Îõ³h*3/Œº      !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJKLMNOPQRSTUVWXYZ[\]^_`abcdefghijklmnopqrstuvwxyz{|}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“”•– — ˜ ™ š › œ  ž Ÿ   ¡ ¢ £ ¤ ¥ ¦ § ¨ © ª « ¬ ­ ® ¯ ° ± ² ³ ´ µ ¶ · ¸ ¹ 1.9.0.0  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 Chromsequence-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.ºsequence-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" ç&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.0sequence-formatsâRead a pileup-formatted file from StdIn, for reading from an external command `samtools mpileup`.1sequence-formatsRead pileup from a file. 01&'()*+,-./ 01&'()*+,-./ Safe-Inferred"W6sequence-formats*A Datatype to denote a single freqSum line8sequence-formatsThe chromosome of the site9sequence-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-formatsÄA list of allele counts in each group. Nothing denotes missing data.?sequence-formats"A Datatype representing the HeaderAsequence-formats#A list of individual or group namesBsequence-formats0A list of haplotype counts per individual/group.Csequence-formatsÊThis function converts a single freqSum entry to a printable freqSum line.Dsequence-formatsïA function to read a freqsum file from StdIn. Returns a pair of a freqSum Header and a Producer over all lines.Esequence-formatsðA function to read a freqsum file from a file. Returns a pair of a freqSum Header and a Producer over all lines.Fsequence-formatsA function to write freqSum data to StdOut. Expects the freqSum header as argument, and then returns a Consumer that accepts freqSum entries.Gsequence-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.DE6789:;<=>?@ABFGCDE6789:;<=>?@ABFGC Safe-Inferred"Lsequence-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).Msequence-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.MLML Safe-Inferred" 1Nsequence-formats;Vector of the genotypes of all individuals at a single SNP.Osequence-formats?A datatype to represent the genotype of an individual at a SNP.Tsequence-formats?@@ABCDEFGHHIJKLMNOPQRSTUVWXYZ[\]^_``aabcdefghijklmnopqrstuvwxyz{||}~€‚ƒ„…†‡ˆ‰Š‹ŒŽ‘’“””•–—˜™ š š › œ  ž Ÿ   ¡ ¢ £ ¤ ¥ ¥ ¦ § ¨ © ª « ¬ ­ ® ¯ ° ± ² ³ ´ µ ¶ · ¸ ¹ º »¼½¾¿ ÀÁ/sequence-formats-1.9.0.0-KELd4T3c8x91VfSl7528TlSequenceFormats.Utils#SequenceFormats.RareAlleleHistogramSequenceFormats.PileupSequenceFormats.FreqSumSequenceFormats.FastaSequenceFormats.EigenstratSequenceFormats.PlinkSequenceFormats.BedSequenceFormats.VCFSequenceFormats.Genomicsequence-formats0streaming-commons-0.2.2.6-JzMOc9rPWI891e49DJYJwxData.Streaming.ZlibDeflateChromunChromSeqFormatExceptionliftParsingErrorsconsumeProducer readFileProdreadFileProdCheckCompressword gzipConsumerwriteFromPopper$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