PedFile (picard 2.26.10 API)

java.lang.Object
- java.util.AbstractMap<K,V>
- - java.util.TreeMap<String,PedFile.PedTrio>
  - - picard.pedigree.PedFile

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

Nested Class Summary

Nested Classes
Modifier and Type Class Description

class PedFile.PedTrio
- 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>

Field Summary

Fields
Modifier and Type Field Description

static Number NO_PHENO

static Sex UNKNOWN_SEX

Constructor Summary

Constructors
Constructor Description

PedFile(boolean isTabMode)

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

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

- Field Detail
  - NO_PHENO
```
public static final Number NO_PHENO
```
  - UNKNOWN_SEX
```
public static final Sex UNKNOWN_SEX
```
- Constructor Detail
  - PedFile
```
public PedFile(boolean isTabMode)
```
- Method Detail
  - add
```
public void add(PedFile.PedTrio trio)
```
    Adds a trio to the PedFile keyed by the individual id.
  - write
```
public void write(File file)
```
    Writes a set of pedigrees out to disk.
  - fromFile
```
public static PedFile fromFile(File file,
                               boolean isTabMode)
```
    Attempts to read a pedigree file into memory.
  - removeIncompleteTrios
```
public PedFile removeIncompleteTrios()
```
    Scans through the pedigrees and removes all entries that do not have both paternal and maternal ids set.
  - fromSexMap
```
public 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.
    
    Parameters:
    
    sampleSexes - a map from sample-name to its sex
    
    Returns:
    
    a PedFile object that contains data.