Package picard.fingerprint
Class Fingerprint
- All Implemented Interfaces:
Serializable
,Cloneable
,Map<HaplotypeBlock,
,HaplotypeProbabilities> NavigableMap<HaplotypeBlock,
,HaplotypeProbabilities> SortedMap<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:
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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> -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
void
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) getInfo()
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) 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, toString
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Constructor Details
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Fingerprint
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Method Details
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getSample
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getSource
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getInfo
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getPrintableId
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add
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merge
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. -
getFingerprintIdDetailsStringFunction
public static Function<FingerprintIdDetails,String> getFingerprintIdDetailsStringFunction(CrosscheckMetric.DataType CROSSCHECK_BY) -
mergeFingerprintsBy
public static Map<FingerprintIdDetails,Fingerprint> mergeFingerprintsBy(Map<FingerprintIdDetails, Fingerprint> fingerprints, Function<FingerprintIdDetails, String> by)
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