Table of Contents - seqtrimnext-2.0.68 Documentation
Pages
- amplicons
- genomics_454
- genomics_454_with_paired
- genomics_short_reads
- genomics_short_reads_2
- only_quality
- sanger
- transcriptomics_454
- transcriptomics_454_plants
- transcriptomics_short_reads
Classes and Modules
- ActionAbAdapter
- ActionAbFarAdapter
- ActionAbLeftAdapter
- ActionEmptyInsert
- ActionIgnoreRepeated
- ActionIndetermination
- ActionInducedLowComplexity
- ActionInsert
- ActionIsContaminated
- ActionKey
- ActionLeftAdapter
- ActionLeftPrimer
- ActionLinker
- ActionLowComplexity
- ActionLowHighSize
- ActionLowQuality
- ActionManager
- ActionMid
- ActionMiddleAdapter
- ActionMultipleLinker
- ActionPairedReads
- ActionPolyA
- ActionPolyT
- ActionRemAditArtifacts
- ActionRightAdapter
- ActionRightPrimer
- ActionSangerLeftAdapter
- ActionSangerRightAdapter
- ActionShortInsert
- ActionTrim
- ActionUnexpectedPolyT
- ActionUnexpectedVector
- ActionUserContaminant
- ActionVectors
- Array
- ExtractSamples
- ExtractStats
- FastaProcessor
- File
- GMatch
- GnuPlotGraph
- GraphStats
- Hash
- InstallDatabase
- InstallRequirements
- JsonUtils
- ListDb
- LoadFastaNamesInHash
- LoadQualInHash
- MakeBlastDb
- Object
- OneBlast
- Params
- Piro
- Plugin
- PluginAbAdapters
- PluginAdapters
- PluginAdaptersOld
- PluginAmplicons
- PluginContaminants
- PluginExtractInserts
- PluginFindPolyAt
- PluginIgnoreRepeated
- PluginIndeterminations
- PluginKey
- PluginLinker
- PluginLowComplexity
- PluginLowHighSize
- PluginLowQuality
- PluginManager
- PluginMids
- PluginRemAditArtifacts
- PluginSangerAdapters
- PluginShortInsert
- PluginSizeTrim
- PluginUserContaminants
- PluginVectors
- RecoverMid
- Regexp
- ScanForRestrSite
- ScbiStats
- Seqtrim
- SeqtrimAction
- SeqtrimWorkManager
- SeqtrimWorker
- Seqtrimnext
- Sequence
- SequenceGroup
- SequenceWithAction
- String
Methods
- ::auto_setup — Plugin
- ::check_param — Plugin
- ::check_params — Plugin
- ::check_params — PluginAbAdapters
- ::check_params — PluginAdapters
- ::check_params — PluginAmplicons
- ::check_params — PluginContaminants
- ::check_params — PluginExtractInserts
- ::check_params — PluginFindPolyAt
- ::check_params — PluginIgnoreRepeated
- ::check_params — PluginIndeterminations
- ::check_params — PluginKey
- ::check_params — PluginLinker
- ::check_params — PluginLowComplexity
- ::check_params — PluginLowHighSize
- ::check_params — PluginLowQuality
- ::check_params — PluginMids
- ::check_params — PluginSangerAdapters
- ::check_params — PluginShortInsert
- ::check_params — PluginSizeTrim
- ::check_params — PluginUserContaminants
- ::check_params — PluginVectors
- ::check_params — PluginAdaptersOld
- ::check_params — PluginRemAditArtifacts
- ::end_work_manager — SeqtrimWorkManager
- ::exit_status — SeqtrimWorkManager
- ::exit_status — Seqtrim
- ::format_db — MakeBlastDb
- ::generate_sample_params — Params
- ::get_graph_filename — Plugin
- ::get_graph_filename — PluginAbAdapters
- ::get_graph_filename — PluginAdapters
- ::get_graph_filename — PluginSangerAdapters
- ::get_graph_title — Plugin
- ::get_graph_title — PluginAbAdapters
- ::get_graph_title — PluginAdapters
- ::get_graph_title — PluginSangerAdapters
- ::get_json_data — JsonUtils
- ::global_error_received — SeqtrimWorkManager
- ::graph_ignored? — Plugin
- ::ignored_graphs — Plugin
- ::init_work_manager — SeqtrimWorkManager
- ::is_zip? — File
- ::list_databases — ListDb
- ::new — ActionAbAdapter
- ::new — ActionAbFarAdapter
- ::new — ActionAbLeftAdapter
- ::new — ActionEmptyInsert
- ::new — ActionIgnoreRepeated
- ::new — ActionIndetermination
- ::new — ActionInducedLowComplexity
- ::new — ActionInsert
- ::new — ActionIsContaminated
- ::new — ActionKey
- ::new — ActionLeftAdapter
- ::new — ActionLeftPrimer
- ::new — ActionLinker
- ::new — ActionLowComplexity
