Îõ³h*2ƒ.–·      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“ ” • – — ˜ ™ š › œ  ž Ÿ   ¡ ¢ £ ¤ ¥ ¦ § ¨ © ª « ¬ ­ ® ¯ ° ± ² ³ ´ µ ¶ 1.8.1.0  Safe-Inferred",sequence-formats(A wrapper datatype for Chromosome names.sequence-formats9An exception type for parsing BioInformatic file formats.sequence-formatsïA function to help with reporting parsing errors to stderr. Returns a clean Producer over the parsed datatype.sequence-formatsÔA helper function to parse a text producer, properly reporting all errors to stderr. sequence-formatsOrd instance for Chrom sequence-formatsShow instance for Chrom    Safe-Inferred" *sequence-formatsÿA 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-formatsÏA 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-formatsÏThe actual data, a dictionary from allele sharing patterns to observed numbers.sequence-formatsìAn 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-formatsˆFunction 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 FilePath sequence-formats$Read a histogram from a File Handle.   Safe-Inferred" Ò#sequence-formats¯A datatype to represent a single pileup row for multiple individuals. The constructor arguments are: Chromosome, Position, Refererence Allelele, Pileup String per individual%sequence-formatsThe chromosome&sequence-formats The position'sequence-formatsThe reference base(sequence-formatsThe base string*sequence-formatsÀA datatype to represent the strand orientation of a single base.-sequence-formatsâRead a pileup-formatted file from StdIn, for reading from an external command `samtools mpileup`..sequence-formatsRead pileup from a file. -.#$%&'()*+, -.#$%&'()*+, Safe-Inferred"B3sequence-formats*A Datatype to denote a single freqSum line5sequence-formatsThe chromosome of the site6sequence-formatsThe position of the site7sequence-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.8sequence-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.9sequence-formatsThe reference allele:sequence-formatsThe alternative allele;sequence-formatsÄA 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-formatsÊThis function converts a single freqSum entry to a printable freqSum line.Asequence-formatsïA function to read a freqsum file from StdIn. Returns a pair of a freqSum Header and a Producer over all lines.Bsequence-formatsðA function to read a freqsum file from a file. Returns a pair of a freqSum Header and a Producer over all lines.Csequence-formatsA function to write freqSum data to StdOut. Expects the freqSum header as argument, and then returns a Consumer that accepts freqSum entries.Dsequence-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.AB3456789:;<=>?CD@AB3456789:;<=>?CD@ Safe-Inferred"íIsequence-formatsÖA 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).Jsequence-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.JIJI Safe-Inferred"°Ksequence-formats;Vector of the genotypes of all individuals at a single SNP.Lsequence-formats?A datatype to represent the genotype of an individual at a SNP.Qsequence-formats?@ABCCDEFGHIJKLMNOPQRSTUVWXYZ[[\\]^_`abcdefghijklmnopqrstuvwwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“” • • – — ˜ ™ š › œ  ž Ÿ     ¡ ¢ £ ¤ ¥ ¦ § ¨ © ª « ¬ ­ ® ¯ ° ± ² ³ ´ µ ¶·¸¹º »¼.sequence-formats-1.8.1.0-E1ysEqoMi1YwH6XDCuDNeSequenceFormats.Utils#SequenceFormats.RareAlleleHistogramSequenceFormats.PileupSequenceFormats.FreqSumSequenceFormats.FastaSequenceFormats.EigenstratSequenceFormats.PlinkSequenceFormats.BedSequenceFormats.VCFSequenceFormats.Genomicsequence-formatsChromunChromSeqFormatExceptionliftParsingErrorsconsumeProducer readFileProdreadFileProdCheckCompressword$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$fShowEigenstratSnpEntryPlinkPopNameModePlinkPopNameAsFamilyPlinkPopNameAsPhenotypePlinkPopNameAsBoth PlinkFamEntry _famFamilyID_famIndividualID _famFatherID _famMotherID _famSexCode _famPhenotypeplinkFam2EigenstratIndeigenstratInd2PlinkFamreadPlinkBedFile readBimStdIn readBimFile readFamFile readPlinkwriteBim writePlink$fEqPlinkPopNameMode$fShowPlinkPopNameMode$fEqPlinkFamEntry$fShowPlinkFamEntryIntervalStatus BedBehindBedOnBedAheadBedEntry bedFileParser readBedFilefilterThroughBed$fShowBedEntry $fEqBedEntryVCFentryvcfChromvcfPosvcfIdvcfRefvcfAltvcfQual vcfFiltervcfInfovcfFormatStringvcfGenotypeInfo VCFheadervcfHeaderCommentsvcfSampleNamesreadVCFfromStdInreadVCFfromFileisBiallelicSnpisTransversionSnp getGenotypes getDosagesvcfToFreqSumEntry$fShowVCFentry $fEqVCFentry$fShowVCFheaderGenomicgenomicPosition genomicChrom genomicBase chromFiltergenomicFilterThroughBed$fGenomicVCFentry$fGenomicPileupRow$fGenomicFreqSumEntry$fGenomicEigenstratSnpEntry showHistogramreadEigenstratGenoFilewriteFamwriteBedreadVCFfromProd