Package picard.fingerprint

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, boolean representativeOnly) 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
      representativeOnly - whether to extract only the representative snps
      Throws:
      IOException - if two snps in the haplotype map have the same "name"

    • createVCSetFromFingerprint

      public static FingerprintUtils.VariantContextSet createVCSetFromFingerprint(Fingerprint fingerPrint, htsjdk.samtools.reference.ReferenceSequenceFile reference, String sample, boolean representativeOnly)
      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
      representativeOnly - A boolean specifying whether to create a VC only for the representative Snp (or for all of them if false)
      Returns:
      VariantContextSet with variants representing the haplotypes in the fingerprint