Class FingerprintUtils


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