Package org.snpeff.ped
Class PedPedigree
java.lang.Object
org.snpeff.ped.PedPedigree
- All Implemented Interfaces:
Comparable<PedPedigree>
,Iterable<TfamEntry>
- Direct Known Subclasses:
PedFamily
A pedigree of PedEntries
- Author:
- pcingola
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
Add an entry to this pedigreeint
compareTo
(PedPedigree ped) families()
Split data into familiesGet a list of sample IDsiterator()
keySet()
void
Load a pedigree from a PED and MAP file pairvoid
Load a TFAM filevoid
Save pedigree as a TFAM filevoid
setVerbose
(boolean verbose) int
size()
toString()
values()
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Constructor Details
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PedPedigree
public PedPedigree() -
PedPedigree
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Method Details
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add
Add an entry to this pedigree- Parameters:
tfamEntry
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compareTo
- Specified by:
compareTo
in interfaceComparable<PedPedigree>
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families
Split data into families- Returns:
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get
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getFamilyId
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getPlinkMap
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getSampleIds
Get a list of sample IDs- Returns:
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iterator
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keySet
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load
Load a pedigree from a PED and MAP file pair- Parameters:
pedFileName
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loadTfam
Load a TFAM file- Parameters:
tfamFileName
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saveTfam
Save pedigree as a TFAM file- Parameters:
fileName
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setVerbose
public void setVerbose(boolean verbose) -
size
public int size() -
toString
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values
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