| Cvdj_pipe::Apply_many | Apply enclosed processing step multiple times to sequence reads of specified kind: forward, reverse, or merged |
| Cvdj_pipe::Apply_one | Apply enclosed processing step once to a sequence read of specified kind: forward, reverse, or merged |
| Cvdj_pipe::step::Apply_to_maker | |
| Cvdj_pipe::detail::Base_id< Super, Val > | |
| ►Cvdj_pipe::detail::Base_id< Id1 > | |
| Cvdj_pipe::test::Id1 | |
| ►Cvdj_pipe::detail::Base_id< Id2 > | |
| Cvdj_pipe::test::Id2 | |
| Cvdj_pipe::Best_match_pair< ID, Score > | |
| ►Cbinary_function | |
| Cvdj_pipe::anonymous_namespace{file_ostream_queue.cpp}::Equal | |
| Cvdj_pipe::anonymous_namespace{histogram_step.cpp}::Compare_vv | |
| Cvdj_pipe::anonymous_namespace{histogram_step.cpp}::Compare_vvv | |
| Cvdj_pipe::detail::Id_bimap< Id, Obj >::Equal_id | |
| Cvdj_pipe::Blank | |
| Cvdj_pipe::Blank_step | |
| Cvdj_pipe::gdst::Branch | |
| Cboost::spirit::traits::char_type_of< boost::string_ref > | |
| Cvdj_pipe::gdst::Children | |
| Cvdj_pipe::Command_line_options | |
| Cvdj_pipe::gdst::Common_subseq | Common subsequence |
| Cvdj_pipe::Config_paired_emid_reads | |
| Cvdj_pipe::Config_paired_reads | |
| Cvdj_pipe::Config_single_reads | |
| Cvdj_pipe::match::Cut_proto | |
| Cvdj_pipe::gdst::Depth_iter | |
| Cvdj_pipe::match::Element_proto | |
| Cvdj_pipe::detail::Id_bimap< Id, Obj >::Equal_obj< ObjCompat > | |
| Cvdj_pipe::detail::Equal_string_ref | |
| ►Cexception | |
| ►Cvdj_pipe::base_exception | |
| Cvdj_pipe::Command_line_options::Err | |
| Cvdj_pipe::detail::Parser_line::Err | |
| Cvdj_pipe::detail::Step_base::Err | |
| Cvdj_pipe::File::Err | |
| Cvdj_pipe::File_istream::Err | |
| Cvdj_pipe::File_ostream::Err | |
| Cvdj_pipe::File_ostream_queue::Err | |
| Cvdj_pipe::File_ostream_variant::Err | |
| Cvdj_pipe::gdst::Gdst::Err | |
| Cvdj_pipe::Get_match_length::Err | |
| Cvdj_pipe::Input_manager::Err | |
| Cvdj_pipe::match::Cut_proto::Err | |
| Cvdj_pipe::match::Element_proto::Err | |
| Cvdj_pipe::match::Match_combination::Err | |
| Cvdj_pipe::match::Match_element_aligned::Err | |
| Cvdj_pipe::match::Match_element_ambiguous::Err | |
| Cvdj_pipe::match::Match_element_battery::Err | |
| Cvdj_pipe::match::Match_element_factory::Err | |
| Cvdj_pipe::match::Match_element_positional::Err | |
| Cvdj_pipe::match::Match_element_short::Err | |
| Cvdj_pipe::Match_fraction_length::Err | |
| Cvdj_pipe::Output_manager::Err | |
| Cvdj_pipe::Pipe_environment::Err | |
| Cvdj_pipe::Pipe_paired_emid_read::Err | |
| Cvdj_pipe::Pipe_paired_read::Err | |
| Cvdj_pipe::Pipe_single_read::Err | |
| Cvdj_pipe::Queable_ofstream::Err | |
| Cvdj_pipe::Read_ginfo_store::Err | |
| Cvdj_pipe::Read_info_store::Err | |
| Cvdj_pipe::Seq_file_entry::Err | |
| Cvdj_pipe::Seq_file_map::Err | |
| Cvdj_pipe::Seq_map_aligned::Err | |
| Cvdj_pipe::Seq_map_full::Err | |
| Cvdj_pipe::Seq_map_short::Err | |
| Cvdj_pipe::step::Apply_to_maker::Err | |
| Cvdj_pipe::Step_registry::Err | |
| Cvdj_pipe::Value_map::Err | |
| Cvdj_pipe::Variable_path::Err | |
| Cvdj_pipe::Vm_access_paired::Err | |