- ::new — ActionLowHighSize
- ::new — ActionLowQuality
- ::new — ActionMid
- ::new — ActionMiddleAdapter
- ::new — ActionMultipleLinker
- ::new — ActionPairedReads
- ::new — ActionPolyA
- ::new — ActionPolyT
- ::new — ActionRemAditArtifacts
- ::new — ActionRightAdapter
- ::new — ActionRightPrimer
- ::new — ActionSangerLeftAdapter
- ::new — ActionSangerRightAdapter
- ::new — ActionShortInsert
- ::new — ActionTrim
- ::new — ActionUnexpectedPolyT
- ::new — ActionUnexpectedVector
- ::new — ActionUserContaminant
- ::new — ActionVectors
- ::new — SeqtrimAction
- ::new — ActionManager
- ::new — ExtractStats
- ::new — GnuPlotGraph
- ::new — GraphStats
- ::new — InstallDatabase
- ::new — InstallRequirements
- ::new — ListDb
- ::new — MakeBlastDb
- ::new — OneBlast
- ::new — Params
- ::new — Piro
- ::new — PluginManager
- ::new — ScanForRestrSite
- ::new — ScbiStats
- ::new — Seqtrim
- ::new — Sequence
- ::new — SequenceGroup
- ::new — SequenceWithAction
- ::new — Plugin
- ::new — ExtractSamples
- ::new_action — ActionManager
- ::plot_setup — Plugin
- ::plot_setup — PluginExtractInserts
- ::unzip — File
- ::valid_graphs — Plugin
- ::valid_graphs — PluginAbAdapters
- ::valid_graphs — PluginAdapters
- ::valid_graphs — PluginSangerAdapters
- ::work_manager_finished — SeqtrimWorkManager
- #action_right — SequenceWithAction
- #action_type — SeqtrimAction
- #add — SequenceGroup
- #add_action — SequenceWithAction
- #add_action_after_high_qual — PluginLowQuality
- #add_action_after_linker — PluginExtractInserts
- #add_action_before_high_qual — PluginLowQuality
- #add_action_before_linker — PluginExtractInserts
- #add_action_inserts — PluginExtractInserts
- #add_actions — SequenceWithAction
- #add_actions_no_left_rigth_parameters — SequenceWithAction
- #add_comment — SequenceWithAction
- #add_file_tag — SequenceWithAction
- #add_key — ExtractStats
- #add_output_data — SeqtrimWorker
- #add_plugin_stats — Plugin
- #add_qv — ExtractStats
- #add_stat — SeqtrimWorker
- #add_stats — Plugin
- #add_stats — Hash
- #add_text_stats — Plugin
- #all_vector_in_linker — PluginVectors
- #apply_decoration — ActionAbAdapter
- #apply_decoration — ActionAbFarAdapter
- #apply_decoration — ActionAbLeftAdapter
- #apply_decoration — ActionEmptyInsert
- #apply_decoration — ActionIgnoreRepeated
- #apply_decoration — ActionIndetermination
- #apply_decoration — ActionInducedLowComplexity
- #apply_decoration — ActionInsert
- #apply_decoration — ActionIsContaminated
- #apply_decoration — ActionKey
- #apply_decoration — ActionLeftAdapter
- #apply_decoration — ActionLeftPrimer
- #apply_decoration — ActionLinker
- #apply_decoration — ActionLowComplexity
- #apply_decoration — ActionLowHighSize
- #apply_decoration — ActionLowQuality
- #apply_decoration — ActionMid
- #apply_decoration — ActionMiddleAdapter
- #apply_decoration — ActionMultipleLinker
- #apply_decoration — ActionPolyA
- #apply_decoration — ActionPolyT
- #apply_decoration — ActionRemAditArtifacts
- #apply_decoration — ActionRightAdapter
- #apply_decoration — ActionRightPrimer
- #apply_decoration — ActionSangerLeftAdapter
- #apply_decoration — ActionSangerRightAdapter
- #apply_decoration — ActionShortInsert
- #apply_decoration — ActionTrim
- #apply_decoration — ActionUnexpectedPolyT
- #apply_decoration — ActionUnexpectedVector
- #apply_decoration — ActionUserContaminant
- #apply_decoration — ActionVectors
- #apply_decoration — SeqtrimAction
- #apply_to — ActionPairedReads
- #apply_to — SeqtrimAction
- #base_count — PluginFindPolyAt
- #base_percent — PluginFindPolyAt
- #can_execute? — Plugin
- #can_execute? — PluginUserContaminants
- #catFasta — MakeBlastDb
- #check_db_param — Params
- #check_global_params — Seqtrim
- #check_install_requirements — InstallRequirements
- #check_param — Params
