Pedigree (SnpEff 5.2 API)

java.lang.Object

org.snpeff.vcf.Pedigree

All Implemented Interfaces:: Iterable<PedigreeEntry>

public class Pedigree extends Object implements Iterable<PedigreeEntry>

A pedigree for cancer samples

Constructor Summary

Constructors

Constructor

Description

Pedigree(VcfFileIterator vcfFile)

Pedigree(VcfFileIterator vcfFile, String cancerSamples)
Method Summary

Modifier and Type

Method

Description

boolean

anyBackToRef(VcfEntry vcfEntry)

Are there any "back to reference" cancer variant

boolean

anyDerived()

Is there any derived sample?

Set<Tuple<Integer,Integer>>

compareCancerGenotypes(VcfEntry vcfEntry)

Analyze which comparisons to make in cancer genomes

List<PedigreeEntry>

derived()

A list of all derived pedigree entries

Iterator<PedigreeEntry>

iterator()

void

setDebug(boolean debug)

void

setVerbose(boolean verbose)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface java.lang.Iterable
forEach, spliterator

Constructor Details
- Pedigree
  
  public Pedigree(VcfFileIterator vcfFile)
- Pedigree
  
  public Pedigree(VcfFileIterator vcfFile, String cancerSamples)
Method Details
- anyBackToRef
  
  public boolean anyBackToRef(VcfEntry vcfEntry)
  
  Are there any "back to reference" cancer variant
- anyDerived
  
  public boolean anyDerived()
  
  Is there any derived sample?
- compareCancerGenotypes
  
  public Set<Tuple<Integer,Integer>> compareCancerGenotypes(VcfEntry vcfEntry)
  
  Analyze which comparisons to make in cancer genomes
- derived
  
  public List<PedigreeEntry> derived()
  
  A list of all derived pedigree entries
- iterator
  
  public Iterator<PedigreeEntry> iterator()
  
  Specified by:
  
  iterator in interface Iterable<PedigreeEntry>
- setDebug
  
  public void setDebug(boolean debug)
- setVerbose
  
  public void setVerbose(boolean verbose)