Class List

Here are the classes, structs, unions and interfaces with brief descriptions:

[detail level 1234]

▼Nboost
Cmulti_array
▼Nvdj_pipe	Main namespace of vdj_pipe library
►Ndetail
CBase_id
CEqual_string_ref
CExternal_mid_base
CFilter_base
CGetter	Extract object by its ID and apply member function
CId_bimap
CId_map
CInterval_checking_policy
CInterval_checking_policy< int >
CNamed_value_map	Store values mapped against name strings and value IDs
►CParser_line	Basic line-based parser; use to derive other parsers
CErr
CQueable_ofstream_types
►CStep_base
CErr
CStep_base_paired
CStep_base_paired_emid
CStep_base_single
CType_name
CVector_set	Collection of unique objects stored in an ordered vector
CWindow_filter_base
►Ngdst
CBranch
CChildren
CCommon_subseq	Common subsequence
CDepth_iter
►CGdst	Generalized DNA suffix tree
CErr
CGdst_stats
CLeaf	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
CMatch	Results of matching pattern to suffix tree
CPattern_iter	Navigate suffix tree according to pattern
►Nstep
►CApply_to_maker
CErr
CFind_maker
CFind_maker< Apply_many >
CFind_maker< Apply_one >
CMaker
CAmbiguous_window_filter
CApply_many	Apply enclosed processing step multiple times to sequence reads of specified kind: forward, reverse, or merged
CApply_one	Apply enclosed processing step once to a sequence read of specified kind: forward, reverse, or merged
CAverage_quality_filter
CAverage_quality_window_filter
Cbase_exception
CBest_match_pair
CBlank
CBlank_step
CCharacter_filter
►CCommand_line_options
CErr
CComposition_stats
CConfig_paired_emid_reads
CConfig_paired_reads
CConfig_single_reads
CExternal_mid_infile	Look for external MIDs in separate files
CExternal_mid_inline	Look for external MIDs in FASTA/Q description lines
►CFile
CErr
CFile_input	File target is supposed to exist at construction time
►CFile_istream
CErr
►CFile_ostream
CErr
►CFile_ostream_queue	Stack of recently used output file streams
CErr
►CFile_ostream_variant	Select output file based on variables in value map
CErr
CFile_output	File target is created if needed at construction time
CFind_shared
CFinish_visitor
►CGet_match_length	Set a fraction of sequence length to match
CErr
CHistogram_1d	Simple unsigned integer-based histogram
CHistogram_step
CHomopolymer_filter
CId_iterator
CIdentity	Why is it not in STL?
►CInput_manager
CErr
CIs_ambiguous
CLength_filter
CLib_info	Library info
►CMatch_fraction_length	Set a fraction of sequence length to match
CErr
CMatch_full_length	Require full sequence to match
CMatch_ignore_ends	Set a minimal sequence length to match allowing for some mismatch at ends
CMatch_min_length	Set a minimal sequence length to match
CMatch_step
CMerge_paired
CMerge_result
CMin_quality_filter
CMin_quality_window_filter
►COutput_manager
CErr
CParser_fasta
CParser_fastq	Parser for FASTQ files
CParser_qual
►CPipe_environment
CErr
►CPipe_paired_emid_read	Process paired reads with external MIDs
CErr
►CPipe_paired_read	Process paired reads with external MIDs
CErr
►CPipe_single_read
CErr
CPipeline
CPipeline_input
CQual_record
CQual_stats
CQuality
►CQueable_ofstream
CErr
CRead_info
►CRead_info_store	Store sequence-related information
CErr
CRun_visitor
CSeq_entry
CSeq_file
►CSeq_file_entry
CErr
►CSeq_file_map
CErr
CSeq_fls	Store short sequence in an integer
CSeq_match
CSeq_meta
CSeq_pos
CSeq_qual_record
CSeq_record
CSeq_store	Store sequence and related information
CStep_variant_store
CSummary_visitor
CSummary_visitor2
CType_index
CUnambiguous_interval_iter
CValue_ids_emid	Provides access to standard eMID values
CValue_ids_paired	Provides access to standard values for paired read pipeline
CValue_ids_single	Provides access to standard values for single read pipeline
►CValue_map	Store values mapped against name strings and value IDs
CErr
CValue_names
►CVariable_path
CErr
►CVm_access_paired	Access to value map for paired read pipeline and processing steps
CErr
CVm_access_paired_emid	Access to value map for paired eMID read pipeline and processing steps
►CVm_access_single
CErr
CWrite_seq
CWrite_value