- #check_plugin_list_param — Params
- #check_plugins_params — PluginManager
- #check_poly_length — PluginIndeterminations
- #check_poly_percent — PluginIndeterminations
- #check_ruby_requirements — InstallRequirements
- #check_system_requirements — InstallRequirements
- #close — OneBlast
- #closing_worker — SeqtrimWorker
- #contains? — SeqtrimAction
- #contains_action? — SeqtrimAction
- #count — SequenceGroup
- #create_sum_window — PluginLowQuality
- #cut_by — PluginShortInsert
- #cut_by_right — PluginAdaptersOld
- #cut_fine_bounds — PluginLowQuality
- #cut_fine_bounds_short — PluginLowQuality
- #decamelize — String
- #decorate — SeqtrimAction
- #delete — SequenceGroup
- #description — SeqtrimAction
- #dirEmpty? — MakeBlastDb
- #do_blast — OneBlast
- #do_blasts — Plugin
- #do_blasts — PluginAbAdapters
- #do_blasts — PluginAdapters
- #do_blasts — PluginAmplicons
- #do_blasts — PluginContaminants
- #do_blasts — PluginLinker
- #do_blasts — PluginLowComplexity
- #do_blasts — PluginMids
- #do_blasts — PluginSangerAdapters
- #do_blasts — PluginUserContaminants
- #do_blasts — PluginVectors
- #do_blasts — PluginAdaptersOld
- #download_and_unzip — InstallDatabase
- #each — SequenceGroup
- #each_slice — SequenceGroup
- #each_with_index — SequenceGroup
- #empty? — SequenceGroup
- #error_received — SeqtrimWorkManager
- #exec_seq — Plugin
- #exec_seq — PluginAbAdapters
- #exec_seq — PluginAdapters
- #exec_seq — PluginAmplicons
- #exec_seq — PluginContaminants
- #exec_seq — PluginExtractInserts
- #exec_seq — PluginFindPolyAt
- #exec_seq — PluginIgnoreRepeated
- #exec_seq — PluginIndeterminations
- #exec_seq — PluginKey
- #exec_seq — PluginLinker
- #exec_seq — PluginLowComplexity
- #exec_seq — PluginLowHighSize
- #exec_seq — PluginLowQuality
- #exec_seq — PluginMids
- #exec_seq — PluginSangerAdapters
- #exec_seq — PluginShortInsert
- #exec_seq — PluginSizeTrim
- #exec_seq — PluginUserContaminants
- #exec_seq — PluginVectors
- #exec_seq — PluginAdaptersOld
- #exec_seq — PluginRemAditArtifacts
- #execute — ScanForRestrSite
- #execute — Plugin
- #execute_no_cut_quality — PluginShortInsert
- #execute_old — PluginRemAditArtifacts
- #execute_plugins — PluginManager
- #exists? — Params
- #exists? — ScanForRestrSite
- #extract_qv_from_sequence — ExtractStats
- #extract_stats_from_sequences — ExtractStats
- #fat_mode — ScbiStats
- #filter_adapters — PluginSangerAdapters
- #filter_hits — PluginAbAdapters
- #filter_hits — PluginAdapters
- #filter_hits — PluginSangerAdapters
- #find_bounds_high_quality — PluginLowQuality
- #find_high_quality — PluginLowQuality
- #find_polyA — PluginFindPolyAt
- #find_polyT — PluginFindPolyAt
- #find_polys — PluginFindPolyAt
- #find_polys — PluginIndeterminations
- #from_json — JsonUtils
- #get_ab_adapter — Params
- #get_actions — SequenceWithAction
- #get_adapter — Params
- #get_cd_hit_cmd — Seqtrim
- #get_comment — Params
- #get_comment_line — SequenceWithAction
- #get_custom_cdhit — Seqtrim
- #get_fasta — Params
- #get_file — SeqtrimWorkManager
- #get_file — SeqtrimWorker
- #get_file_tag_path — SequenceWithAction
- #get_inserts — SequenceWithAction
- #get_linker — Params
- #get_low_qual_regions — PluginLowQuality
- #get_max_key — ExtractStats
- #get_mid — Params
- #get_mid_message — SeqtrimWorker
- #get_next_seq_from_file — SeqtrimWorkManager
- #get_param — Params
- #get_param — ScanForRestrSite
- #get_plugin — Params
- #get_qual_inserts — SequenceWithAction
- #get_type_adapter — PluginAdaptersOld
- #get_window_value — ScbiStats
- #global_match — Regexp
- #include? — SequenceGroup
- #insert_bounds — SequenceWithAction
- #inspect — SeqtrimAction
- #inspect — SequenceGroup
- #install — InstallRequirements
- #integer? — String
- #json_file — SeqtrimWorker
- #lcs — String
- #left_action? — SeqtrimAction
- #load_ab_adapters — Params
