  shore::aa | Amino acid symbols |
| shore::read::accessory | Additional read information, usually represented as optional tags |
| shore::alignment::accessory | Additional alignment information, usually represented as optional tags |
| shore::alignment | Alignment, e.g. map.list file entry |
| shore::alignment_3px | Move the 3' end of alignments, but keep them sorted by position |
| shore::alignment_builder | Build an alignment string base by base |
| shore::alignment_helper | Alignment string utilities |
| shore::alignment_queue | Read alignment storage queue |
| shore::alignment_reader | Merged read of alignment files in various formats |
| shore::alignment_statistic | Collect statistics on alignments |
| shore::alignment_token | Stretch of an alignment that corresponds to a single AlignmentOperation |
| shore::alignment_tokenizer | Tokenize an alignment string into alignment_tokens |
| shore::aln_writer | Writes alignments in cisgenome ALN format |
| shore::annotation_entry | GFF3 annotation entry |
| shore::av_parser | Command line option parser |
| shore::basic_line_reader | Read plain text files line by line (basic interface) |
| shore::basic_qseq_reader | Reader for Illumina QSEQ files |
| shore::basic_refdict_reader | Reads reference sequence dictionary files |
| shore::basic_sff_reader | 454 SFF (Standard Flowgram Format) file reader |
| shore::bed_writer | Writer for BED formatted files |
| shore::bedgraph_writer | Writer for BEDGraph formatted files |
| shore::berry | Class for finding the optimal log-transformation constant for ANOVA-type models uing the method proposed by Berry |
| shore::besthit_filter | Discards redundant or suboptimal alignments |
| shore::binomial | Binomial distribution |
| shore::blockcmp_end | Comparator that compares the end positions of blocks (used with d2tree) |
| shore::blockcmp_pos | Comparator that compares the start positions of blocks (used with d2tree) |
| shore::blockcmp_posend | Comparator that compares the start position of a block with the end position of another block (used with d2tree) |
 shore::buffer_chain< T > | Base class for data sources that support adding plugin objects |
 shore::dp_aligner_pipe< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type > | |
| shore::dp_multialigner_pipe< shore::shore::dna_iterator > | |
 shore::monolithic< S, T, Cmp > | Turns a data source without an internal buffer into one with an internal buffer |
| shore::buffer_chain< dp_alignment< RefIter, QryIter, Scoring > > | |
| shore::dp_aligner_pipe< RefIter, QryIter, Scoring > | Dynamic programming aligner |
| shore::dp_multialigner_pipe< RefIter, QryIter, Scoring > | Dynamic programming aligner (multiple reference sequences) |
| shore::buffer_chain< dp_alignment< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type > > | |
| shore::buffer_chain< dp_alignment< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type > > | |
| shore::buffer_chain< dp_trace > | |
| shore::dp_backtracer_pipe< shore::shore::dna_iterator > | |
| shore::dp_backtracer_pipe< RefIter, QryIter, Scoring, AlnBuilder > | Dynamic programming alignment backtracer class |
| shore::buffer_chain< read > | |
| shore::sff_flatten_pipe | Convert SFF file records obtained from sff_reader into regular raw read records |
| shore::buffer_chain< typename source_traits< basic_line_reader >::current_type > | |
 shore::monolithic< basic_line_reader > | |
 shore::line_reader | Read plain text files line by line (monolithic interface) |
| shore::buffer_chain< U > | |
| shore::conversion_pipe< T, U, Converter > | Simply pass the data on, but perform a type conversion |
| shore::xzbase::buffer_t | Inflater buffer accessible as different types |
| shore::twodex::build_spec | Parameters for index creation |
| shore::twodex::bytecount | Helper for keeping track of the number of bytes read |
| shore::chardna_iterator | Iterate over DNA sequences in different encodings |
| shore::chartable< conv_type, initfunc > | String conversion tables |
| shore::chisquare | Chi square distribution |
| shore::cmp_tokens | General purpose line comparator |
| shore::color2seq | Converts raw read sequences from SOLiD color space to sequence space |
| shore::sff_read::commonhead | SFF (Standard Flowgram Format) Common Header Section as documented in the GS FLX documentation |
| shore::alignment_reader::config | Configuration that may be passed to the alignment_reader constructor |
| shore::sam_base::config | Configuration struct that may be passed to sam_reader or bam_reader |
| shore::intpack::const_iterator | Iterator proxy class |
| shore::intpack::const_reference | Const reference proxy class |
| shore::conv_base2char | Conversion functor for use with conversion_proxy |
| shore::conv_base2char_compl | Conversion functor for use with conversion_proxy |
| shore::conv_base2packed | Conversion functor for use with conversion_proxy |
| shore::conv_base2packed_compl | Conversion functor for use with conversion_proxy |
| shore::conv_base_compl | Conversion functor for use with conversion_proxy |