| Cvdj_pipe::Vm_access_single::Err | |
| ►Cstd::exception | STL class |
| Cvdj_pipe::base_exception | |
| Cvdj_pipe::test::Exception_fixture | |
| ►Cvdj_pipe::detail::External_mid_base | |
| Cvdj_pipe::External_mid_infile | Look for external MIDs in separate files |
| Cvdj_pipe::External_mid_inline | Look for external MIDs in FASTA/Q description lines |
| ►Cvdj_pipe::File | |
| ►Cvdj_pipe::File_input | File target is supposed to exist at construction time |
| Cvdj_pipe::Seq_file | |
| ►Cvdj_pipe::File_output | File target is created if needed at construction time |
| Cvdj_pipe::File_ostream | |
| Cvdj_pipe::File_istream | |
| Cvdj_pipe::File_ostream_queue | Stack of recently used output file streams |
| Cvdj_pipe::File_ostream_variant | Select output file based on variables in value map |
| Cvdj_pipe::step::Find_maker< Step > | |
| Cvdj_pipe::step::Find_maker< Apply_many > | |
| Cvdj_pipe::step::Find_maker< Apply_one > | |
| Cvdj_pipe::anonymous_namespace{pipe_paired_emid_read.cpp}::Four_file_ids | |
| Cvdj_pipe::gdst::Gdst | Generalized DNA suffix tree |
| Cvdj_pipe::gdst::Gdst_stats | |
| Cvdj_pipe::detail::Getter< Stor, Id, Obj, Result, MemFunPtr > | Extract object by its ID and apply member function |
| ►Cgrammar | |
| Cvdj_pipe::anonymous_namespace{sanitize_string.cpp}::Escape< Iter > | |
| Cvdj_pipe::Group_count | |
| Cvdj_pipe::Group_unique | |
| Cvdj_pipe::Histogram_1d | Simple unsigned integer-based histogram |
| Cvdj_pipe::detail::Id_bimap< Id, Obj > | |
| Cvdj_pipe::detail::Id_bimap< Id, std::string > | |
| Cvdj_pipe::detail::Id_bimap< Mapped_id, val_vector > | |
| Cvdj_pipe::detail::Id_bimap< Mid_id, seq_type > | |
| Cvdj_pipe::detail::Id_bimap< Seq_id, std::string > | |
| Cvdj_pipe::detail::Id_map< Id, Obj, Stor > | |
| Cvdj_pipe::detail::Id_map< Branch_id, Branch > | |
| Cvdj_pipe::detail::Id_map< Children_id, Children > | |
| Cvdj_pipe::detail::Id_map< Id, Val > | |
| Cvdj_pipe::detail::Id_map< Leaf_id, Leaf > | |
| Cvdj_pipe::detail::Id_map< Mid_id, std::string > | |
| Cvdj_pipe::detail::Id_map< Read_id, Read_info > | |
| Cvdj_pipe::detail::Id_map< Read_id, super_seq_set > | |
| Cvdj_pipe::detail::Id_map< Seq_id, sub_seq_set > | |
| Cvdj_pipe::Input_manager | |
| Cvdj_pipe::step::Step_builder_registry< Config >::Insert | |
| Cvdj_pipe::detail::Inserter | |
| Cvdj_pipe::detail::Interval_checking_policy< T > | |
| Cvdj_pipe::detail::Interval_checking_policy< int > | |
| ►Citerator_facade | |
| Cvdj_pipe::Id_iterator< Path_id > | |
| Cvdj_pipe::Id_iterator< Id > | |
| Cvdj_pipe::Lib_info | Library info |
| Cvdj_pipe::step::Maker< Step > | |
| Cvdj_pipe::gdst::Match | Results of matching pattern to suffix tree |
| Cvdj_pipe::Seq_map_aligned::Match | |
| Cvdj_pipe::match::Match_combination | |
| Cvdj_pipe::match::Match_element_aligned | Identify DNA sequence interval by finding the best alignment |
| Cvdj_pipe::match::Match_element_ambiguous | Find best match between DNA sequence interval and a set of sequences without gaps that may include ambiguous nucleotides |
