Package org.snpeff.vcf
Class Pedigree
java.lang.Object
org.snpeff.vcf.Pedigree
- All Implemented Interfaces:
Iterable<PedigreeEntry>
A pedigree for cancer samples
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Constructor Summary
ConstructorsConstructorDescriptionPedigree
(VcfFileIterator vcfFile) Pedigree
(VcfFileIterator vcfFile, String cancerSamples) -
Method Summary
Modifier and TypeMethodDescriptionboolean
anyBackToRef
(VcfEntry vcfEntry) Are there any "back to reference" cancer variantboolean
Is there any derived sample?compareCancerGenotypes
(VcfEntry vcfEntry) Analyze which comparisons to make in cancer genomesderived()
A list of all derived pedigree entriesiterator()
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
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Constructor Details
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Pedigree
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Pedigree
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Method Details
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anyBackToRef
Are there any "back to reference" cancer variant -
anyDerived
public boolean anyDerived()Is there any derived sample? -
compareCancerGenotypes
Analyze which comparisons to make in cancer genomes -
derived
A list of all derived pedigree entries -
iterator
- Specified by:
iterator
in interfaceIterable<PedigreeEntry>
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setDebug
public void setDebug(boolean debug) -
setVerbose
public void setVerbose(boolean verbose)
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