Package picard.pedigree
Class PedFile
- java.lang.Object
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- java.util.AbstractMap<K,V>
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- java.util.TreeMap<String,PedFile.PedTrio>
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- picard.pedigree.PedFile
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- All Implemented Interfaces:
Serializable
,Cloneable
,Map<String,PedFile.PedTrio>
,NavigableMap<String,PedFile.PedTrio>
,SortedMap<String,PedFile.PedTrio>
public class PedFile extends TreeMap<String,PedFile.PedTrio>
Represents a .ped file of family information as documented here: http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml Stores the information in memory as a map of individualId -> Pedigree information for that individual- See Also:
- Serialized Form
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Nested Class Summary
Nested Classes Modifier and Type Class Description class
PedFile.PedTrio
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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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Field Summary
Fields Modifier and Type Field Description static Number
NO_PHENO
static Sex
UNKNOWN_SEX
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Constructor Summary
Constructors Constructor Description PedFile(boolean isTabMode)
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(PedFile.PedTrio trio)
Adds a trio to the PedFile keyed by the individual id.static PedFile
fromFile(File file, boolean isTabMode)
Attempts to read a pedigree file into memory.static PedFile
fromSexMap(Map<String,Sex> sampleSexes)
Function that accepts a map from sample-name to its sex and creates a PEDFile documenting the sexes.PedFile
removeIncompleteTrios()
Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.void
write(File file)
Writes a set of pedigrees out to disk.-
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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add
public void add(PedFile.PedTrio trio)
Adds a trio to the PedFile keyed by the individual id.
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write
public void write(File file)
Writes a set of pedigrees out to disk.
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fromFile
public static PedFile fromFile(File file, boolean isTabMode)
Attempts to read a pedigree file into memory.
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removeIncompleteTrios
public PedFile removeIncompleteTrios()
Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.
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