Table of Contents - BioDSL-1.0.2 Documentation
Classes and Modules
- Array
- BioDSL
- BioDSL::AddKey
- BioDSL::AlignSeqMothur
- BioDSL::Ambiguity
- BioDSL::AnalyzeResidueDistribution
- BioDSL::Assemble
- BioDSL::AssemblePairs
- BioDSL::AssembleSeqIdba
- BioDSL::AssembleSeqRay
- BioDSL::AssembleSeqSpades
- BioDSL::AuxHelper
- BioDSL::BackTrack
- BioDSL::BackTrack::Match
- BioDSL::BackTrackError
- BioDSL::CAry
- BioDSL::CAryError
- BioDSL::CSV
- BioDSL::CSV::IO
- BioDSL::CSVError
- BioDSL::Channel
- BioDSL::ClassifySeq
- BioDSL::ClassifySeqMothur
- BioDSL::ClipPrimer
- BioDSL::ClusterOtus
- BioDSL::CollapseOtus
- BioDSL::CollectOtus
- BioDSL::Command
- BioDSL::Commands
- BioDSL::ComplementSeq
- BioDSL::Config
- BioDSL::Count
- BioDSL::CountValues
- BioDSL::DegapSeq
- BioDSL::DereplicateSeq
- BioDSL::Digest
- BioDSL::Dump
- BioDSL::Dynamic
- BioDSL::DynamicError
- BioDSL::EmailHelper
- BioDSL::Fasta
- BioDSL::Fasta::IO
- BioDSL::FastaError
- BioDSL::Fastq
- BioDSL::Fastq::IO
- BioDSL::FastqError
- BioDSL::Filesys
- BioDSL::FilesysError
- BioDSL::FilterRrna
- BioDSL::Fork
- BioDSL::Genecall
- BioDSL::Grab
- BioDSL::Hamming
- BioDSL::HistoryHelper
- BioDSL::Homopolymer
- BioDSL::HomopolymerError
- BioDSL::HtmlReport
- BioDSL::IndexTaxonomy
- BioDSL::Kmer
- BioDSL::KmerError
- BioDSL::Levenshtein
- BioDSL::LogHelper
- BioDSL::MaskSeq
- BioDSL::Math
- BioDSL::MeanScores
- BioDSL::MergePairSeq
- BioDSL::MergeTable
- BioDSL::MergeValues
- BioDSL::Mummer
- BioDSL::OptionsHelper
- BioDSL::Pipeline
- BioDSL::PlotHeatmap
- BioDSL::PlotHistogram
- BioDSL::PlotMatches
- BioDSL::PlotResidueDistribution
- BioDSL::PlotScores
- BioDSL::Random
- BioDSL::ReadFasta
- BioDSL::ReadFastq
- BioDSL::ReadTable
- BioDSL::ReverseSeq
- BioDSL::Seq
- BioDSL::SeqError
- BioDSL::Serializer
- BioDSL::SliceAlign
- BioDSL::SliceAlign::PosIndex
- BioDSL::SliceSeq
- BioDSL::Sort
- BioDSL::SplitPairSeq
- BioDSL::SplitValues
- BioDSL::StatusHelper
- BioDSL::Stream
- BioDSL::Taxonomy
- BioDSL::Taxonomy::Index
- BioDSL::Taxonomy::Index::TaxNode
- BioDSL::Taxonomy::Search
- BioDSL::Taxonomy::Search::TaxPath
- BioDSL::TaxonomyError
- BioDSL::TmpDir
- BioDSL::Translate
- BioDSL::Trim
- BioDSL::TrimError
- BioDSL::TrimPrimer
- BioDSL::TrimSeq
- BioDSL::UchimeRef
- BioDSL::Uclust
- BioDSL::UniqueValues
- BioDSL::Usearch
- BioDSL::Usearch::IO
- BioDSL::UsearchError
- BioDSL::UsearchGlobal
- BioDSL::UsearchLocal
- BioDSL::WriteFasta
- BioDSL::WriteFastq
- BioDSL::WriteTable
- BioDSL::WriteTree
- Numeric
- Object
- String
Methods
- ::check_name_pair — BioDSL::Seq
- ::check_strings — BioDSL::Hamming
- ::cluster_otus — BioDSL::Usearch
- ::cluster_smallmem — BioDSL::Usearch
- ::create — BioDSL::TmpDir
- ::debug — BioDSL
- ::debug= — BioDSL
- ::dist_point2line — BioDSL::Math
- ::dist_point2point — BioDSL::Math
- ::distance — BioDSL::Hamming
- ::distance — BioDSL::Levenshtein
- ::each_mem — BioDSL::Mummer
- ::execute — BioDSL::Fork
- ::generate_oligos — BioDSL::Seq
- ::new — BioDSL::CAry
- ::new — BioDSL::Command
- ::new — BioDSL::AddKey
- ::new — BioDSL::AlignSeqMothur
- ::new — BioDSL::AnalyzeResidueDistribution
- ::new — BioDSL::AssemblePairs
- ::new — BioDSL::AssembleSeqIdba
- ::new — BioDSL::AssembleSeqRay
- ::new — BioDSL::AssembleSeqSpades
- ::new — BioDSL::ClassifySeq
- ::new — BioDSL::ClassifySeqMothur
- ::new — BioDSL::ClipPrimer
- ::new — BioDSL::ClusterOtus
- ::new — BioDSL::CollapseOtus
- ::new — BioDSL::CollectOtus
- ::new — BioDSL::ComplementSeq
- ::new — BioDSL::Count
- ::new — BioDSL::CountValues
- ::new — BioDSL::DegapSeq
- ::new — BioDSL::DereplicateSeq
