!      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~None sequence-formats9An exception type for parsing BioInformatic file formats.sequence-formats(A wrapper datatype for Chromosome names.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$sequence-formatsA simple type synonym for the SitePattern, represented as a list of Integers that represents each pattern across the branches.sequence-formats4A datatype to represent an Allele Sharing Histogram:sequence-formatsA list of branch namessequence-formatsA list of haploid sample sizes.sequence-formatsThe minimum allele countsequence-formatsThe maximum allele countsequence-formatsPA list of branch indices that were used to condition the allele sharing patternsequence-formats%A list of patterns that are excluded.sequence-formats4The total number of non-missing sites in the genome.sequence-formatsOThe actual data, a dictionary from allele sharing patterns to observed numbers.sequence-formatslAn optional dictionary that contains Jackknife estimates and standard deviations for each pattern frequency.sequence-formats5A simple function to convert a pattern into a String.sequence-formats Function to convert a Rare Allele Histogram to text. Returns an error if attempting to print a histogram with non-standard settings. Many settings, such as minAf>1, are only meant for in-memory representations, but are not compatible with the file format itself.sequence-formatsWrite a histogram to the stdoutsequence-formatsWrite a histogram to a filesequence-formats Read a histogram from a FilePathsequence-formats$Read a histogram from a File Handle.None*e!sequence-formatsA datatype to represent a single pileup row for multiple individuals. The constructor arguments are: Chromosome, Position, Refererence Allelele, Pileup String per individual#sequence-formatsbRead a pileup-formatted file from StdIn, for reading from an external command `samtools mpileup`.$sequence-formatsRead pileup from a file.!"#$#$!"None= 'sequence-formats*A Datatype to denote a single freqSum line)sequence-formatsThe chromosome of the site*sequence-formatsThe position of the site+sequence-formatsThe reference allele,sequence-formatsThe alternative allele-sequence-formatsDA list of allele counts in each group. Nothing denotes missing data..sequence-formats"A Datatype representing the Header0sequence-formats#A list of individual or group names1sequence-formats0A list of haplotype counts per individual/group.2sequence-formatsJThis function converts a single freqSum entry to a printable freqSum line.3sequence-formatsoA function to read a freqsum file from StdIn. Returns a pair of a freqSum Header and a Producer over all lines.4sequence-formatspA function to read a freqsum file from a file. Returns a pair of a freqSum Header and a Producer over all lines.5sequence-formatsA function to write freqSum data to StdOut. Expects the freqSum header as argument, and then returns a Consumer that accepts freqSum entries.6sequence-formatsA function that writes a freqSum file. Expects the FilePath and the freqSum header as arguments, and then returns a Consumer that accepts freqSum entries.'()*+,-./012345634'()*+,-./01562NoneG);sequence-formatsXA 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).<sequence-formatsThis 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.;<<;Nonem,=sequence-formats;Vector of the genotypes of all individuals at a single SNP.>sequence-formats?A datatype to represent the genotype of an individual at a SNP.Csequence-formats<A datatype to represent Sex in an Eigenstrat Individual fileGsequence-formatsjA datatype to represent a single individual. The constructor arguments are: Name, Sex and Population NameIsequence-formatsA datatype to represent a single genomic SNP. The constructor arguments are: Chromosome, Position, Reference Allele, Alternative Allele.Qsequence-formatsbFunction to read an Eigenstrat individual file. Returns the Eigenstrat Individual Entries as list.Rsequence-formats_Function to read a Snp File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries.Ssequence-formats`Function to read a Snp File from a file. Returns a Pipes-Producer over the EigenstratSnpEntries.Tsequence-formats_Function to read a Bim File from StdIn. Returns a Pipes-Producer over the EigenstratSnpEntries.Usequence-formats`Function to read a Bim File from a file. Returns a Pipes-Producer over the EigenstratSnpEntries.Vsequence-formatsFunction 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.Wsequence-formats)Function to write an Eigenstrat Ind file.Xsequence-formats\Function to write an Eigenstrat Snp File. Returns a consumer expecting EigenstratSnpEntries.Ysequence-formatsPFunction to write a Bim file. Returns a consumer expecting EigenstratSnpEntries.Zsequence-formats\Function to write an Eigentrat Geno File. Returns a consumer expecting Eigenstrat Genolines.