FingerprintUtils (picard 2.18.2 API)

java.lang.Object
- picard.fingerprint.FingerprintUtils

```
public class FingerprintUtils
extends Object
```
A set of utilities used in the fingerprinting environment

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class FingerprintUtils.VariantContextSet
A class that holds VariantContexts sorted by genomic position

Nested Classes
Modifier and Type	Class	Description
`static class`	`FingerprintUtils.VariantContextSet`	A class that holds VariantContexts sorted by genomic position

Constructor Summary

Constructors
Constructor Description

FingerprintUtils()

Constructors
Constructor	Description
`FingerprintUtils()`

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 fingerprint
`static 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

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

Constructor Detail
- FingerprintUtils
```
public FingerprintUtils()
```

Method Detail

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 write; outputFile - the file to write to; referenceSequenceFileName - the reference sequence (file); sample - the sample name to use in the vcf; source - a "source" comment to use in the VCF
Throws:: IOException

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 fingerprint

reference - A reference sequence that will be used to create the VariantContexts

sample - A sample name that will be used for the genotype field

Returns:

VariantContextSet with variants representing the haplotypes in the fingerprint

Class FingerprintUtils

Nested Class Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

FingerprintUtils

Method Detail

writeFingerPrint

createVCSetFromFingerprint