- ::new — BioDSL::Dump
- ::new — BioDSL::FilterRrna
- ::new — BioDSL::Genecall
- ::new — BioDSL::Grab
- ::new — BioDSL::IndexTaxonomy
- ::new — BioDSL::MaskSeq
- ::new — BioDSL::MeanScores
- ::new — BioDSL::MergePairSeq
- ::new — BioDSL::MergeTable
- ::new — BioDSL::MergeValues
- ::new — BioDSL::PlotHeatmap
- ::new — BioDSL::PlotHistogram
- ::new — BioDSL::PlotMatches
- ::new — BioDSL::PlotResidueDistribution
- ::new — BioDSL::PlotScores
- ::new — BioDSL::Random
- ::new — BioDSL::ReadFasta
- ::new — BioDSL::ReadFastq
- ::new — BioDSL::ReadTable
- ::new — BioDSL::ReverseSeq
- ::new — BioDSL::SliceAlign
- ::new — BioDSL::SliceAlign::PosIndex
- ::new — BioDSL::SliceSeq
- ::new — BioDSL::Sort
- ::new — BioDSL::SplitPairSeq
- ::new — BioDSL::SplitValues
- ::new — BioDSL::TrimPrimer
- ::new — BioDSL::TrimSeq
- ::new — BioDSL::UchimeRef
- ::new — BioDSL::Uclust
- ::new — BioDSL::UniqueValues
- ::new — BioDSL::UsearchGlobal
- ::new — BioDSL::UsearchLocal
- ::new — BioDSL::WriteFasta
- ::new — BioDSL::WriteFastq
- ::new — BioDSL::WriteTable
- ::new — BioDSL::WriteTree
- ::new — BioDSL::CSV
- ::new — BioDSL::Fasta
- ::new — BioDSL::Fastq
- ::new — BioDSL::Filesys
- ::new — BioDSL::Fork
- ::new — BioDSL::HtmlReport
- ::new — BioDSL::Mummer
- ::new — BioDSL::Pipeline
- ::new — BioDSL::Seq
- ::new — BioDSL::Assemble
- ::new — BioDSL::BackTrack::Match
- ::new — BioDSL::Serializer
- ::new — BioDSL::Stream
- ::new — BioDSL::Channel
- ::new — BioDSL::Taxonomy::Index
- ::new — BioDSL::Taxonomy::Index::TaxNode
- ::new — BioDSL::Taxonomy::Search
- ::new — BioDSL::Taxonomy::Search::TaxPath
- ::new — BioDSL::Usearch
- ::new_bp — BioDSL::Seq
- ::open — BioDSL::CSV
- ::open — BioDSL::Fasta
- ::open — BioDSL::Fastq
- ::open — BioDSL::Filesys
- ::open — BioDSL::Usearch
- ::pair — BioDSL::Assemble
- ::pair — BioDSL::Channel
- ::pipe — BioDSL::Stream
- ::read — BioDSL::Fasta
- ::read_array — BioDSL::CSV
- ::read_hash — BioDSL::CSV
- ::retrieve — BioDSL::CAry
- ::store — BioDSL::CAry
- ::test — BioDSL
- ::test= — BioDSL
- ::tmpfile — BioDSL::Filesys
- ::to_oligos — BioDSL::Kmer
- ::uchime_ref — BioDSL::Usearch
- ::usearch_global — BioDSL::Usearch
- ::usearch_local — BioDSL::Usearch
- ::verbose — BioDSL
- ::verbose= — BioDSL
- ::which — BioDSL::Filesys
- #& — BioDSL::CAry
- #+ — BioDSL::Pipeline
- #+ — BioDSL::Seq
- #<< — BioDSL::Pipeline
- #<< — BioDSL::Seq
- #<< — BioDSL::Serializer
- #<< — BioDSL::Stream
- #<< — BioDSL::Channel
- #[] — BioDSL::SliceAlign::PosIndex
- #[] — BioDSL::Seq
- #[] — BioDSL::Taxonomy::Index::TaxNode
- #[]= — BioDSL::Seq
- #[]= — BioDSL::Taxonomy::Index::TaxNode
- #^ — BioDSL::CAry
- #add — BioDSL::Taxonomy::Index
- #add_ambiguity_macro — BioDSL::Ambiguity
- #add_row — BioDSL::MergeTable
- #add_stats — BioDSL::AssembleSeqRay
- #add_to_count_hash — BioDSL::CollectOtus
- #add_to_index — BioDSL::IndexTaxonomy
- #add_to_options — BioDSL::OptionsHelper
- #add_to_rc_options — BioDSL::OptionsHelper
- #align_columns — BioDSL::WriteTable
- #analyze_residues — BioDSL::AnalyzeResidueDistribution
- #assemble_entries — BioDSL::AssemblePairs
- #assemble_pairs — BioDSL::AssemblePairs
- #assembled2record — BioDSL::AssemblePairs
- #assert_uneven — BioDSL::AssembleSeqRay
- #aux_exist — BioDSL::AuxHelper
- #calc_del — BioDSL::ClipPrimer
- #calc_delta — BioDSL::Command
- #calc_diff — BioDSL::Assemble
- #calc_dist — BioDSL::AnalyzeResidueDistribution
- #calc_dist_count — BioDSL::AnalyzeResidueDistribution
- #calc_dist_percent — BioDSL::AnalyzeResidueDistribution
- #calc_ins — BioDSL::ClipPrimer
- #calc_mean — BioDSL::MeanScores