[sequence-formatseFunction to write an Eigenstrat Database. Returns a consumer expecting joint Snp- and Genotype lines.Vsequence-formatsThe Genotype filesequence-formats The Snp Filesequence-formats The Ind fileXsequence-formatsThe Eigenstrat Snp File Handle.sequence-formats'A consumer to read EigenstratSnpEntriesYsequence-formatsThe Eigenstrat Snp File handle.sequence-formats'A consumer to read EigenstratSnpEntriesZsequence-formatsThe Genotype file handlesequence-formats$A consumer to read Genotype entries.[sequence-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.=>?@ABCFDEGHIJKLMNOPQRSTUVWXYZ[IJKLMNOPGHQ>?@AB=CFDERSTUV[WXYZNoneDdsequence-formats+A Datatype representing a single VCF entry.fsequence-formatsThe chromosomegsequence-formats The positionhsequence-formatsThe SNP ID if non-missingisequence-formatsGThe reference allele (supports also multi-character alleles for Indels)jsequence-formatsBThe alternative alleles, each one possible of multiple characters ksequence-formatsThe quality valuelsequence-formats!The Filter value, if non-missing.msequence-formatsA list of Info fieldsnsequence-formatsA list of format tagsosequence-formats(A list of format fields for each sample.psequence-formatsA 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 outrsequence-formats9A list of containing all comments starting with a single #ssequence-formatsKThe list of sample names parsed from the last comment line starting with ##tsequence-formats6reads a VCFheader and VCFentries from a text producer.usequence-formatsMReading a VCF from StdIn. Returns a VCFHeader and a Producer over VCFentries.vsequence-formatsNReading a VCF from a file. Returns a VCFHeader and a Producer over VCFentries.wsequence-formats%returns True if the SNP is biallelic.xsequence-formatsFreturns True if the SNp is a biallelic Transversion SNP (i.e. one of GT, GC, AT, AC)ysequence-formats?Extracts the genotype fields (for each sapmle) from a VCF entryzsequence-formatsfExtracts the dosages (the sum of non-reference alleles) per sample (returns a Left Error if it fails.){sequence-formatsUConverts a VCFentry to the simpler FreqSum format (returns a Left Error if it fails.)defghijklmnopqrstuvwxyz{pqrsdefghijklmnouvtyzx{w       !"#$%&&'()*++,-./01123456789:;<=>?@ABCDEFGHIIJJKLMNOPQRSTUVWXYZ[\]^_`abcddefghijklmnoopqrstuvwxyz{|}~-sequence-formats-1.3.3-DqVzhtKrYz3GVd8k9HbLOSSequenceFormats.Utils#SequenceFormats.RareAlleleHistogramSequenceFormats.PileupSequenceFormats.FreqSumSequenceFormats.FastaSequenceFormats.EigenstratSequenceFormats.VCFSeqFormatExceptionChromunChromliftParsingErrorsconsumeProducer readFileProdword $fOrdChrom $fShowChrom$fExceptionSeqFormatException $fEqChrom$fShowSeqFormatException SitePatternRareAlleleHistogramraNamesraNVecraMinAfraMaxAf raConditionOnraExcludePatternsraTotalNrSitesraCountsraJackknifeEstimatesshowSitePatternwriteHistogramStdOutwriteHistogramFile readHistogramreadHistogramFromHandle$fEqRareAlleleHistogram$fShowRareAlleleHistogram PileupRowreadPileupFromStdInreadPileupFromFile $fEqPileupRow$fShowPileupRow FreqSumEntryfsChromfsPosfsReffsAltfsCounts FreqSumHeaderfshNames fshCountsfreqSumEntryToTextreadFreqSumStdInreadFreqSumFileprintFreqSumStdOutprintFreqSumFile$fEqFreqSumHeader$fShowFreqSumHeader$fEqFreqSumEntry$fShowFreqSumEntryloadFastaChromreadNextFastaEntryGenoLine GenoEntryHomRefHetHomAltMissingSexMaleFemaleUnknownEigenstratIndEntryEigenstratSnpEntrysnpChromsnpPos snpGeneticPossnpIdsnpRefsnpAltreadEigenstratIndreadEigenstratSnpStdInreadEigenstratSnpFile readBimStdIn readBimFilereadEigenstratwriteEigenstratIndFilewriteEigenstratSnpwriteBimwriteEigenstratGenowriteEigenstrat$fEqEigenstratSnpEntry$fShowEigenstratSnpEntry$fEqSex $fShowSex$fEqEigenstratIndEntry$fShowEigenstratIndEntry $fEqGenoEntry$fShowGenoEntryVCFentryvcfChromvcfPosvcfIdvcfRefvcfAltvcfQual vcfFiltervcfInfovcfFormatStringvcfGenotypeInfo VCFheadervcfHeaderCommentsvcfSampleNamesreadVCFfromProdreadVCFfromStdInreadVCFfromFileisBiallelicSnpisTransversionSnp getGenotypes getDosagesvcfToFreqSumEntry$fShowVCFheader$fShowVCFentry $fEqVCFentry showHistogram