picard.fingerprint

Class Fingerprint

java.lang.Object

java.util.AbstractMap<K,V>

java.util.TreeMap<HaplotypeBlock,HaplotypeProbabilities>

picard.fingerprint.Fingerprint

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, java.util.Map<HaplotypeBlock,HaplotypeProbabilities>, java.util.NavigableMap<HaplotypeBlock,HaplotypeProbabilities>, java.util.SortedMap<HaplotypeBlock,HaplotypeProbabilities>

public class Fingerprint
extends java.util.TreeMap<HaplotypeBlock,HaplotypeProbabilities>

Small class to represent a genetic fingerprint as a set of HaplotypeProbabilities objects that give the relative probabilities of each of the possible haplotypes at a locus.

Author:

Tim Fennell

See Also:

Serialized Form

Nested Class Summary

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

java.util.AbstractMap.SimpleEntry<K,V>, java.util.AbstractMap.SimpleImmutableEntry<K,V>

Constructor Summary

Constructors

Constructor and Description
Fingerprint(java.lang.String sample, java.io.File source, java.lang.String info)

Method Summary

Modifier and Type	Method and Description
void	add(HaplotypeProbabilities h)
void	filterSuspectSites() Attempts to filter out haplotypes that may have suspect genotyping by removing haplotypes that reach a minimum confidence score yet have a significant fraction of observations from a third or fourth allele.
java.lang.String	getInfo()
java.lang.String	getPrintableId()
java.lang.String	getSample()
java.io.File	getSource()
void	merge(Fingerprint other) Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.

Methods inherited from class java.util.TreeMap

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

Methods inherited from class java.util.AbstractMap

equals, hashCode, isEmpty, toString

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Map

compute, computeIfAbsent, computeIfPresent, equals, getOrDefault, hashCode, isEmpty, merge, putIfAbsent, remove

Constructor Detail

Fingerprint

public Fingerprint(java.lang.String sample,
                   java.io.File source,
                   java.lang.String info)

Method Detail

getSample

public java.lang.String getSample()

getSource

public java.io.File getSource()

getInfo

public java.lang.String getInfo()

getPrintableId

public java.lang.String getPrintableId()

add

public void add(HaplotypeProbabilities h)

merge

public void merge(Fingerprint other)

Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.

filterSuspectSites

public void filterSuspectSites()

Attempts to filter out haplotypes that may have suspect genotyping by removing haplotypes that reach a minimum confidence score yet have a significant fraction of observations from a third or fourth allele.