| shore::conv_char2base | Conversion functor for use with conversion_proxy |
| shore::conv_char2base_compl | Conversion functor for use with conversion_proxy |
| shore::conv_char2packed | Conversion functor for use with conversion_proxy |
| shore::conv_char2packed_compl | Conversion functor for use with conversion_proxy |
| shore::conv_char_compl | Conversion functor for use with conversion_proxy |
| shore::conv_int2base | Conversion functor for use with conversion_proxy |
| shore::conv_int2base_compl | Conversion functor for use with conversion_proxy |
| shore::conv_int2char | Conversion functor for use with conversion_proxy |
| shore::conv_int2char_compl | Conversion functor for use with conversion_proxy |
| shore::conv_int2packed | Conversion functor for use with conversion_proxy |
| shore::conv_int2packed_compl | Conversion functor for use with conversion_proxy |
| shore::conv_packed2base | Conversion functor for use with conversion_proxy |
| shore::conv_packed2base_compl | Conversion functor for use with conversion_proxy |
| shore::conv_packed2char | Conversion functor for use with conversion_proxy |
| shore::conv_packed2char_compl | Conversion functor for use with conversion_proxy |
| shore::conv_packed_compl | Conversion functor for use with conversion_proxy |
| shore::conversion< T, U > | Specializable assignment functor for use with conversion_pipe |
| shore::conversion_proxy< Iter, Converted, ConversionFunc > | Proxy iterator that converts the referenced values using a user-defined functor / function |
| shore::conversion_proxy< Iter, char, conv_base2char > | |
| shore::base2char_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, char, conv_base2char_compl > | |
| shore::base2char_compl_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, char, conv_char_compl > | |
| shore::char_compl_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, char, conv_int2char > | |
| shore::int2char_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, char, conv_int2char_compl > | |
| shore::int2char_compl_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, char, conv_packed2char > | |
| shore::packed2char_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, char, conv_packed2char_compl > | |
| shore::packed2char_compl_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::base, conv_base_compl > | |
| shore::base_compl_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::base, conv_char2base > | |
| shore::char2base_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::base, conv_char2base_compl > | |
| shore::char2base_compl_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::base, conv_int2base > | |
| shore::int2base_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::base, conv_int2base_compl > | |
| shore::int2base_compl_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::base, conv_packed2base > | |
| shore::packed2base_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::base, conv_packed2base_compl > | |
| shore::packed2base_compl_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::packed_base, conv_base2packed > | |
| shore::base2packed_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::packed_base, conv_base2packed_compl > | |
| shore::base2packed_compl_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::packed_base, conv_char2packed > | |
| shore::char2packed_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::packed_base, conv_char2packed_compl > | |
| shore::char2packed_compl_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::packed_base, conv_int2packed > | |
| shore::int2packed_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::packed_base, conv_int2packed_compl > | |
| shore::int2packed_compl_iterator< Iter > | Conversion iterator |
| shore::conversion_proxy< Iter, shore::nuc::packed_base, conv_packed_compl > | |
| shore::packed_compl_iterator< Iter > | Conversion iterator |
| shore::d2tree< XCompare, YCompare, XYCompare > | 2d-tree: index-sort containers of 2-dimensional data for range queries |
| shore::d2tree< shore::blockcmp_pos, shore::blockcmp_end, shore::blockcmp_posend > | |
| shore::delta_reader | Reader for NUCMER / PROMER delta files |
| shore::delta_record | NUCMER or PROMER alignment record |
| shore::desync< T > | Gathers the data generated by the serial processing steps and multiplexes it to downstream after the mutex is unlocked |
| shore::desync< U > | |
| shore::xzindex::iterator::detail | Priviledged access for xzinflater |
| shore::dna_iterator | Iterate over DNA sequences in different encodings |
| shore::dp_aligner_config | Configuration for dp_aligner_pipe |
| shore::dp_alignment< RefIter, QryIter, Scoring > | Representation of a dynamic programming alignment |
| shore::dp_alignment< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type > | |
| shore::dp_alignment_matrix | Matrix representation of an alignment |
| shore::dp_backtracer_config | Dynamic programming alignment backtracer configuration |
