Package picard.fingerprint
Class FingerprintUtils
java.lang.Object
picard.fingerprint.FingerprintUtils
A set of utilities used in the fingerprinting environment
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Nested Class Summary
Nested ClassesModifier and TypeClassDescriptionstatic class
A class that holds VariantContexts sorted by genomic position -
Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptioncreateVCSetFromFingerprint
(Fingerprint fingerPrint, htsjdk.samtools.reference.ReferenceSequenceFile reference, String sample) A utility function that takes a fingerprint and returns a VariantContextSet with variants representing the haplotypes in the fingerprintstatic void
writeFingerPrint
(Fingerprint fingerprint, File outputFile, File referenceSequenceFileName, String sample, String source) A function that takes a Fingerprint and writes it as a VCF to a file
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Constructor Details
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FingerprintUtils
public FingerprintUtils()
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Method Details
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writeFingerPrint
public static void writeFingerPrint(Fingerprint fingerprint, File outputFile, File referenceSequenceFileName, String sample, String source) throws IOException A function that takes a Fingerprint and writes it as a VCF to a file- Parameters:
fingerprint
- the fingerprint to writeoutputFile
- the file to write toreferenceSequenceFileName
- the reference sequence (file)sample
- the sample name to use in the vcfsource
- a "source" comment to use in the VCF- Throws:
IOException
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createVCSetFromFingerprint
public static FingerprintUtils.VariantContextSet createVCSetFromFingerprint(Fingerprint fingerPrint, htsjdk.samtools.reference.ReferenceSequenceFile reference, String sample) A utility function that takes a fingerprint and returns a VariantContextSet with variants representing the haplotypes in the fingerprint- Parameters:
fingerPrint
- A fingerprintreference
- A reference sequence that will be used to create the VariantContextssample
- A sample name that will be used for the genotype field- Returns:
- VariantContextSet with variants representing the haplotypes in the fingerprint
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