úÎ%x"#9      !"#$%&'()*+,-./01234567 8 None <Adds the length of a sequence to the header of that sequence+Adds filler germlines to normal fasta files9Get the field of a fasta sequence, 1 indexed split by "|"9:9:Safe    None4NoneJTakes a clone entry and returns a formatted text with or without germlineNone  Convert sequences to amino acids >Fill in the sequence with corrected nucleotides or amino acids!©Change a field to a match, so a regex "ch.*_" to field 2 of ">abc|brie_cheese_dude" would result in ">abc|cheese_". Useful for getting specific properties from a field"7Change all fields to their matches based on changeField;!Get a region of a text, 0 indexed#%Get a region of a sequence, 1 indexed<ÿ,Trim the sequence. For default, trim the extra nucleotides off the end. Otherwise, use UCSC frames (0, 1, 2) to cut off the beginning (0 means in frame) or the end (0 means the nucleotide AFTER the end of the sequence is in frame). For amino acids, if it's not in frame, just cut that amino acid.$‘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  !";#<$% !"#$% !"#$%  !";#<$%None4&&&&Safe'()*+'()*+'()*+'()*+None4 ,-./0123456 ,-./0123456 ,-./0123456 ,-./0123456 None=6Return True if there are no gap characters in the text>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=78>?@7878=78>?@A     !"#$%&'()*+,-./0123456789:;<=>?@ A BCDEF G H I JKmodif_H4PoSOl3AtL6GkYlnMeDFkUtilityTypesFilterFastaListPrintTransformFastaListFilterCloneList DiversityFilterCloneMapTransformCloneListaddLengthHeaderaddFillerGermlines replaceCharsgetFieldCodonMutationsCountMapMutation FillInValue CloneEntryFramePositionStopStartFieldCodonMutCodonID FrameTypeInFrameOutFrame GeneticUnit AminoAcid Nucleotide hasNoStops isInFramehasCustomFilterhasAllCustomFilters printFastaprintFastaNoGermlineprintSequenceCountprintCloneEntry convertToAminoAcidsFastaSequencefillInSequence changeFieldchangeAllFieldsgetRegionSequence trimFastaremoveUnknownNucsfilterHighlyMutatedEntryhamming diversitychooserarefactionCurverarefactionViableisRight' listToMaybe'filterHighlyMutatedremoveCodonMutCountremoveStopsCloneMapremoveDuplicatesCloneMapremoveOutOfFrameSeqsremoveCustomFilterremoveAllCustomFiltersremoveEmptyCloneconvertToAminoAcidsCloneMap onlyMutationsfrequentMutations zipWithRetainzipWithRetainText getRegiontrimnoGaps replaceCodonpositionalCodons getCountMap