- #calc_mis — BioDSL::ClipPrimer
- #calc_n50 — BioDSL::AssembleSeqIdba
- #calc_n50 — BioDSL::AssembleSeqRay
- #calc_n50 — BioDSL::AssembleSeqSpades
- #calc_overlap — BioDSL::Assemble
- #calc_status — BioDSL::AssemblePairs
- #calc_time_elapsed — BioDSL::Command
- #call — BioDSL::Command
- #check_direction — BioDSL::Mummer
- #check_duplicate — BioDSL::MergeTable
- #check_entry — BioDSL::ReadFastq
- #check_input_files — BioDSL::ReadFastq
- #check_length — BioDSL::DegapSeq
- #check_length — BioDSL::PlotScores
- #check_length_min_type — BioDSL::Mummer
- #check_length_min_value — BioDSL::Mummer
- #check_options — BioDSL::AddKey
- #check_options — BioDSL::AlignSeqMothur
- #check_options — BioDSL::AnalyzeResidueDistribution
- #check_options — BioDSL::AssemblePairs
- #check_options — BioDSL::AssembleSeqIdba
- #check_options — BioDSL::AssembleSeqRay
- #check_options — BioDSL::AssembleSeqSpades
- #check_options — BioDSL::ClassifySeq
- #check_options — BioDSL::ClassifySeqMothur
- #check_options — BioDSL::ClipPrimer
- #check_options — BioDSL::ClusterOtus
- #check_options — BioDSL::CollapseOtus
- #check_options — BioDSL::CollectOtus
- #check_options — BioDSL::ComplementSeq
- #check_options — BioDSL::Count
- #check_options — BioDSL::CountValues
- #check_options — BioDSL::DegapSeq
- #check_options — BioDSL::DereplicateSeq
- #check_options — BioDSL::Dump
- #check_options — BioDSL::FilterRrna
- #check_options — BioDSL::Genecall
- #check_options — BioDSL::Grab
- #check_options — BioDSL::IndexTaxonomy
- #check_options — BioDSL::MaskSeq
- #check_options — BioDSL::MeanScores
- #check_options — BioDSL::MergePairSeq
- #check_options — BioDSL::MergeTable
- #check_options — BioDSL::MergeValues
- #check_options — BioDSL::PlotHeatmap
- #check_options — BioDSL::PlotHistogram
- #check_options — BioDSL::PlotMatches
- #check_options — BioDSL::PlotResidueDistribution
- #check_options — BioDSL::PlotScores
- #check_options — BioDSL::Random
- #check_options — BioDSL::ReadFasta
- #check_options — BioDSL::ReadFastq
- #check_options — BioDSL::ReadTable
- #check_options — BioDSL::ReverseSeq
- #check_options — BioDSL::SliceAlign
- #check_options — BioDSL::SliceSeq
- #check_options — BioDSL::Sort
- #check_options — BioDSL::SplitPairSeq
- #check_options — BioDSL::SplitValues
- #check_options — BioDSL::TrimPrimer
- #check_options — BioDSL::TrimSeq
- #check_options — BioDSL::UchimeRef
- #check_options — BioDSL::Uclust
- #check_options — BioDSL::UniqueValues
- #check_options — BioDSL::UsearchGlobal
- #check_options — BioDSL::UsearchLocal
- #check_options — BioDSL::WriteFasta
- #check_options — BioDSL::WriteFastq
- #check_options — BioDSL::WriteTable
- #check_options — BioDSL::WriteTree
- #check_options — BioDSL::Mummer
- #check_options — BioDSL::Pipeline
- #check_options — BioDSL::Assemble
- #check_output_files — BioDSL::IndexTaxonomy
- #check_score_range — BioDSL::ReadFastq
- #check_trim_args — BioDSL::Trim
- #children_ids — BioDSL::Taxonomy::Index::TaxNode
- #choose_compression — BioDSL::WriteFastq
- #choose_compression — BioDSL::WriteTable
- #choose_encoding — BioDSL::WriteFastq
- #classify_seq — BioDSL::ClassifySeq
- #clip_primer — BioDSL::ClipPrimer
- #clip_primer_forward — BioDSL::ClipPrimer
- #clip_primer_reverse — BioDSL::ClipPrimer
- #close — BioDSL::Filesys
- #close — BioDSL::Stream
- #closed? — BioDSL::Stream
- #cluster_otus — BioDSL::Usearch
- #cluster_smallmem — BioDSL::Usearch
- #collapse_tax — BioDSL::CollapseOtus
- #collect_plot_data — BioDSL::PlotScores
- #collect_samples — BioDSL::CollectOtus
- #command_runner — BioDSL::Pipeline
