Package picard.fingerprint

Class FingerprintChecker

java.lang.Object
picard.fingerprint.FingerprintChecker
public class FingerprintChecker extends Object
Major class that coordinates the activities involved in comparing genetic fingerprint data whether the source is from a genotyping platform or derived from sequence data.

  • Field Details

    • DEFAULT_GENOTYPING_ERROR_RATE

      public static final double DEFAULT_GENOTYPING_ERROR_RATE
      See Also:

    • DEFAULT_MINIMUM_MAPPING_QUALITY

      public static final int DEFAULT_MINIMUM_MAPPING_QUALITY
      See Also:

    • DEFAULT_MINIMUM_BASE_QUALITY

      public static final int DEFAULT_MINIMUM_BASE_QUALITY
      See Also:

  • Constructor Details

    • FingerprintChecker

      public FingerprintChecker(File haplotypeData)
      Creates a fingerprint checker that will work with the set of haplotypes stored in the supplied file.

    • FingerprintChecker

      public FingerprintChecker(HaplotypeMap haplotypes)
      Creates a fingerprint checker that will work with the set of haplotyped provided.

  • Method Details

    • getValidationStringency

      public htsjdk.samtools.ValidationStringency getValidationStringency()

    • setValidationStringency

      public void setValidationStringency(htsjdk.samtools.ValidationStringency validationStringency)

    • getReferenceFasta

      public File getReferenceFasta()

    • setMinimumBaseQuality

      public void setMinimumBaseQuality(int minimumBaseQuality)
      Sets the minimum base quality for bases used when computing a fingerprint from sequence data.

    • setMinimumMappingQuality

      public void setMinimumMappingQuality(int minimumMappingQuality)
      Sets the minimum mapping quality for reads used when computing fingerprints from sequence data.

    • setGenotypingErrorRate

      public void setGenotypingErrorRate(double genotypingErrorRate)
      Sets the assumed genotyping error rate used when accurate error rates are not available.

    • getHeader

      public htsjdk.samtools.SAMFileHeader getHeader()

    • setAllowDuplicateReads

      public void setAllowDuplicateReads(boolean allowDuplicateReads)
      Sets whether duplicate reads should be allowed when calling genotypes from SAM files. This is useful when comparing read groups within a SAM file and individual read groups show artifactually high duplication (e.g. a single-ended read group mixed in with paired-end read groups).
      Parameters:
      allowDuplicateReads - should fingerprinting use duplicate reads?

    • setpLossofHet

      public void setpLossofHet(double pLossofHet)

    • loadFingerprints

      public Map<String,Fingerprint> loadFingerprints(Path fingerprintFile, Path indexPath, boolean forceIndex, String specificSample)
      Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
      Parameters:
      fingerprintFile - - VCF file containing genotypes for one or more samples
      specificSample - - null to load genotypes for all samples contained in the file or the name of an individual sample to load (and exclude all others).
      Returns:
      a Map of Sample name to Fingerprint

    • loadFingerprintsFromNonIndexedVcf

      public Map<String,Fingerprint> loadFingerprintsFromNonIndexedVcf(Path fingerprintFile, String specificSample)
      Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
      Parameters:
      fingerprintFile - - VCF file containing genotypes for one or more samples
      specificSample - - null to load genotypes for all samples contained in the file or the name of an individual sample to load (and exclude all others).
      Returns:
      a Map of Sample name to Fingerprint

    • loadFingerprintsFromVariantContexts

      public Map<String,Fingerprint> loadFingerprintsFromVariantContexts(Iterable<htsjdk.variant.variantcontext.VariantContext> iterable, String specificSample, Path source)
      Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
      Parameters:
      iterable - - an iterable over variantContexts containing genotypes for one or more samples
      specificSample - - null to load genotypes for all samples contained in the file or the name of an individual sample to load (and exclude all others).
      source - The path of the source file used. used to emit errors, and annotate the fingerprints.
      Returns:
      a Map of Sample name to Fingerprint

    • loadFingerprintsFromIndexedVcf

      public Map<String,Fingerprint> loadFingerprintsFromIndexedVcf(Path fingerprintFile, String specificSample)
      Loads genotypes from the supplied file into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
      Parameters:
      fingerprintFile - - VCF file containing genotypes for one or more samples
      specificSample - - null to load genotypes for all samples contained in the file or the name of an individual sample to load (and exclude all others).
      Returns:
      a Map of Sample name to Fingerprint

    • loadFingerprintsFromQueriableReader

      public Map<String,Fingerprint> loadFingerprintsFromQueriableReader(htsjdk.variant.vcf.VCFFileReader reader, String specificSample, Path source)
      Loads genotypes from the supplied reader into one or more Fingerprint objects and returns them in a Map of Sample->Fingerprint.
      Parameters:
      reader - - VCF reader containing genotypes for one or more samples
      specificSample - - null to load genotypes for all samples contained in the file or the name of an individual sample to load (and exclude all others).
      source - The path of the source file used. used to emit errors.
      Returns:
      a Map of Sample name to Fingerprint

    • getLociToGenotype

      public htsjdk.samtools.util.IntervalList getLociToGenotype(Collection<Fingerprint> fingerprints)
      Takes a set of fingerprints and returns an IntervalList containing all the loci that can be productively examined in sequencing data to compare to one or more of the fingerprints.

