Package org.snpeff.vcf
Class Pedigree
- java.lang.Object
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- org.snpeff.vcf.Pedigree
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- All Implemented Interfaces:
java.lang.Iterable<PedigreeEntry>
public class Pedigree extends java.lang.Object implements java.lang.Iterable<PedigreeEntry>
A pedigree for cancer samples
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Constructor Summary
Constructors Constructor Description Pedigree(VcfFileIterator vcfFile)
Pedigree(VcfFileIterator vcfFile, java.lang.String cancerSamples)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
anyBackToRef(VcfEntry vcfEntry)
Are there any "back to reference" cancer variantboolean
anyDerived()
Is there any derived sample?java.util.Set<Tuple<java.lang.Integer,java.lang.Integer>>
compareCancerGenotypes(VcfEntry vcfEntry)
Analyze which comparisons to make in cancer genomesjava.util.List<PedigreeEntry>
derived()
A list of all derived pedigree entriesjava.util.Iterator<PedigreeEntry>
iterator()
void
setDebug(boolean debug)
void
setVerbose(boolean verbose)
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Constructor Detail
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Pedigree
public Pedigree(VcfFileIterator vcfFile)
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Pedigree
public Pedigree(VcfFileIterator vcfFile, java.lang.String cancerSamples)
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Method Detail
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anyBackToRef
public boolean anyBackToRef(VcfEntry vcfEntry)
Are there any "back to reference" cancer variant
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anyDerived
public boolean anyDerived()
Is there any derived sample?
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compareCancerGenotypes
public java.util.Set<Tuple<java.lang.Integer,java.lang.Integer>> compareCancerGenotypes(VcfEntry vcfEntry)
Analyze which comparisons to make in cancer genomes
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derived
public java.util.List<PedigreeEntry> derived()
A list of all derived pedigree entries
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iterator
public java.util.Iterator<PedigreeEntry> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<PedigreeEntry>
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setDebug
public void setDebug(boolean debug)
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setVerbose
public void setVerbose(boolean verbose)
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