- #commify — Numeric
- #commify — BioDSL::WriteTable
- #compile_cmd_line — BioDSL::AssembleSeqIdba
- #compile_cmd_line — BioDSL::AssembleSeqRay
- #compile_command — BioDSL::AssembleSeqSpades
- #compile_command — BioDSL::WriteTree
- #compile_command — BioDSL::Mummer
- #compile_consensus — BioDSL::Taxonomy::Search
- #compile_exact — BioDSL::Grab
- #compile_exact_file — BioDSL::Grab
- #compile_exact_patterns — BioDSL::Grab
- #compile_headings — BioDSL::WriteTable
- #compile_keys — BioDSL::Grab
- #compile_regex_file — BioDSL::Grab
- #compile_regex_patterns — BioDSL::Grab
- #compile_regexes — BioDSL::Grab
- #complement — BioDSL::ComplementSeq
- #complement — BioDSL::Seq
- #complement! — BioDSL::Seq
- #compose_mail — BioDSL::EmailHelper
- #composition — BioDSL::Seq
- #compress — BioDSL::WriteFasta
- #confidence_filter — BioDSL::ClassifySeqMothur
- #convert_types — Array
- #count_residues — BioDSL::PlotResidueDistribution
- #create_mask — BioDSL::DegapSeq
- #create_output_dir — BioDSL::IndexTaxonomy
- #decide_wanted — BioDSL::Random
- #decide_wanted_pairs — BioDSL::Random
- #decompose_consensus — BioDSL::Taxonomy::Search
- #default — BioDSL::PlotScores
- #default_options — BioDSL::Mummer
- #defaults — BioDSL::AlignSeqMothur
- #defaults — BioDSL::AssemblePairs
- #defaults — BioDSL::AssembleSeqIdba
- #defaults — BioDSL::AssembleSeqRay
- #defaults — BioDSL::AssembleSeqSpades
- #defaults — BioDSL::ClassifySeq
- #defaults — BioDSL::ClassifySeqMothur
- #defaults — BioDSL::ClipPrimer
- #defaults — BioDSL::ClusterOtus
- #defaults — BioDSL::Genecall
- #defaults — BioDSL::IndexTaxonomy
- #defaults — BioDSL::MaskSeq
- #defaults — BioDSL::MeanScores
- #defaults — BioDSL::MergeTable
- #defaults — BioDSL::MergeValues
- #defaults — BioDSL::PlotHeatmap
- #defaults — BioDSL::PlotHistogram
- #defaults — BioDSL::PlotMatches
- #defaults — BioDSL::PlotResidueDistribution
- #defaults — BioDSL::SliceAlign
- #defaults — BioDSL::TrimSeq
- #degap_all — BioDSL::DegapSeq
- #degap_columns — BioDSL::DegapSeq
- #degap_seq — BioDSL::DegapSeq
- #delta — BioDSL::Command
- #delta_percent — BioDSL::Command
- #determine_encoding — BioDSL::ReadFastq
- #determine_headings — BioDSL::PlotHeatmap
- #determine_skip_keys — BioDSL::PlotHeatmap
- #determine_types — BioDSL::SplitValues
- #determine_types — BioDSL::CSV
- #disambiguate — BioDSL::Digest
- #dna? — BioDSL::Seq
- #dump_all — BioDSL::Dump
- #dump_first — BioDSL::Dump
- #dump_last — BioDSL::Dump
- #each — BioDSL::Fasta
- #each — BioDSL::Fasta::IO
- #each — BioDSL::Fastq
- #each — BioDSL::Fastq::IO
- #each — BioDSL::Filesys
- #each — BioDSL::Serializer
- #each — BioDSL::Stream
- #each — BioDSL::Channel
- #each — BioDSL::Usearch::IO
- #each_array — BioDSL::CSV
- #each_digest — BioDSL::Digest
- #each_hash — BioDSL::CSV
- #each_homopolymer — BioDSL::Homopolymer
- #each_mem — BioDSL::Mummer
- #each_orf — BioDSL::Seq
- #each_uc — BioDSL::Usearch::IO
- #edit_distance — BioDSL::Seq
- #emit_match — BioDSL::Grab
- #entry2record — BioDSL::AssemblePairs
- #entry_left — BioDSL::Assemble
- #entry_overlap — BioDSL::Assemble
- #entry_right — BioDSL::Assemble
- #eof? — BioDSL::Filesys
- #eval_match? — BioDSL::Grab
- #exact_match? — BioDSL::Grab
- #exact_match_key_values? — BioDSL::Grab
- #exact_match_keys? — BioDSL::Grab
- #exact_match_values? — BioDSL::Grab
- #execute — BioDSL::Fork
- #execute — BioDSL::Mummer
- #execute — BioDSL::Taxonomy::Search
- #execute — BioDSL::Usearch
- #execute_idba — BioDSL::AssembleSeqIdba
- #execute_ray — BioDSL::AssembleSeqRay
- #execute_sortmerna — BioDSL::FilterRrna
