úÎJ—Gi6      !"#$%&'()*+,-./01234 5 None <Adds the length of a sequence to the header of that sequence+Adds filler germlines to normal fasta files6pLike zipWith, but if one if one list is longer than the other than use the remaining, needs to be the same type7 Like zipWithRetain, but for text˜Replace characters in the first string with another in the second string if they are equal to a certain character and they aren't replaced with a gap.9Get the field of a fasta sequence, 1 indexed split by "|"6767Safe    None4KRemove clone sequences that have stop codons in the first stopRange codonsRemove out of frame sequencesÿñRemove sequences that do not contain the string customFilter in the customField location, split by "|". Note that this is 1 indexed and 0 means to search the entire header for the customFilter. If the customRemove option is enabled, this function will instead remove sequences that have headers which match the custom filter, as opposed to the other way around (this is defined in the "equal" function). Also takes into account whether to filter on the germline versus the actual sequences.NoneGReturn the results of the filtration in text form for saving to a file^Return the results of the filtration in text form for saving to a file and excluding germlineJTakes a clone entry and returns a formatted text with or without germlineNone  Convert sequences to amino acids!>Fill in the sequence with corrected nucleotides or amino acids"©Change a field to a match, so a regex "ch.*_" to field 2 of ">abc|brie_cheese_dude" would result in ">abc|cheese_". Useful for getting specific properties from a field#7Change all fields to their matches based on changeField8!Get a region of a text, 0 indexed$%Get a region of a sequence, 1 indexed9ÿ,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.%‘Trim off extra nucleotides (or amino acids) from a fasta sequence. If inframe and outframe are specified, instead cut off based on those frames.&(Convert non standard nucleotides to gaps !"#8$9%& !"#$%& !"#$%& !"#8$9%&None4'dRemove highly mutated sequences (sequences with more than a third of their sequence being mutated).''''Safe(+Takes two strings, returns Hamming distance((((None4 )$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 sequences0ÿñRemove 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.2BRemove clones that do not have any sequences after the filtrations3 Convert sequences to amino acids )*+,-./0123 )*+,-./0123 )*+,-./0123 )*+,-./0123 None:6Return True if there are no gap characters in the text4lReplace codons that have more than CodonMut mutations (make them "---" codons) and don't have gaps in them.5NOnly include codons containing mutations found in a certain number of mutants;ÿReplace 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.<NGet the complete mutation codons with a position provided for each nucleotide=-Get the number of times each mutation appears:45;<=4545:45;<=>     !"#$%&'()*+,-./0123456789:;<= > ?@ABC D E F GHmodif_1ObK7zhBQXBH127YTqWqAQUtilityTypesFilterFastaListPrintTransformFastaListFilterCloneList DiversityFilterCloneMapTransformCloneListaddLengthHeaderaddFillerGermlines replaceCharsgetFieldCodonMutationsCountMapMutation CodonTable FillInValue CloneEntryFramePositionStopStartFieldCodonMutCodonID FrameTypeInFrameOutFrame GeneticUnit AminoAcid Nucleotide hasNoStops isInFramehasCustomFilterhasAllCustomFilters printFastaprintFastaNoGermlineprintSequenceCountprintCloneEntry convertToAminoAcidsFastaSequencefillInSequence changeFieldchangeAllFieldsgetRegionSequence trimFastaremoveUnknownNucsfilterHighlyMutatedEntryhammingisRight' listToMaybe'filterHighlyMutatedremoveCodonMutCountremoveStopsCloneMapremoveDuplicatesCloneMapremoveOutOfFrameSeqsremoveCustomFilterremoveAllCustomFiltersremoveEmptyCloneconvertToAminoAcidsCloneMap onlyMutationsfrequentMutations zipWithRetainzipWithRetainText getRegiontrimnoGaps replaceCodonpositionalCodons getCountMap