úÎ!ąPšhŽ      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒNone„sequence-formats(A wrapper datatype for Chromosome names.sequence-formats9An exception type for parsing BioInformatic file formats.sequence-formatspA function to help with reporting parsing errors to stderr. Returns a clean Producer over the parsed datatype.sequence-formatsTA helper function to parse a text producer, properly reporting all errors to stderr. sequence-formatsOrd instance for Chrom sequence-formatsShow instance for Chrom  None$àsequence-formats€A simple type synonym for the SitePattern, represented as a list of Integers that represents each pattern across the branches.sequence-formats4A datatype to represent an Allele Sharing Histogram:sequence-formatsA list of branch namessequence-formatsA list of haploid sample sizes.sequence-formatsThe minimum allele countsequence-formatsThe maximum allele countsequence-formatsPA list of branch indices that were used to condition the allele sharing patternsequence-formats%A list of patterns that are excluded.sequence-formats4The total number of non-missing sites in the genome.sequence-formatsOThe actual data, a dictionary from allele sharing patterns to observed numbers.sequence-formatslAn optional dictionary that contains Jackknife estimates and standard deviations for each pattern frequency.sequence-formats5A simple function to convert a pattern into a String.Žsequence-formatsÿ Function to convert a Rare Allele Histogram to text. Returns an error if attempting to print a histogram with non-standard settings. Many settings, such as minAf>1, are only meant for in-memory representations, but are not compatible with the file format itself.sequence-formatsWrite a histogram to the stdoutsequence-formatsWrite a histogram to a filesequence-formats Read a histogram from a FilePathsequence-formats$Read a histogram from a File Handle.None.†"sequence-formatsŻA datatype to represent a single pileup row for multiple individuals. The constructor arguments are: Chromosome, Position, Refererence Allelele, Pileup String per individual$sequence-formatsThe chromosome%sequence-formats The position&sequence-formatsThe reference base'sequence-formatsThe base string)sequence-formats@A datatype to represent the strand orientation of a single base.,sequence-formatsbRead a pileup-formatted file from StdIn, for reading from an external command `samtools mpileup`.-sequence-formatsRead pileup from a file. "#$%&'()*+,- ,-"#$%&'()*+NoneFš2sequence-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-formatsDA 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-formatsJThis function converts a single freqSum entry to a printable freqSum line.@sequence-formatsoA function to read a freqsum file from StdIn. Returns a pair of a freqSum Header and a Producer over all lines.Asequence-formatspA 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?NonePÖHsequence-formatsÿXA 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-formatsÚThis 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.HIIHNonep 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<A datatype to represent Sex in an Eigenstrat Individual fileTsequence-formatsjA datatype to represent a single individual. The constructor arguments are: Name, Sex and Population NameVsequence-formats‰A datatype to represent a single genomic SNP. The constructor arguments are: Chromosome, Position, Reference Allele, Alternative Allele.^sequence-formatsbFunction to read an Eigenstrat individual file. Returns the Eigenstrat Individual Entries as list._sequence-formats_Function to read a Snp File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries.`sequence-formats`Function to read a Snp File from a file. Returns a Pipes-Producer over the EigenstratSnpEntries.asequence-formats©Function to read a full Eigenstrat database from files. Returns a pair of the Eigenstrat Individual Entries, and a joint Producer over the snp entries and the genotypes.bsequence-formats)Function to write an Eigenstrat Ind file.csequence-formats\Function to write an Eigenstrat Snp File. Returns a consumer expecting EigenstratSnpEntries.dsequence-formats\Function to write an Eigentrat Geno File. Returns a consumer expecting Eigenstrat Genolines.esequence-formatseFunction to write an Eigenstrat Database. Returns a consumer expecting joint Snp- and Genotype lines.asequence-formatsThe Genotype filesequence-formats The Snp Filesequence-formats The Ind filecsequence-formatsThe Eigenstrat Snp File Handle.sequence-formats'A consumer to read EigenstratSnpEntriesdsequence-formatsThe Genotype file handlesequence-formats$A consumer to read Genotype entries.esequence-formatsThe Genotype filesequence-formats The Snp Filesequence-formats The Ind filesequence-formatsThe list of individual entriessequence-formats.A consumer to read