- #execute_spades — BioDSL::AssembleSeqSpades
- #exit_gracefully — BioDSL::Pipeline
- #fastq_files — BioDSL::ReadFastq
- #fill — BioDSL::CAry
- #fill! — BioDSL::CAry
- #fill_pqueue — BioDSL::Sort
- #fill_table — BioDSL::WriteTable
- #find_match — BioDSL::SliceAlign
- #fix_seq_names — BioDSL::SplitPairSeq
- #fork_process — BioDSL::Fork
- #forward — BioDSL::SliceAlign
- #generate — BioDSL::Seq
- #get_fields — BioDSL::CSV
- #get_header — BioDSL::CSV
- #get_match — BioDSL::Mummer
- #get_node — BioDSL::Taxonomy::Index
- #get_split_pos — BioDSL::SplitPairSeq
- #gets — BioDSL::CSV::IO
- #gets — BioDSL::Filesys
- #glob_check — BioDSL::OptionsHelper
- #hamming_distance — BioDSL::Seq
- #hard_mask — BioDSL::Seq
- #help_url — BioDSL::HtmlReport
- #indels — BioDSL::Seq
- #indels_remove — BioDSL::Seq
- #index_positions — BioDSL::SliceAlign::PosIndex
- #input? — BioDSL::HtmlReport
- #kmers_lookup — BioDSL::Taxonomy::Search
- #leaf? — BioDSL::Taxonomy::Index
- #len — BioDSL::Seq
- #length — BioDSL::Seq
- #lmb — BioDSL::AddKey
- #lmb — BioDSL::AlignSeqMothur
- #lmb — BioDSL::AnalyzeResidueDistribution
- #lmb — BioDSL::AssemblePairs
- #lmb — BioDSL::AssembleSeqIdba
- #lmb — BioDSL::AssembleSeqRay
- #lmb — BioDSL::AssembleSeqSpades
- #lmb — BioDSL::ClassifySeq
- #lmb — BioDSL::ClassifySeqMothur
- #lmb — BioDSL::ClipPrimer
- #lmb — BioDSL::ClusterOtus
- #lmb — BioDSL::CollapseOtus
- #lmb — BioDSL::CollectOtus
- #lmb — BioDSL::ComplementSeq
- #lmb — BioDSL::Count
- #lmb — BioDSL::CountValues
- #lmb — BioDSL::DegapSeq
- #lmb — BioDSL::DereplicateSeq
- #lmb — BioDSL::Dump
- #lmb — BioDSL::FilterRrna
- #lmb — BioDSL::Genecall
- #lmb — BioDSL::Grab
- #lmb — BioDSL::IndexTaxonomy
- #lmb — BioDSL::MaskSeq
- #lmb — BioDSL::MeanScores
- #lmb — BioDSL::MergePairSeq
- #lmb — BioDSL::MergeTable
- #lmb — BioDSL::MergeValues
- #lmb — BioDSL::PlotHeatmap
- #lmb — BioDSL::PlotHistogram
- #lmb — BioDSL::PlotMatches
- #lmb — BioDSL::PlotResidueDistribution
- #lmb — BioDSL::PlotScores
- #lmb — BioDSL::Random
- #lmb — BioDSL::ReadFasta
- #lmb — BioDSL::ReadFastq
- #lmb — BioDSL::ReadTable
- #lmb — BioDSL::ReverseSeq
- #lmb — BioDSL::SliceAlign
- #lmb — BioDSL::SliceSeq
- #lmb — BioDSL::Sort
- #lmb — BioDSL::SplitPairSeq
- #lmb — BioDSL::SplitValues
- #lmb — BioDSL::TrimPrimer
- #lmb — BioDSL::TrimSeq
- #lmb — BioDSL::UchimeRef
- #lmb — BioDSL::Uclust
- #lmb — BioDSL::UniqueValues
- #lmb — BioDSL::UsearchGlobal
- #lmb — BioDSL::UsearchLocal
- #lmb — BioDSL::WriteFasta
- #lmb — BioDSL::WriteFastq
- #lmb — BioDSL::WriteTable
- #lmb — BioDSL::WriteTree
- #load_kmer_index — BioDSL::Taxonomy::Search
- #load_tax_index — BioDSL::Taxonomy::Search
- #log_error — BioDSL::LogHelper
- #log_ok — BioDSL::LogHelper
- #mask_add — BioDSL::DegapSeq
- #mask_seq — BioDSL::MaskSeq
- #mask_seq_hard — BioDSL::MaskSeq
- #mask_seq_hard! — BioDSL::Seq
- #mask_seq_soft — BioDSL::MaskSeq
- #mask_seq_soft! — BioDSL::Seq
- #match — BioDSL::Assemble
- #match_forward — BioDSL::TrimPrimer
- #match_options — BioDSL::TrimPrimer
- #match_reverse — BioDSL::TrimPrimer
- #mean_vec — BioDSL::PlotScores
- #merge_forward — BioDSL::TrimPrimer
- #merge_overlap — BioDSL::Assemble
- #merge_pair_seq — BioDSL::MergePairSeq
- #merge_record_entry — BioDSL::ClipPrimer
- #merge_reverse — BioDSL::TrimPrimer
- #method_missing — BioDSL::Pipeline
- #naive — BioDSL::Kmer
- #naive_bin — BioDSL::Kmer
- #new_record — BioDSL::MergePairSeq
- #next_entry — BioDSL::Fasta
- #next_entry — BioDSL::Fastq
- #next_entry — BioDSL::Serializer
- #open_block_files — BioDSL::Sort
- #options_allowed — BioDSL::OptionsHelper
