public class Fingerprint extends TreeMap<HaplotypeBlock,HaplotypeProbabilities>
AbstractMap.SimpleEntry<K,V>, AbstractMap.SimpleImmutableEntry<K,V>
Constructor and Description |
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Fingerprint(String sample,
File source,
String info) |
Modifier and Type | Method and Description |
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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.
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String |
getInfo() |
String |
getPrintableId() |
String |
getSample() |
File |
getSource() |
void |
merge(Fingerprint other)
Merges the likelihoods from the supplied Fingerprint into the likelihoods for this fingerprint.
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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
equals, hashCode, isEmpty, toString
finalize, getClass, notify, notifyAll, wait, wait, wait
compute, computeIfAbsent, computeIfPresent, equals, getOrDefault, hashCode, isEmpty, merge, putIfAbsent, remove
public String getSample()
public File getSource()
public String getInfo()
public String getPrintableId()
public void add(HaplotypeProbabilities h)
public void merge(Fingerprint other)
public void filterSuspectSites()