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vdj_pipe
pipeline for processing DNA sequence data
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vdj_pipe
pipeline for processing DNA sequence data
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| ►Nboost | |
| ►Nspirit | |
| ►Ntraits | |
| Cchar_type_of< boost::string_ref > | |
| Cis_string< boost::string_ref > | |
| Cmulti_array | |
| ►Nvdj_pipe | Main namespace of vdj_pipe library |
| ►Nanonymous_namespace{file_ostream_queue.cpp} | |
| CEqual | |
| CHash | |
| ►Nanonymous_namespace{histogram_step.cpp} | |
| CCompare_vv | |
| CCompare_vvv | |
| ►Nanonymous_namespace{pipe_paired_emid_read.cpp} | |
| CFour_file_ids | |
| ►Nanonymous_namespace{sanitize_string.cpp} | |
| CEscape | |
| ►Ndetail | |
| CBase_id | |
| CEqual_string_ref | |
| CExternal_mid_base | |
| CFilter_base | |
| CGetter | Extract object by its ID and apply member function |
| ►CId_bimap | |
| CEqual_id | |
| CEqual_obj | |
| CHash_id | |
| CId_map | |
| CInserter | |
| 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 | |
| CSeq_props | |
| ►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 |
| CUkkonen_inserter | According to: http://www.cise.ufl.edu/~sahni/dsaaj/enrich/c16/suffix.htm http://stackoverflow.com/questions/9452701 |
| ►Nmatch | |
| ►Nanonymous_namespace{me_battery.cpp} | |
| CFinish_visitor | |
| ►CCut_proto | |
| CErr | |
| ►CElement_proto | |
| CErr | |
| ►CMatch_combination | |
| CErr | |
| ►CMatch_element_aligned | Identify DNA sequence interval by finding the best alignment |
| CErr | |
| ►CMatch_element_ambiguous | Find best match between DNA sequence interval and a set of sequences without gaps that may include ambiguous nucleotides |
| CErr | |
| ►CMatch_element_battery | |
| CErr | |
| ►CMatch_element_factory | |
| CErr | |
| ►CMatch_element_positional | Identify DNA sequence interval by position only |
| CErr | |
| ►CMatch_element_short | Find best match between DNA sequence interval and a set of short sequences without gaps |
| CErr | |
| CMatch_element_visitor | |
| CRelative_interval | |
| CRelative_position | Sequence position defined relatively to an interval |
| CTruncate | |
| ►Nstep | |
| ►CApply_to_maker | |
| CErr | |
| CFind_maker | |
| CFind_maker< Apply_many > | |
| CFind_maker< Apply_one > | |
| CMaker | |
| ►CStep_builder_registry | |
| CInsert | |
| ►Ntest | Namespace for unit-tests |
| CException_fixture | |
| CId1 | |
| CId2 | |
| CStep_harness | |
| CAmbiguous_window_filter | |
| ►CApply_many | Apply enclosed processing step multiple times to sequence reads of specified kind: forward, reverse, or merged |
| CVisitor | |
| 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 | |
| CGroup_count | |
| CGroup_unique | |
| 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 | |
| CNull_buff | |
| ►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_ginfo | Read ID and group ID |
| ►CRead_ginfo_store | Read ID and group ID |
| 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 | |
| CPair | |
| CSeq_fls | Store short sequence in an integer |
| ►CSeq_map_aligned | |
| CErr | |
| CMatch | |
| ►CSeq_map_full | |
| CErr | |
| ►CSeq_map_short | |
| CErr | |
| CSeq_match | |
| CSeq_meta | |
| CSeq_pos | |
| CSeq_qual_record | |
| CSeq_record | |
| CSeq_store | Store sequence and related information |
| CSequence_bstats | |
| CSequence_gstats | |
| ►CStep_registry | |
| CErr | |
| CMeta | |
| 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 | |
| CWrap | |
| CWrite_seq | |
| CWrite_value |
1.8.11