- #options_allowed_values — BioDSL::OptionsHelper
- #options_assert — BioDSL::OptionsHelper
- #options_conflict — BioDSL::OptionsHelper
- #options_dirs_exist — BioDSL::OptionsHelper
- #options_files_exist — BioDSL::OptionsHelper
- #options_files_exist_force — BioDSL::OptionsHelper
- #options_glob — BioDSL::OptionsHelper
- #options_list_unique — BioDSL::OptionsHelper
- #options_load_rc — BioDSL::OptionsHelper
- #options_required — BioDSL::OptionsHelper
- #options_required_unique — BioDSL::OptionsHelper
- #options_string — BioDSL::Pipeline
- #options_tie — BioDSL::OptionsHelper
- #options_unique — BioDSL::OptionsHelper
- #output? — BioDSL::HtmlReport
- #output_assembled — BioDSL::AssemblePairs
- #output_buffer — BioDSL::ReadFastq
- #output_buffer — BioDSL::ReadTable
- #output_entries — BioDSL::AssemblePairs
- #output_entry — BioDSL::Uclust
- #output_header — BioDSL::WriteTable
- #output_last — BioDSL::WriteTable
- #output_merged — BioDSL::AssemblePairs
- #output_pqueue — BioDSL::Sort
- #output_pretty — BioDSL::WriteTable
- #output_record — BioDSL::AssemblePairs
- #output_record — BioDSL::FilterRrna
- #output_record? — BioDSL::UniqueValues
- #output_row — BioDSL::WriteTable
- #overlap_possible? — BioDSL::AssemblePairs
- #paired? — BioDSL::AssembleSeqRay
- #parent_id — BioDSL::Taxonomy::Index::TaxNode
- #parse_entry — BioDSL::Genecall
- #parse_input_tables — BioDSL::MergeTable
- #parse_output — BioDSL::Uclust
- #parse_result — BioDSL::AssembleSeqRay
- #parse_sortme_output — BioDSL::FilterRrna
- #parse_template_file — BioDSL::SliceAlign
- #patmatch — BioDSL::BackTrack
- #patmatch — BioDSL::Dynamic
- #patscan — BioDSL::BackTrack
- #patscan — BioDSL::Dynamic
- #pattern — BioDSL::TrimPrimer
- #plot_colors — BioDSL::PlotResidueDistribution
- #plot_count — BioDSL::PlotResidueDistribution
- #plot_count — BioDSL::PlotScores
- #plot_create — BioDSL::PlotHistogram
- #plot_create — BioDSL::PlotResidueDistribution
- #plot_dataset — BioDSL::PlotHeatmap
- #plot_defaults — BioDSL::PlotHistogram
- #plot_defaults — BioDSL::PlotMatches
- #plot_defaults — BioDSL::PlotResidueDistribution
- #plot_defaults — BioDSL::PlotScores
- #plot_empty — BioDSL::PlotHistogram
- #plot_fix_xtics — BioDSL::PlotHistogram
- #plot_fix_ylogscale — BioDSL::PlotHistogram
- #plot_match — BioDSL::PlotMatches
- #plot_match_direction — BioDSL::PlotMatches
- #plot_match_strand — BioDSL::PlotMatches
- #plot_numeric — BioDSL::PlotHistogram
- #plot_options — BioDSL::PlotHeatmap
- #plot_output — BioDSL::PlotHeatmap
- #plot_output — BioDSL::PlotHistogram
- #plot_output — BioDSL::PlotMatches
- #plot_output — BioDSL::PlotResidueDistribution
- #plot_output — BioDSL::PlotScores
- #plot_residue — BioDSL::PlotResidueDistribution
- #plot_scores — BioDSL::PlotScores
- #plot_string — BioDSL::PlotHistogram
- #plot_xtics_rotate — BioDSL::PlotHistogram
- #png? — BioDSL::HtmlReport
- #pop — BioDSL::Pipeline
- #pqueue_init — BioDSL::Sort
- #prefix_output_dir — BioDSL::Pipeline
- #prepare_plot_data — BioDSL::PlotScores
- #prime_variables — BioDSL::Pipeline
- #primer — BioDSL::ClipPrimer
- #print_status — BioDSL::Pipeline
- #process_first — BioDSL::WriteTable
- #process_input — BioDSL::AlignSeqMothur
- #process_input — BioDSL::AssembleSeqIdba
- #process_input — BioDSL::AssembleSeqRay
- #process_input — BioDSL::AssembleSeqSpades
- #process_input — BioDSL::ClassifySeqMothur
- #process_input — BioDSL::ClusterOtus
- #process_input — BioDSL::CollectOtus
- #process_input — BioDSL::Count
- #process_input — BioDSL::CountValues
- #process_input — BioDSL::DegapSeq
- #process_input — BioDSL::DereplicateSeq
