Ξυ³h$,ς*      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽNone Xsequence-formats(A wrapper datatype for Chromosome names.sequence-formats9An exception type for parsing BioInformatic file formats.sequence-formatsπA function to help with reporting parsing errors to stderr. Returns a clean Producer over the parsed datatype.sequence-formatsΤA helper function to parse a text producer, properly reporting all errors to stderr. sequence-formatsOrd instance for Chrom sequence-formatsShow instance for Chrom  None ,sequence-formats€A simple type synonym for the SitePattern, represented as a list of Integers that represents each pattern across the branches.sequence-formats4A datatype to represent an Allele Sharing Histogram:sequence-formatsA list of branch namessequence-formatsA list of haploid sample sizes.sequence-formatsThe minimum allele countsequence-formatsThe maximum allele countsequence-formatsΠA list of branch indices that were used to condition the allele sharing patternsequence-formats%A list of patterns that are excluded.sequence-formats4The total number of non-missing sites in the genome.sequence-formatsΟThe actual data, a dictionary from allele sharing patterns to observed numbers.sequence-formatsμAn optional dictionary that contains Jackknife estimates and standard deviations for each pattern frequency.sequence-formats5A simple function to convert a pattern into a String.sequence-formatsWrite a histogram to the stdoutsequence-formatsWrite a histogram to a filesequence-formats Read a histogram from a FilePathsequence-formats$Read a histogram from a File Handle.None Λ"sequence-formats―A datatype to represent a single pileup row for multiple individuals. The constructor arguments are: Chromosome, Position, Refererence Allelele, Pileup String per individual$sequence-formatsThe chromosome%sequence-formats The position&sequence-formatsThe reference base'sequence-formatsThe base string)sequence-formatsΐA datatype to represent the strand orientation of a single base.,sequence-formatsβRead a pileup-formatted file from StdIn, for reading from an external command `samtools mpileup`.-sequence-formatsRead pileup from a file. "#$%&'()*+,- ,-"#$%&'()*+None 22sequence-formats*A Datatype to denote a single freqSum line4sequence-formatsThe chromosome of the site5sequence-formatsThe position of the site6sequence-formats’An optional parameter to take the snpId. This is not parsed from or printed to freqSum format but is used in internal conversions from Eigenstrat.7sequence-formats˜An optional parameter to take the genetic pos. This is not parsed from or printed to freqSum format but is used in internal conversions from Eigenstrat.8sequence-formatsThe reference allele9sequence-formatsThe alternative allele:sequence-formatsΔA list of allele counts in each group. Nothing denotes missing data.;sequence-formats"A Datatype representing the Header=sequence-formats#A list of individual or group names>sequence-formats0A list of haplotype counts per individual/group.?sequence-formatsΚThis function converts a single freqSum entry to a printable freqSum line.@sequence-formatsοA function to read a freqsum file from StdIn. Returns a pair of a freqSum Header and a Producer over all lines.Asequence-formatsπA function to read a freqsum file from a file. Returns a pair of a freqSum Header and a Producer over all lines.Bsequence-formatsA function to write freqSum data to StdOut. Expects the freqSum header as argument, and then returns a Consumer that accepts freqSum entries.Csequence-formatsšA function that writes a freqSum file. Expects the FilePath and the freqSum header as arguments, and then returns a Consumer that accepts freqSum entries.23456789:;<=>?@ABC@A23456789:;<=>BC?None ΦHsequence-formatsΨA function to select out a specific chromosome from a Fasta File. Expects a file handle to the file and a chromosome. Note that by Chromosome I simply denote a fasta header line, as is the case for example for the human reference genome. Returns a Bytestring-Producer over the single sequence followed the specified header (the chromosome).Isequence-formatsΪThis function takes a Bytestring-Producer over a Fasta-file, reads in the first header and then returns a produer over its sequence. The return of that producer is the Bytestring-Producer of the rest of the fasta file.HIIHNone ! Jsequence-formats;Vector of the genotypes of all individuals at a single SNP.Ksequence-formats?A datatype to represent the genotype of an individual at a SNP.Psequence-formats??@ABCDEFGHIJKLMNOPQRSTUVWWXXYZ[\]^_`abcdefghijklmnopqrstuvvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ-sequence-formats-1.6.3-Ciw6oN5cbR6IlvtY976cHYSequenceFormats.Utils#SequenceFormats.RareAlleleHistogramSequenceFormats.PileupSequenceFormats.FreqSumSequenceFormats.FastaSequenceFormats.EigenstratSequenceFormats.PlinkSequenceFormats.VCFChromunChromSeqFormatExceptionliftParsingErrorsconsumeProducer readFileProdword$fExceptionSeqFormatException $fOrdChrom $fShowChrom $fEqChrom$fShowSeqFormatException$fEqSeqFormatException SitePatternRareAlleleHistogramraNamesraNVecraMinAfraMaxAf raConditionOnraExcludePatternsraTotalNrSitesraCountsraJackknifeEstimatesshowSitePatternwriteHistogramStdOutwriteHistogramFile readHistogramreadHistogramFromHandle$fEqRareAlleleHistogram$fShowRareAlleleHistogram PileupRow pileupChrom pileupPos pileupRef pileupBasespileupStrandInfoStrand ForwardStrand ReverseStrandreadPileupFromStdInreadPileupFromFile $fEqPileupRow$fShowPileupRow $fEqStrand $fShowStrand FreqSumEntryfsChromfsPosfsSnpId fsGeneticPosfsReffsAltfsCounts FreqSumHeaderfshNames fshCountsfreqSumEntryToTextreadFreqSumStdInreadFreqSumFileprintFreqSumStdOutprintFreqSumFile$fEqFreqSumEntry$fShowFreqSumEntry$fEqFreqSumHeader$fShowFreqSumHeaderloadFastaChromreadNextFastaEntryGenoLine GenoEntryHomRefHetHomAltMissingSexMaleFemaleUnknownEigenstratIndEntryEigenstratSnpEntrysnpChromsnpPos snpGeneticPossnpIdsnpRefsnpAltreadEigenstratIndreadEigenstratSnpStdInreadEigenstratSnpFilereadEigenstratwriteEigenstratIndFilewriteEigenstratSnpwriteEigenstratGenowriteEigenstrat $fEqGenoEntry$fShowGenoEntry$fEqEigenstratIndEntry$fShowEigenstratIndEntry$fEqSex $fShowSex$fEqEigenstratSnpEntry$fShowEigenstratSnpEntryreadPlinkBedFile readBimStdIn readBimFile readFamFile readPlinkwriteBim writePlinkVCFentryvcfChromvcfPosvcfIdvcfRefvcfAltvcfQual vcfFiltervcfInfovcfFormatStringvcfGenotypeInfo VCFheadervcfHeaderCommentsvcfSampleNamesreadVCFfromProdreadVCFfromStdInreadVCFfromFileisBiallelicSnpisTransversionSnp getGenotypes getDosagesvcfToFreqSumEntry$fShowVCFentry $fEqVCFentry$fShowVCFheader