joint Snp/Genotype entries.JKLMNOPSQRTUVWXYZ[\]^_`abcdeVWXYZ[\]TU^KLMNOJPSQR_`aebcdNonea\nsequence-formatsMA function to read a bed file from a file. Returns a Producer over all lines.osequence-formats_Function to read a Bim File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries.psequence-formats`Function to read a Bim File from a file. Returns a Pipes-Producer over the EigenstratSnpEntries.qsequence-formatsUFunction to read a Plink fam file. Returns the Eigenstrat Individual Entries as list.sequence-formatsžFunction to read a full Plink dataset from files. Returns a pair of the Plink Individual Entries, and a joint Producer over the snp entries and the genotypes.rsequence-formatsPFunction to write a Bim file. Returns a consumer expecting EigenstratSnpEntries.sequence-formats The Bed filesequence-formats The Bim Filesequence-formats The Fam filersequence-formatsThe Eigenstrat Snp File handle.sequence-formats'A consumer to read EigenstratSnpEntriesnopqroprqnNone™€ssequence-formats+A Datatype representing a single VCF entry.usequence-formatsThe chromosomevsequence-formats The positionwsequence-formatsThe SNP ID if non-missingxsequence-formatsGThe reference allele (supports also multi-character alleles for Indels)ysequence-formatsBThe alternative alleles, each one possible of multiple characters zsequence-formatsThe quality value{sequence-formats!The Filter value, if non-missing.|sequence-formatsA list of Info fields}sequence-formatsA list of format tags~sequence-formats(A list of format fields for each sample.sequence-formatsŠA datatype to represent the VCF Header. Most comments are simply parsed as entire lines, but the very last comment line, containing the sample names, is separated outsequence-formats9A list of containing all comments starting with a single #‚sequence-formatsKThe list of sample names parsed from the last comment line starting with ##ƒsequence-formats6reads a VCFheader and VCFentries from a text producer.„sequence-formatsMReading a VCF from StdIn. Returns a VCFHeader and a Producer over VCFentries.…sequence-formatsNReading a VCF from a file. Returns a VCFHeader and a Producer over VCFentries.†sequence-formats%returns True if the SNP is biallelic.‡sequence-formatsFreturns True if the SNp is a biallelic Transversion SNP (i.e. one of GT, GC, AT, AC)ˆsequence-formats?Extracts the genotype fields (for each sapmle) from a VCF entry‰sequence-formatsfExtracts the dosages (the sum of non-reference alleles) per sample (returns a Left Error if it fails.)Šsequence-formatsUConverts a VCFentry to the simpler FreqSum format (returns a Left Error if it fails.)stuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š€‚stuvwxyz{|}~„…ƒˆ‰‡Š†        !"#$%&'(()*+,-./01234567789:;<=>??@ABCDEFGHIJKLMNOPQRSTUVWWXXYZ[\]^_`abcdefghijklmnopqrsttuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ-sequence-formats-1.5.1-9h5rHjgnIxCF6XNQtpUtLESequenceFormats.Utils#SequenceFormats.RareAlleleHistogramSequenceFormats.PileupSequenceFormats.FreqSumSequenceFormats.FastaSequenceFormats.EigenstratSequenceFormats.PlinkSequenceFormats.VCFChromunChromSeqFormatExceptionliftParsingErrorsconsumeProducer readFileProdword$fExceptionSeqFormatException $fOrdChrom $fShowChrom$fShowSeqFormatException$fEqSeqFormatException $fEqChrom SitePatternRareAlleleHistogramraNamesraNVecraMinAfraMaxAf raConditionOnraExcludePatternsraTotalNrSitesraCountsraJackknifeEstimatesshowSitePatternwriteHistogramStdOutwriteHistogramFile readHistogramreadHistogramFromHandle$fEqRareAlleleHistogram$fShowRareAlleleHistogram PileupRow pileupChrom pileupPos pileupRef pileupBasespileupStrandInfoStrand ForwardStrand ReverseStrandreadPileupFromStdInreadPileupFromFile $fEqStrand $fShowStrand $fEqPileupRow$fShowPileupRow FreqSumEntryfsChromfsPosfsSnpId fsGeneticPosfsReffsAltfsCounts FreqSumHeaderfshNames fshCountsfreqSumEntryToTextreadFreqSumStdInreadFreqSumFileprintFreqSumStdOutprintFreqSumFile$fEqFreqSumHeader$fShowFreqSumHeader$fEqFreqSumEntry$fShowFreqSumEntryloadFastaChromreadNextFastaEntryGenoLine GenoEntryHomRefHetHomAltMissingSexMaleFemaleUnknownEigenstratIndEntryEigenstratSnpEntrysnpChromsnpPos snpGeneticPossnpIdsnpRefsnpAltreadEigenstratIndreadEigenstratSnpStdInreadEigenstratSnpFilereadEigenstratwriteEigenstratIndFilewriteEigenstratSnpwriteEigenstratGenowriteEigenstrat$fEqEigenstratSnpEntry$fShowEigenstratSnpEntry$fEqSex $fShowSex$fEqEigenstratIndEntry$fShowEigenstratIndEntry $fEqGenoEntry$fShowGenoEntryreadPlinkBedFile readBimStdIn readBimFile readFamFilewriteBimVCFentryvcfChromvcfPosvcfIdvcfRefvcfAltvcfQual vcfFiltervcfInfovcfFormatStringvcfGenotypeInfo VCFheadervcfHeaderCommentsvcfSampleNamesreadVCFfromProdreadVCFfromStdInreadVCFfromFileisBiallelicSnpisTransversionSnp getGenotypes getDosagesvcfToFreqSumEntry$fShowVCFheader$fShowVCFentry $fEqVCFentry showHistogram readPlink