Package picard.fingerprint
Class FingerprintUtils
- java.lang.Object
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- picard.fingerprint.FingerprintUtils
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public class FingerprintUtils extends Object
A set of utilities used in the fingerprinting environment
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Nested Class Summary
Nested Classes Modifier and Type Class Description static class
FingerprintUtils.VariantContextSet
A class that holds VariantContexts sorted by genomic position
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Constructor Summary
Constructors Constructor Description FingerprintUtils()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description 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 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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Method Detail
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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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