- #load_actions_from_files — ActionManager
- #load_adapters — Params
- #load_db_fastas — Params
- #load_linkers — Params
- #load_mids — Params
- #load_plugins_from_files — PluginManager
- #load_plugins_from_files_old — PluginManager
- #load_repeated_seqs — Params
- #load_requirements — InstallRequirements
- #load_user_checkpoint — SeqtrimWorkManager
- #low_complexity_file — SeqtrimWorker
- #low_sffinfo_file — SeqtrimWorker
- #merge_db_files — MakeBlastDb
- #merge_hits — Plugin
- #merge_hits_with_same_qbeg_and_qend — PluginLinker
- #near_left? — SeqtrimAction
- #near_to_extrem — PluginContaminants
- #near_to_extrem — PluginUserContaminants
- #near_to_extrem — PluginVectors
- #new_action — SequenceWithAction
- #next_low_qual_region — PluginLowQuality
- #next_work — SeqtrimWorkManager
- #ns_present? — Sequence
- #on_begin_process — ExtractSamples
- #on_begin_process — FastaProcessor
- #on_begin_process — LoadFastaNamesInHash
- #on_begin_process — LoadQualInHash
- #on_end_process — Piro
- #on_end_process — ExtractSamples
- #on_end_process — FastaProcessor
- #on_end_process — LoadFastaNamesInHash
- #on_end_process — LoadQualInHash
- #on_process_sequence — Piro
- #on_process_sequence — ExtractSamples
- #on_process_sequence — FastaProcessor
- #on_process_sequence — LoadFastaNamesInHash
- #on_process_sequence — LoadQualInHash
- #overlap — Object
- #overlap — PluginIndeterminations
- #overlapX? — Plugin
- #paired_file — SeqtrimWorker
- #paired_file_ilu1 — SeqtrimWorker
- #paired_file_ilu2 — SeqtrimWorker
- #part_left_overlap? — PluginExtractInserts
- #part_right_overlap? — PluginExtractInserts
- #plot_lengths — ExtractStats
- #plot_qualities — ExtractStats
- #poly_near_end — PluginIndeterminations
- #print_global_stats — ExtractStats
- #print_parameters — Params
- #print_parameters — ScanForRestrSite
- #process_object — SeqtrimWorker
- #push — SequenceGroup
- #range_inside_action_type? — SequenceWithAction
- #read_file — Params
- #read_file — ScanForRestrSite
- #receive_initial_config — SeqtrimWorker
- #recover_mid — RecoverMid
- #rejected_output_file — SeqtrimWorker
- #remove_all_seqs — SequenceGroup
- #repeated_seq? — Params
- #reverse_each — SequenceGroup
- #right_action? — SeqtrimAction
- #save_empty_insert — SeqtrimWorker
- #save_file — Params
- #save_files — SeqtrimWorkManager
- #save_one_insert — SeqtrimWorker
- #save_rejected_empty_or_single — SeqtrimWorker
- #save_rejected_seq — SeqtrimWorker
- #save_to_file — SequenceWithAction
- #save_two_inserts — SeqtrimWorker
- #save_two_inserts_tuple — SeqtrimWorker
- #save_user_checkpoint — SeqtrimWorkManager
- #select_the_best — PluginExtractInserts
- #select_the_best — PluginShortInsert
- #select_the_best_with_linker — PluginExtractInserts
- #seq_is_long_enough — Sequence
- #sequence_file — SeqtrimWorker
- #set_comment — Params
- #set_mid — Params
- #set_param — Params
- #set_param — ScanForRestrSite
- #set_params_and_results — ExtractStats
- #sffinfo_file — SeqtrimWorker
- #split_by — PluginExtractInserts
- #starting_worker — SeqtrimWorker
- #sum — Array
- #sum_hits_by_id — PluginUserContaminants
- #sum_quals — PluginLinker
- #title — SeqtrimAction
- #to_fasta — Sequence
- #to_hash — SeqtrimAction
- #to_human — SeqtrimAction
- #to_json — SequenceWithAction
- #to_pretty_json — JsonUtils
- #to_qual — Sequence
- #to_text — SequenceWithAction
- #to_text_seq_fasta — SequenceWithAction
- #too_many_errors_received — SeqtrimWorkManager
- #trash_checkpointed_work — SeqtrimWorkManager
- #type — SeqtrimAction
- #update_dbs — MakeBlastDb
- #valid_low_qual_region? — PluginLowQuality
- #work_received — SeqtrimWorkManager
- #worker_initial_config — SeqtrimWorkManager
- #write_seq_to_files_normal — SeqtrimWorker
- #write_seq_to_files_tuple — SeqtrimWorker
- #xs_present? — Sequence