- #process_input — BioDSL::FilterRrna
- #process_input — BioDSL::Genecall
- #process_input — BioDSL::PlotHistogram
- #process_input — BioDSL::Random
- #process_input — BioDSL::ReadFastq
- #process_input — BioDSL::ReadTable
- #process_input — BioDSL::UchimeRef
- #process_input — BioDSL::Uclust
- #process_input — BioDSL::UsearchGlobal
- #process_input — BioDSL::UsearchLocal
- #process_input — BioDSL::WriteFastq
- #process_input_records — BioDSL::Uclust
- #process_last — BioDSL::WriteTable
- #process_output — BioDSL::AlignSeqMothur
- #process_output — BioDSL::AssembleSeqIdba
- #process_output — BioDSL::AssembleSeqRay
- #process_output — BioDSL::AssembleSeqSpades
- #process_output — BioDSL::ClassifySeqMothur
- #process_output — BioDSL::ClusterOtus
- #process_output — BioDSL::CollectOtus
- #process_output — BioDSL::CountValues
- #process_output — BioDSL::DegapSeq
- #process_output — BioDSL::DereplicateSeq
- #process_output — BioDSL::FilterRrna
- #process_output — BioDSL::Genecall
- #process_output — BioDSL::PlotHistogram
- #process_output — BioDSL::PlotMatches
- #process_output — BioDSL::Random
- #process_output — BioDSL::UchimeRef
- #process_output — BioDSL::Uclust
- #process_output — BioDSL::UsearchGlobal
- #process_output — BioDSL::UsearchLocal
- #process_output_align — BioDSL::Uclust
- #process_output_serial — BioDSL::Uclust
- #process_ref_files — BioDSL::FilterRrna
- #progress_print — BioDSL::StatusHelper
- #protein? — BioDSL::Seq
- #puts — BioDSL::Fasta
- #puts — BioDSL::Filesys
- #qual_base33? — BioDSL::Seq
- #qual_base64? — BioDSL::Seq
- #qual_coerce! — BioDSL::Seq
- #qual_convert! — BioDSL::Seq
- #qual_valid? — BioDSL::Seq
- #quality_trim — BioDSL::Trim
- #quality_trim! — BioDSL::Trim
- #quality_trim_left — BioDSL::Trim
- #quality_trim_left! — BioDSL::Trim
- #quality_trim_right — BioDSL::Trim
- #quality_trim_right! — BioDSL::Trim
- #read — BioDSL::Filesys
- #read — BioDSL::Fork
- #read — BioDSL::Stream
- #read — BioDSL::Channel
- #read_all — BioDSL::ReadFasta
- #read_all — BioDSL::ReadTable
- #read_all_pair — BioDSL::ReadFastq
- #read_all_single — BioDSL::ReadFastq
- #read_first — BioDSL::ReadFasta
- #read_first — BioDSL::ReadTable
- #read_first_pair — BioDSL::ReadFastq
- #read_first_single — BioDSL::ReadFastq
- #read_input — BioDSL::ReadFasta
- #read_last — BioDSL::ReadFasta
- #read_last — BioDSL::ReadTable
- #read_last_pair — BioDSL::ReadFastq
- #read_last_single — BioDSL::ReadFastq
- #read_options — BioDSL::ReadTable
- #record2entry — BioDSL::ClusterOtus
- #record2entry — BioDSL::FilterRrna
- #record2entry — BioDSL::WriteFasta
- #records2entries — BioDSL::AssemblePairs
- #regex_match? — BioDSL::Grab
- #regex_match_key_values? — BioDSL::Grab
- #regex_match_keys? — BioDSL::Grab
- #regex_match_values? — BioDSL::Grab
- #remove_residues — BioDSL::DegapSeq
- #render — BioDSL::HtmlReport
- #render_command — BioDSL::HtmlReport
- #render_css — BioDSL::HtmlReport
- #render_input_files — BioDSL::HtmlReport
- #render_output_files — BioDSL::HtmlReport
- #render_overview — BioDSL::HtmlReport
- #render_pipeline — BioDSL::HtmlReport
- #render_png — BioDSL::HtmlReport
- #render_status — BioDSL::HtmlReport
- #render_time — BioDSL::HtmlReport
- #replace_keys — BioDSL::ReadTable
- #require_file — BioDSL::Pipeline
- #reset — BioDSL::ClipPrimer
- #reverse — BioDSL::ReverseSeq
- #reverse — BioDSL::SliceAlign
- #reverse — BioDSL::Seq
- #reverse! — BioDSL::Seq
- #reverse_complement — BioDSL::ReadFastq
- #rna? — BioDSL::Seq
- #root_dir — BioDSL::HtmlReport
- #run — BioDSL::Pipeline
- #run_add_enumerators — BioDSL::Pipeline
