public class FingerprintUtils extends Object
| Modifier and Type | Class | Description |
|---|---|---|
static class |
FingerprintUtils.VariantContextSet |
A class that holds VariantContexts sorted by genomic position
|
| Constructor | Description |
|---|---|
FingerprintUtils() |
| 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
|
public static void writeFingerPrint(Fingerprint fingerprint, File outputFile, File referenceSequenceFileName, String sample, String source) throws IOException
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 VCFIOExceptionpublic static FingerprintUtils.VariantContextSet createVCSetFromFingerprint(Fingerprint fingerPrint, htsjdk.samtools.reference.ReferenceSequenceFile reference, String sample)
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