Îõ³h*2¿.¦¾      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•–— ˜ ™ š › œ  ž Ÿ   ¡ ¢ £ ¤ ¥ ¦ § ¨ © ª « ¬ ­ ® ¯ ° ± ² ³ ´ µ ¶ · ¸ ¹ º » ¼ ½ 1.11.0.0  Safe-Inferred"Psequence-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 Chromsequence-formatsShow instance for Chrom       Safe-Inferred" Vsequence-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.¾sequence-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 stdout"sequence-formatsWrite a histogram to a file#sequence-formats Read a histogram from a FilePath$sequence-formats$Read a histogram from a File Handle.$#!" $#!"  Safe-Inferred" þ'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.1sequence-formatsâRead a pileup-formatted file from StdIn, for reading from an external command `samtools mpileup`.2sequence-formatsRead pileup from a file. 12'()*+,-./0 12'()*+,-./0 Safe-Inferred"£7sequence-formats*A Datatype to denote a single freqSum line9sequence-formatsThe chromosome of the site:sequence-formatsThe position of the site;sequence-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.<sequence-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.=sequence-formatsThe reference allele>sequence-formatsThe alternative allele?sequence-formatsùA list of tuples with non-reference allele counts in each group and the total allele count. Nothing denotes missing data.@sequence-formats"A Datatype representing the HeaderBsequence-formats#A list of individual or group namesCsequence-formats0A list of haplotype counts per individual/group.Dsequence-formatsÊThis function converts a single freqSum entry to a printable freqSum line.Esequence-formatsïA function to read a freqsum file from StdIn. Returns a pair of a freqSum Header and a Producer over all lines.Fsequence-formatsðA function to read a freqsum file from a file. Returns a pair of a freqSum Header and a Producer over all lines.Gsequence-formatsA function to write freqSum data to StdOut. Expects the freqSum header as argument, and then returns a Consumer that accepts freqSum entries.Hsequence-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.EF789:;<=>?@ABCGHDEF789:;<=>?@ABCGHD Safe-Inferred"NMsequence-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).Nsequence-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.NMNM Safe-Inferred" Osequence-formats;Vector of the genotypes of all individuals at a single SNP.Psequence-formats?A datatype to represent the genotype of an individual at a SNP.Usequence-formats?@AABCDEFGHIIJKLMNOPQRSTUVWXYZ[\]^_`aabbcdefghijklmnopqrstuvwxyz{|}}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”••–—˜™š › › œ  ž Ÿ   ¡ ¢ £ ¤ ¥ ¥ ¦ § ¨ © ª « ¬ ­ ® ¯ ° ± ² ³ ´ µ ¶ · ¸ ¹ º » ¼ ½ ¾ ¿ÀÁÂà ÄÅ0sequence-formats-1.11.0.0-5rbzHrtrwqA4L0txRa5j6gSequenceFormats.Utils#SequenceFormats.RareAlleleHistogramSequenceFormats.PileupSequenceFormats.FreqSumSequenceFormats.FastaSequenceFormats.EigenstratSequenceFormats.PlinkSequenceFormats.BedSequenceFormats.VCFSequenceFormats.Genomicsequence-formats0streaming-commons-0.2.3.0-FLmMps0qO1lDxG2H6phYk5Data.Streaming.ZlibDeflateChromunChromSeqFormatExceptionliftParsingErrorsconsumeProducer readFileProdreadFileProdCheckCompressword gzipConsumerwriteFromPopperdeflateFinaliser$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 $fEqBedEntryVCFentryvcfChromvcfPosvcfIdvcfRefvcfAltvcfQual vcfFiltervcfInfovcfGenotypeInfo VCFheadervcfHeaderCommentsvcfSampleNamesreadVCFfromStdInreadVCFfromFilevcfHeaderParserisBiallelicSnpisTransversionSnp getGenotypes getDosagesvcfToFreqSumEntryprintVCFtoStdOut writeVCFfile$fShowVCFentry $fEqVCFentry$fShowVCFheader $fEqVCFheaderGenomicgenomicPosition genomicChrom genomicBase chromFiltergenomicFilterThroughBed$fGenomicVCFentry$fGenomicPileupRow$fGenomicFreqSumEntry$fGenomicEigenstratSnpEntry showHistogramreadEigenstratGenoFilewriteFamwriteBedreadVCFfromProd