| Cvdj_pipe::match::Match_element_battery | |
| Cvdj_pipe::match::Match_element_factory | |
| Cvdj_pipe::match::Match_element_positional | Identify DNA sequence interval by position only |
| Cvdj_pipe::match::Match_element_short | Find best match between DNA sequence interval and a set of short sequences without gaps |
| Cvdj_pipe::Merge_result | |
| Cvdj_pipe::Step_registry::Meta | |
| Cboost::multi_array< typename, size_t, typename > | |
| Cboost::multi_array< std::size_t, 2 > | |
| Cvdj_pipe::detail::Named_value_map< Id, Val > | Store values mapped against name strings and value IDs |
| ►Cnoncopyable | |
| Cvdj_pipe::Read_info_store | Store sequence-related information |
| Cvdj_pipe::Output_manager | |
| Cvdj_pipe::Seq_file_map::Pair | |
| ►Cvdj_pipe::detail::Parser_line | Basic line-based parser; use to derive other parsers |
| Cvdj_pipe::Parser_fasta | |
| Cvdj_pipe::Parser_fastq | Parser for FASTQ files |
| Cvdj_pipe::Parser_qual | |
| Cvdj_pipe::gdst::Pattern_iter | Navigate suffix tree according to pattern |
| Cvdj_pipe::Pipe_environment | |
| Cvdj_pipe::Pipe_paired_emid_read | Process paired reads with external MIDs |
| Cvdj_pipe::Pipe_paired_read | Process paired reads with external MIDs |
| Cvdj_pipe::Pipe_single_read | |
| Cvdj_pipe::Pipeline< Config > | |
| Cvdj_pipe::Pipeline_input< Config > | |
| ►Cpredicate_facade | |
| Cvdj_pipe::Is_ambiguous | |
| Cvdj_pipe::Queable_ofstream | |
| Cvdj_pipe::detail::Queable_ofstream_types | |
| Cvdj_pipe::Read_ginfo | Read ID and group ID |
| Cvdj_pipe::Read_ginfo_store | Read ID and group ID |
| Cvdj_pipe::Read_info | |
| Cvdj_pipe::match::Relative_interval | |
| Cvdj_pipe::match::Relative_position | Sequence position defined relatively to an interval |
| Cvdj_pipe::Seq_entry | |
| Cvdj_pipe::Seq_file_entry | |
| Cvdj_pipe::Seq_file_map | |
| Cvdj_pipe::Seq_fls< N, S > | Store short sequence in an integer |
| Cvdj_pipe::Seq_map_aligned | |
| Cvdj_pipe::Seq_map_full | |
| Cvdj_pipe::Seq_map_short | |
| Cvdj_pipe::Seq_match | |
| ►Cvdj_pipe::Seq_meta | |
| Cvdj_pipe::Qual_record | |
| Cvdj_pipe::Seq_qual_record | |
| Cvdj_pipe::Seq_record | |
| Cvdj_pipe::Seq_pos< Id > | |
| Cvdj_pipe::detail::Seq_props | |
| Cvdj_pipe::Seq_store | Store sequence and related information |
| Cvdj_pipe::Sequence_bstats | |
| Cvdj_pipe::Sequence_gstats | |
| ►Cstatic_visitor | |
| Cvdj_pipe::Apply_many::Visitor | |
| Cvdj_pipe::detail::Type_name | |
| Cvdj_pipe::Finish_visitor | |
| Cvdj_pipe::match::anonymous_namespace{me_battery.cpp}::Finish_visitor | |
| Cvdj_pipe::match::Match_element_visitor | |
| Cvdj_pipe::Run_visitor | |
| Cvdj_pipe::Summary_visitor | |
| Cvdj_pipe::Summary_visitor2 | |
| ►Cvdj_pipe::detail::Step_base | |
| ►Cvdj_pipe::detail::Step_base_paired | |
| Cvdj_pipe::Merge_paired | |
| ►Cvdj_pipe::detail::Step_base_paired_emid | |
| Cvdj_pipe::External_mid_infile | Look for external MIDs in separate files |
| ►Cvdj_pipe::detail::Step_base_single | |
| Cvdj_pipe::Composition_stats | |
| ►Cvdj_pipe::detail::Filter_base | |
