Class FingerprintUtils

java.lang.Object
picard.fingerprint.FingerprintUtils

public class FingerprintUtils extends Object
A set of utilities used in the fingerprinting environment
  • Constructor Details

    • FingerprintUtils

      public FingerprintUtils()
  • Method Details

    • 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