class AbstractMap<Integer,htsjdk.variant.variantcontext.VariantContext>

buildEventMapsForHaplotypes

public static TreeSet<Integer> buildEventMapsForHaplotypes(List<Haplotype> haplotypes,
 byte[] ref,
 htsjdk.samtools.util.Locatable refLoc,
 boolean debug,
 int maxMnpDistance)

Build event maps for each haplotype, returning the sorted set of all of the starting positions of all events across all haplotypes

Parameters:

haplotypes - a list of haplotypes

ref - the reference bases

refLoc - the span of the reference bases

debug - if true, we'll emit debugging information during this operation

maxMnpDistance - Phased substitutions separated by this distance or less are merged into MNPs. More than two substitutions occuring in the same alignment block (ie the same M/X/EQ CIGAR element) are merged until a substitution is separated from the previous one by a greater distance. That is, if maxMnpDistance = 1, substitutions at 10,11,12,14,15,17 are partitioned into a MNP at 10-12, a MNP at 14-15, and a SNP at 17. May not be negative.

Returns:

a sorted set of start positions of all events among all haplotypes

getOverlappingEvents

public List<htsjdk.variant.variantcontext.VariantContext> getOverlappingEvents(int loc)

Returns any events in the map that overlap loc, including spanning deletions and events that start at loc.