    • fingerprintVcf

      @Deprecated public Map<FingerprintIdDetails,Fingerprint> fingerprintVcf(Path vcfFile)
      Deprecated.

    • fingerprintVcf

      public Map<FingerprintIdDetails,Fingerprint> fingerprintVcf(Path vcfFile, Path indexPath, boolean forceIndex)

    • fingerprintSamFile

      @Deprecated public Map<FingerprintIdDetails,Fingerprint> fingerprintSamFile(Path samFile, htsjdk.samtools.util.IntervalList loci)
      Deprecated.
      use fingerprintSamFile(Path, Path, boolean, Function) instead.
      Does same thing as fingerprintSamFile(Path, Path, boolean, Function) but in the old way that required that you pass in the loci of interest. Since the loci are always the same as in haplotypes there's no need for this method signature anymore

    • fingerprintSamFile

      @Deprecated public Map<FingerprintIdDetails,Fingerprint> fingerprintSamFile(Path samFile, Function<HaplotypeBlock,HaplotypeProbabilities> blockToProbMapper)
      Deprecated.
      Generates a Fingerprint per read group in the supplied SAM file using the loci provided in the interval list.

    • fingerprintSamFile

      public Map<FingerprintIdDetails,Fingerprint> fingerprintSamFile(Path samFile, Path indexPath, boolean forceIndex, Function<HaplotypeBlock,HaplotypeProbabilities> blockToProbMapper)

    • identifyContaminant

      public Map<String,Fingerprint> identifyContaminant(Path samFile, double contamination)
      Generates a per-sample Fingerprint for the contaminant in the supplied SAM file. Data is aggregated by sample, not read-group.

    • fingerprintFiles

      @Deprecated public Map<FingerprintIdDetails,Fingerprint> fingerprintFiles(Collection<Path> files, int threads, int waitTime, TimeUnit waitTimeUnit)
      Deprecated.
      Fingerprints one or more SAM/BAM/VCF files at all available loci within the haplotype map, using multiple threads to speed up the processing.

    • fingerprintFiles

      public Map<FingerprintIdDetails,Fingerprint> fingerprintFiles(Collection<Path> files, Map<Path,Path> indexPathMap, Boolean forceIndex, int threads, int waitTime, TimeUnit waitTimeUnit)

    • checkFingerprints

      public List<FingerprintResults> checkFingerprints(List<Path> samFiles, List<Path> genotypeFiles, String specificSample, boolean ignoreReadGroups)
      Top level method to take a set of one or more SAM files and one or more Genotype files and compare each read group in each SAM file to each set of fingerprint genotypes.
      Parameters:
      samFiles - the list of SAM files to fingerprint
      genotypeFiles - the list of genotype files from which to pull fingerprint genotypes
      specificSample - an optional single sample who's genotypes to load from the supplied files
      ignoreReadGroups - aggregate data into one fingerprint per file, instead of splitting by RG

    • checkFingerprintsFromPaths

      public List<FingerprintResults> checkFingerprintsFromPaths(List<Path> observedGenotypeFiles, List<Path> expectedGenotypeFiles, String observedSample, String expectedSample)
      Top level method to take a set of one or more observed genotype (VCF) files and one or more expected genotype (VCF) files and compare one or more sample in the observed genotype file with one or more in the expected file and generate results for each set.
      Parameters:
      observedGenotypeFiles - The list of genotype files containing observed calls, from which to pull fingerprint genotypes
      expectedGenotypeFiles - The list of genotype files containing expected calls, from which to pull fingerprint genotypes
      observedSample - an optional single sample whose genotypes to load from the observed genotype file (if null, use all)
      expectedSample - an optional single sample whose genotypes to load from the expected genotype file (if null, use all)

    • calculateMatchResults

      public static MatchResults calculateMatchResults(Fingerprint observedFp, Fingerprint expectedFp, double minPExpected, double pLoH)

    • calculateMatchResults

      public static MatchResults calculateMatchResults(Fingerprint observedFp, Fingerprint expectedFp, double minPExpected, double pLoH, boolean calculateLocusInfo, boolean calculateTumorAwareLod)
      Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample.

      If comparing sequencing data to genotype data then the sequencing data should be passed as the observedFp and the genotype data as the expectedFp in order to get the best output.

      In the cases where the most likely genotypes from the two fingerprints do not match the lExpectedSample is Max(actualpExpectedSample, minPExpected).

    • calculateMatchResults

      public static MatchResults calculateMatchResults(Fingerprint observedFp, Fingerprint expectedFp)
      Compares two fingerprints and calculates a MatchResults object which contains detailed information about the match (or mismatch) between fingerprints including the LOD score for whether or not the two are likely from the same sample.

      If comparing sequencing data to genotype data then the sequencing data should be passed as the observedFp and the genotype data as the expectedFp in order to get the best output.

    • setReferenceFasta

      public void setReferenceFasta(File referenceFasta)

    • getLocusMaxReads

      public int getLocusMaxReads()

    • setLocusMaxReads

      public void setLocusMaxReads(int locusMaxReads)

    • getDefaultSampleID

      public String getDefaultSampleID()

    • setDefaultSampleID

      public void setDefaultSampleID(String defaultSampleID)