Package picard.fingerprint
Class Fingerprint
- java.lang.Object
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- java.util.AbstractMap<K,V>
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- java.util.TreeMap<HaplotypeBlock,HaplotypeProbabilities>
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- picard.fingerprint.Fingerprint
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- All Implemented Interfaces:
Serializable
,Cloneable
,Map<HaplotypeBlock,HaplotypeProbabilities>
,NavigableMap<HaplotypeBlock,HaplotypeProbabilities>
,SortedMap<HaplotypeBlock,HaplotypeProbabilities>
public class Fingerprint extends TreeMap<HaplotypeBlock,HaplotypeProbabilities>
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.- See Also:
- Serialized Form
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Nested Class Summary
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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>
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Constructor Summary
Constructors Constructor Description Fingerprint(String sample, Path source, String info)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method 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.static Function<FingerprintIdDetails,String>
getFingerprintIdDetailsStringFunction(CrosscheckMetric.DataType CROSSCHECK_BY)
String
getInfo()
String
getPrintableId()
String
getSample()
Path
getSource()
void
merge(Fingerprint other)
Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.static Map<FingerprintIdDetails,Fingerprint>
mergeFingerprintsBy(Map<FingerprintIdDetails,Fingerprint> fingerprints, Function<FingerprintIdDetails,String> by)
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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
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Methods inherited from class java.util.AbstractMap
equals, hashCode, isEmpty, toString
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Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
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Methods inherited from interface java.util.Map
compute, computeIfAbsent, computeIfPresent, equals, getOrDefault, hashCode, isEmpty, merge, putIfAbsent, remove
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Method Detail
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getSample
public String getSample()
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getSource
public Path getSource()
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getInfo
public String getInfo()
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getPrintableId
public String getPrintableId()
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add
public void add(HaplotypeProbabilities h)
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merge
public void merge(Fingerprint other)
Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.
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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.
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getFingerprintIdDetailsStringFunction
public static Function<FingerprintIdDetails,String> getFingerprintIdDetailsStringFunction(CrosscheckMetric.DataType CROSSCHECK_BY)
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mergeFingerprintsBy
public static Map<FingerprintIdDetails,Fingerprint> mergeFingerprintsBy(Map<FingerprintIdDetails,Fingerprint> fingerprints, Function<FingerprintIdDetails,String> by)
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