- #run_assemblies — BioDSL::AssembleSeqRay
- #run_assertions — BioDSL::ClassifySeq
- #run_commands — BioDSL::Pipeline
- #run_enumerate — BioDSL::Pipeline
- #run_mothur — BioDSL::AlignSeqMothur
- #run_mothur — BioDSL::ClassifySeqMothur
- #run_prodigal — BioDSL::Genecall
- #run_time_start — BioDSL::Pipeline
- #run_uchime_ref — BioDSL::UchimeRef
- #run_uclust — BioDSL::Uclust
- #run_usearch_global — BioDSL::UsearchGlobal
- #run_usearch_local — BioDSL::UsearchLocal
- #running? — BioDSL::Fork
- #save — BioDSL::Taxonomy::Index
- #save_block — BioDSL::Sort
- #save_history — BioDSL::HistoryHelper
- #save_kmer_index — BioDSL::Taxonomy::Index
- #save_report — BioDSL::Pipeline
- #save_tax_index — BioDSL::Taxonomy::Index
- #scores_max — BioDSL::Seq
- #scores_mean — BioDSL::Seq
- #scores_mean_local — BioDSL::Seq
- #scores_min — BioDSL::Seq
- #search_distance — BioDSL::ClipPrimer
- #send_email — BioDSL::EmailHelper
- #serialize — BioDSL::DereplicateSeq
- #serialize_records — BioDSL::Sort
- #setup_slice — BioDSL::SliceAlign
- #setup_template_slice — BioDSL::SliceAlign
- #setup_template_slice_primers — BioDSL::SliceAlign
- #setup_template_slice_range — BioDSL::SliceAlign
- #shuffle — BioDSL::Seq
- #shuffle! — BioDSL::Seq
- #size — BioDSL::Pipeline
- #skip — BioDSL::CSV
- #skip_headings — BioDSL::WriteTable
- #slice_align — BioDSL::SliceAlign
- #slice_seq — BioDSL::SliceSeq
- #soft_mask — BioDSL::Seq
- #sort_keys — BioDSL::PlotHeatmap
- #sort_keys — BioDSL::WriteTable
- #split_entry — BioDSL::SplitPairSeq
- #split_pair_seq — BioDSL::SplitPairSeq
- #split_values — BioDSL::SplitValues
- #start — BioDSL::BackTrack::Match
- #status — BioDSL::Pipeline
- #status_init — BioDSL::StatusHelper
- #status_progress — BioDSL::StatusHelper
- #status_rows — BioDSL::StatusHelper
- #status_tabulate — BioDSL::StatusHelper
- #stop — BioDSL::ClipPrimer
- #stop — BioDSL::BackTrack::Match
- #taxonomy_backtrack — BioDSL::Taxonomy::Search::TaxPath
- #terminate — BioDSL::Channel
- #to_bp — BioDSL::Seq
- #to_dna — BioDSL::Seq
- #to_fasta — BioDSL::Seq
- #to_fastq — BioDSL::Seq
- #to_html — BioDSL::HtmlReport
- #to_key — BioDSL::Seq
- #to_kmers — BioDSL::Kmer
- #to_num — String
- #to_protein — BioDSL::Translate
- #to_protein! — BioDSL::Translate
- #to_rna — BioDSL::Seq
- #to_s — BioDSL::CAry
- #to_s — BioDSL::Command
- #to_s — BioDSL::Pipeline
- #to_s — BioDSL::BackTrack::Match
- #to_s — BioDSL::Taxonomy::Search::TaxPath
- #translate — BioDSL::Translate
- #translate! — BioDSL::Translate
- #tree_union — BioDSL::Taxonomy::Index
- #trim_forward — BioDSL::TrimPrimer
- #trim_record — BioDSL::MergeTable
- #trim_reverse — BioDSL::TrimPrimer
- #trim_seq — BioDSL::TrimSeq
- #type_guess — BioDSL::Seq
- #type_guess! — BioDSL::Seq
- #uchime_ref — BioDSL::Usearch
- #update_time — BioDSL::StatusHelper
- #usearch_global — BioDSL::Usearch
- #usearch_local — BioDSL::Usearch
- #wait — BioDSL::Fork
- #write — BioDSL::Filesys
- #write — BioDSL::Fork
- #write — BioDSL::Stream
- #write — BioDSL::Channel
- #write_buffer — BioDSL::ReadFasta
- #write_entry — BioDSL::AlignSeqMothur
- #write_fastq — BioDSL::WriteFastq
- #write_file — BioDSL::WriteFasta
- #write_output — BioDSL::Count
- #write_output — BioDSL::PlotScores
- #write_output — BioDSL::WriteFasta
- #write_seq — BioDSL::WriteTree
- #write_sequence — BioDSL::AssembleSeqSpades
- #write_stdout — BioDSL::WriteFasta
- #write_table — BioDSL::WriteTable
- #write_tax — BioDSL::CollapseOtus
- #write_tree — BioDSL::WriteTree
- #writei — BioDSL::Serializer
- #zero — BioDSL::CAry
- #zero! — BioDSL::CAry
- #| — BioDSL::CAry
- #~ — BioDSL::CAry