| Cvdj_pipe::Average_quality_filter | |
| Cvdj_pipe::Character_filter | |
| ►Cvdj_pipe::detail::Window_filter_base | |
| Cvdj_pipe::Ambiguous_window_filter | |
| Cvdj_pipe::Average_quality_window_filter | |
| Cvdj_pipe::Length_filter | |
| Cvdj_pipe::Min_quality_window_filter | |
| Cvdj_pipe::Homopolymer_filter | |
| Cvdj_pipe::Min_quality_filter | |
| Cvdj_pipe::External_mid_inline | Look for external MIDs in FASTA/Q description lines |
| Cvdj_pipe::Find_shared | |
| Cvdj_pipe::Match_step | |
| Cvdj_pipe::Qual_stats | |
| Cvdj_pipe::Write_seq | |
| Cvdj_pipe::Histogram_step | |
| Cvdj_pipe::Write_value | |
| Cvdj_pipe::step::Step_builder_registry< Config > | |
| Cvdj_pipe::test::Step_harness< Step > | |
| Cvdj_pipe::Step_registry | |
| Cvdj_pipe::Step_variant_store | |
| ►Cstreambuf | |
| Cvdj_pipe::Null_buff | |
| ►Ctrue_ | |
| Cboost::spirit::traits::is_string< boost::string_ref > | |
| Cvdj_pipe::match::Truncate | |
| ►Ctype | |
| Cvdj_pipe::Type_index< T > | |
| Cvdj_pipe::gdst::Ukkonen_inserter | According to: http://www.cise.ufl.edu/~sahni/dsaaj/enrich/c16/suffix.htm http://stackoverflow.com/questions/9452701 |
| Cvdj_pipe::Unambiguous_interval_iter | |
| ►Cunary_function | |
| Cvdj_pipe::anonymous_namespace{file_ostream_queue.cpp}::Hash | |
| Cvdj_pipe::detail::Id_bimap< Id, Obj >::Hash_id | |
| Cvdj_pipe::Get_match_length | Set a fraction of sequence length to match |
| Cvdj_pipe::Identity< T > | Why is it not in STL? |
| Cvdj_pipe::Match_fraction_length | Set a fraction of sequence length to match |
| Cvdj_pipe::Match_full_length | Require full sequence to match |
| Cvdj_pipe::Match_ignore_ends | Set a minimal sequence length to match allowing for some mismatch at ends |
| Cvdj_pipe::Match_min_length | Set a minimal sequence length to match |
| Cvdj_pipe::Value_ids_emid | Provides access to standard eMID values |
| Cvdj_pipe::Value_ids_paired | Provides access to standard values for paired read pipeline |
| Cvdj_pipe::Value_ids_single | Provides access to standard values for single read pipeline |
| ►Cvdj_pipe::Value_map | Store values mapped against name strings and value IDs |
| ►Cvdj_pipe::Vm_access_paired | Access to value map for paired read pipeline and processing steps |
| Cvdj_pipe::Vm_access_paired_emid | Access to value map for paired eMID read pipeline and processing steps |
| Cvdj_pipe::Vm_access_single | |
| Cvdj_pipe::Value_names | |
| Cvdj_pipe::Variable_path | |
| ►Cstd::vector< T > | STL class |
| Cvdj_pipe::Quality | |
| Cvdj_pipe::detail::Vector_set< T, Alloc > | Collection of unique objects stored in an ordered vector |
| Cvdj_pipe::detail::Vector_set< id_type > | |
| ►Cvdj_pipe::detail::Vector_set< Seq_id > | |
| Cvdj_pipe::gdst::Leaf | Store suffixes Each leaf is attached to a branch and stores suffixes that have the length of the branch' index. Since the length of the suffixes is known, only the sequence ID is stored |
| Cvdj_pipe::detail::Vector_set< std::string > | |
| Cvdj_pipe::detail::Vector_set< vdj_pipe::Seq_pos > | |
| Cvdj_pipe::Wrap< Step > | |
1.8.11
