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