| shore::dp_trace | Dynamic programming alignment backtrace |
| shore::dp_traits< RefType, QryType > | Dynamic programming type traits |
| shore::dp_traits< shore::nuc::base, shore::nuc::base > | Dynamic programming type traits for shore::nuc::base |
| shore::dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type > | |
| shore::eland_reader | Reader for Illumina ELAND alignment files |
| std::exception | STL class |
| std::runtime_error | STL class |
| shore::av_parser::usage_error | Thrown to indicate a mistake by the user, to trigger displaying the usage page |
| shore::sorting_check< T, Cmp >::error | Exception thrown on invalid sort order |
| shore::exponential | Exponential distribution |
| shore::extractor< T > | Manually get data from the end of a pipeline |
| shore::extractor< S > | |
| shore::extractor< shore::dp_trace > | |
| shore::extractor< shore::shore::alignment > | |
| shore::fasta_reader | FastA file reader |
| shore::fasta_writer | Writer for FastA files |
| shore::fastq_writer | FastQ file writer |
| shore::feed< T > | Manually append data to the start of a pipeline |
| shore::feed< dp_sequence< QryIter > > | |
| shore::feed< dp_sequence< shore::shore::dna_iterator > > | |
| shore::feed< shore::shore::alignment > | |
| shore::feed< shore::shore::read > | |
| shore::feed< shore::shore::sff_read > | |
| shore::filter< T > | Takes up functors for filtering items from a pipeline |
| shore::flatread_tags_parser | Parser for SHORE FlatRead tags |
| shore::basic_fastq_reader | Fastq file reader (basic interface) |
| shore::basic_flatread_reader | Reader for SHORE FlatRead files (basic interface) |
| shore::flatread_writer | Writer for SHORE FlatRead files |
| shore::frag_vector< Iterator > | Pseudo container combining a set of iterator ranges |
| shore::genomic_coor | Genomic coordinates |
| shore::genomic_range | Range on a genomic sequence where start and end may be on different chromosomes |
| shore::genomic_region | Range on a genomic sequence with start and end on the same chromosome |
| shore::geometric | Geometric distribution |
| shore::gff_reader | Read genomic features from a GFF files |
| shore::gff_writer | Write genomic features to a gff file |
| shore::glht | Linear hypothesis test |
| shore::glm | General Linear Model |
| shore::gzx_istream | Istream wrapper for GZIP decompression |
| shore::gzx_ostream | Block-wise GZIP compressing ostream wrapper |
| shore::gzxbase | Base for gzx... classes |
| shore::gzxdeflater | GZIP compress a stream in blocks |
| shore::gzxindex | Read and access the index extension of a gzip file |
| shore::gzxindex::iterator | Iterator over the blocks of the streams |
| shore::gzxinflater | Decode or seek in a GZIP compressed stream |
| shore::gzxdeflater_sink | Sink device for GZIP block-wise compression |
| shore::gzxinflater_source | Source device for GZIP decompression |
| shore::twodex::header | Index header record |
| shore::iless | A case insensitive string comparator |
| shore::suffix_index::incremental_hash | Update the hash value of a sequence incrementally |
| shore::incremental_mean_var | Online calculation of mean, variance and standard deviation |
| shore::suffix_index::incremental_query | Incrementally elongate a query while keeping track of the suffix array range |
| shore::suffix_index::incremental_reverse_query | Incrementally elongate a query while keeping track of the suffix array range (queries the reverse index) |
| shore::index_comparator< DataIter, Comparator > | Compare indexes referring to another data structure |
| shore::index_comparator< DataIter, void > | Compare indexes referring to another data structure |
| shore::index_generator< T > | A generator that increments its value after each call |
| shore::intpack | Vector for dynamic bit-width integer storage |
| std::ios_base | STL class |
| std::basic_ios< Char > | STL class |
| std::basic_ostream< Char > | STL class |
| std::ostream | STL class |
| shore::ostreams | Manages an array of output streams |
| shore::ipipe | Stream source for an input pipe |
| shore::suffix_index::iterator | Iterator that decodes raw suffix array coordinates into chromosome-position pairs |
| shore::intpack::iterator | Iterator proxy class |
| shore::line_sorter< StrictWeakOrdering > | ASCII text file sorting |
| shore::line_writer | Plain text file writer |
| shore::local_variant | Quality_variant.txt file record |
| shore::ltok_occurrence< iter_type, delim_iter_type > | Tokenizer for strings and other containers. Splits at delimiter occurences, where the delimiter consists of multiple characters/items |
| shore::ltok_transition< iter_type, delim_iter_type > | Tokenizer for strings and other containers. Splits at no-delimiter-delimiter transitions (and vice versa), where the delimiter consists of multiple characters/items |
| shore::manipd< T > | Class that associates values with stream manipulators and formatting |
| shore::maplist_tags_parser | Parser class for MapList tags |
| shore::basic_maplist_reader | Reader for SHORE MapList files (basic interface) |
