úÎLÚHâ<      !"#$%&'()*+,-./0123456789: ; Safe+Takes two strings, returns Hamming distanceSafeB  None GReturn the results of the filtration in text form for saving to a file^Return the results of the filtration in text form for saving to a file and excluding germlineJTakes a clone entry and returns a formatted text with or without germlineNone<KRemove clone sequences that have stop codons in the first stopRange codonsRemove out of frame sequencesÿñRemove sequences that do not contain the string customFilter in the customField location, split by "|". Note that this is 1 indexed and 0 means to search the entire header for the customFilter. If the customRemove option is enabled, this function will instead remove sequences that have headers which match the custom filter, as opposed to the other way around (this is defined in the "equal" function). Also takes into account whether to filter on the germline versus the actual sequences.  None<"ð !$Check if the data structure is Right"Altered version of listToMaybe#dRemove highly mutated sequences (sequences with more than a third of their sequence being mutated).$PReplace codons that have more than CodonMut mutations (make them "---" codons).%KRemove clone sequences that have stop codons in the first stopRange codons&Remove duplicate sequences'Remove out of frame sequences(ÿñRemove sequences that do not contain the string customFilter in the customField location, split by "|". Note that this is 1 indexed and 0 means to search the entire header for the customFilter. If the customRemove option is enabled, this function will instead remove sequences that have headers which match the custom filter, as opposed to the other way around (this is defined in the "equal" function). Also takes into account whether to filter on the germline versus the actual sequences.*BRemove clones that do not have any sequences after the filtrations+ Convert sequences to amino acids !"#$%&'()*+ !"#$%&'()*+None<%0,dRemove highly mutated sequences (sequences with more than a third of their sequence being mutated).,,None%/0 -<Adds the length of a sequence to the header of that sequence.?Adds the mutations of a sequence to the header of that sequence<Print the mutations=Filter for the true mutations>(Returns the difference between two texts? Sees if an element is in a tuple/+Adds filler germlines to normal fasta files@pLike zipWith, but if one if one list is longer than the other than use the remaining, needs to be the same typeA Like zipWithRetain, but for text0˜Replace characters in the first string with another in the second string if they are equal to a certain character and they aren't replaced with a gap.1Error for left-./01-./01None>$ 2 Convert sequences to amino acids3>Fill in the sequence with corrected nucleotides or amino acids4#Insert a sequence into a reference.5©Change a field to a match, so a regex "ch.*_" to field 2 of ">abc|brie_cheese_dude" would result in ">abc|cheese_". Useful for getting specific properties from a field67Change all fields to their matches based on changeFieldB!Get a region of a text, 0 indexed7%Get a region of a sequence, 1 indexedCÿ,Trim the sequence. For default, trim the extra nucleotides off the end. Otherwise, use UCSC frames (0, 1, 2) to cut off the beginning (0 means in frame) or the end (0 means the nucleotide AFTER the end of the sequence is in frame). For amino acids, if it's not in frame, just cut that amino acid.8‘Trim off extra nucleotides (or amino acids) from a fasta sequence. If inframe and outframe are specified, instead cut off based on those frames.9(Convert non standard nucleotides to gaps 023456789 203456789 NoneHÌD6Return True if there are no gap characters in the text:lReplace codons that have more than CodonMut mutations (make them "---" codons) and don't have gaps in them.;NOnly include codons containing mutations found in a certain number of mutantsEÿReplace codons that are not valid with a gap "---". Important to note that the predicates return False if we have what we want because the monoid instance of Any has True trumping False, but we want False to trump True, so invert it all and invert it back at the end.FNGet the complete mutation codons with a position provided for each nucleotideG-Get the number of times each mutation appears:;:;H     !"#$%&'()*+,-./0123456789:;<=>?@ABC D EFGHIJKLM N O P QR+modify-fasta-0.8.3.0-KhkeuY6FOVqI5weHozf0ow DiversityTypesPrintFilterFastaListFilterCloneMapFilterCloneListUtilityTransformFastaListTransformCloneListhammingCodonMutationsCountMapMutation CodonTable FillInValue CloneEntryFramePositionStopStartFieldCodonMutCodonID FrameTypeInFrameOutFrame GeneticUnit AminoAcid Nucleotide$fReadGeneticUnit$fShowGeneticUnit$fReadFrameType$fShowFrameType printFastaprintFastaNoGermlineprintSequenceCountprintCloneEntry hasNoStops isInFramehasCustomFilterhasAllCustomFiltersisRight' listToMaybe'filterHighlyMutatedremoveCodonMutCountremoveStopsCloneMapremoveDuplicatesCloneMapremoveOutOfFrameSeqsremoveCustomFilterremoveAllCustomFiltersremoveEmptyCloneconvertToAminoAcidsCloneMapfilterHighlyMutatedEntryaddLengthHeaderaddMutationsHeaderaddFillerGermlines replaceChars fromEither convertToAminoAcidsFastaSequencefillInSequenceinsertSequence changeFieldchangeAllFieldsgetRegionSequence trimFastaremoveUnknownNucs onlyMutationsfrequentMutationsprintMutations getMutationsgetDiffinTuple zipWithRetainzipWithRetainText getRegiontrimnoGaps replaceCodonpositionalCodons getCountMap