| shore::maplist_reader | Reader for SHORE MapList files (monolithic interface) |
| shore::maplist_writer | Writer for SHORE MapList files |
| shore::md5_sum | MD5 checksum calculation |
| shore::merge< T, Cmp > | Merge sorted data from multiple inputs |
| shore::merge< shore::shore::read, shore::shore::read::compare_type > | |
| shore::mmapping | Memory mapped file handling |
| shore::mmapping_ifstream | Stream that reads from an mmapped file |
| shore::mmapping_source | Stream source that reads from an mmapped file |
| shore::mpi | Interface to the Message Passing Interface |
| shore::mtc | Multiple testing correction |
| shore::nuc | Base symbol conversions |
| shore::opipe | Stream source for an output pipe |
| shore::opt_base | Helper for av_parser |
| shore::opt_base1< bool > | |
| shore::opt_base2< bool > | |
| shore::av_option< bool > | Helper for av_parser |
| shore::opt_base1< std::pair< T, U > > | |
| shore::av_option< std::pair< T, U > > | Helper for av_parser |
| shore::opt_base1< std::set< T > > | |
| shore::av_option< std::set< T > > | Helper for av_parser |
| shore::opt_base1< std::vector< std::vector< T > > > | |
| shore::av_option< std::vector< std::vector< T > > > | Helper for av_parser |
| shore::opt_base1< std::vector< T > > | |
| shore::av_option< std::vector< T > > | Helper for av_parser |
| shore::opt_base1< unary > | |
| shore::av_option< unary > | Helper for av_parser |
| shore::opt_base1< T > | Helper for av_parser |
| shore::opt_base2< T > | Helper for av_parser |
| shore::av_option< T > | Helper for av_parser |
| shore::packeddna_iterator | Iterate over DNA sequences in different encodings |
| shore::parallel< T > | Parallel part of a pipeline |
| shore::parallel< U > | |
| shore::parallel_log | Logging for parallel operations |
| shore::parallelizer< T > | Pipeline parallelization |
| shore::pefilter | Filter element for selecting reads with a certain paired end index |
| shore::pipe< Chnaf, S, T > | Template for turning a class into a pipe element |
| shore::pipe< shore::shore::alignment_3px > | |
| shore::pipe< shore::shore::poissonifier > | |
| shore::pipe_facade< Derived, InputType, OutputType, UNCHECKED_PIPE > | Template to aid implementing pipe elements |
| shore::dp_aligner_pipe< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type > | |
| shore::dp_backtracer_pipe< shore::shore::dna_iterator > | |
| shore::dp_multialigner_pipe< shore::shore::dna_iterator > | |
| shore::splitter< shore::shore::alignment > | |
| shore::thru< shore::shore::alignment > | |
| shore::thru< shore::shore::read > | |
| shore::pipe_facade< alignment_condenser_pipe, shore::alignment, shore::alignment > | |
| shore::alignment_condenser_pipe | Replaces 'match' streches in the alignment string with their length, and reduces their quality resolution |
| shore::pipe_facade< alignment_filter_pipe, shore::alignment, shore::alignment > | |
| shore::alignment_filter_pipe | Combines various alignment filters |
| shore::pipe_facade< alignment_trimmer_pipe, shore::alignment, shore::alignment > | |
| shore::alignment_trimmer_pipe | Trim alignments that overlap range boundaries |
| shore::pipe_facade< conversion_pipe< T, U >, T, U > | |
| shore::conversion_pipe< T, U, Converter > | Simply pass the data on, but perform a type conversion |
| shore::pipe_facade< dp_aligner_pipe< RefIter, QryIter, Scoring >, dp_sequence< QryIter >, dp_alignment< RefIter, QryIter, Scoring > > | |
| shore::dp_aligner_pipe< RefIter, QryIter, Scoring > | Dynamic programming aligner |
| shore::pipe_facade< dp_aligner_pipe< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type >, dp_sequence< shore::shore::dna_iterator >, dp_alignment< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type > > | |
| shore::pipe_facade< dp_backtracer_pipe< RefIter, QryIter, Scoring, AlnBuilder >, dp_alignment< RefIter, QryIter, Scoring >, dp_trace > | |
| shore::dp_backtracer_pipe< RefIter, QryIter, Scoring, AlnBuilder > | Dynamic programming alignment backtracer class |
| shore::pipe_facade< dp_backtracer_pipe< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::alignment_builder_type >, dp_alignment< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type >, dp_trace > | |
| shore::pipe_facade< dp_mapper_pipe, shore::read, dp_mapping > | |
| shore::pipe_facade< dp_multialigner_pipe< RefIter, QryIter, Scoring >, dp_sequence< QryIter >, dp_alignment< RefIter, QryIter, Scoring > > | |
| shore::dp_multialigner_pipe< RefIter, QryIter, Scoring > | Dynamic programming aligner (multiple reference sequences) |
| shore::pipe_facade< dp_multialigner_pipe< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type >, dp_sequence< shore::shore::dna_iterator >, dp_alignment< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type > > | |
| shore::pipe_facade< leftover_pipe, shore::read, shore::read > | |
| shore::pipe_facade< lock_buffer, append_type, current_type, true > | |
| shore::pipe_facade< mapping_pair_finder_pipe, shore::alignment, std::vector< shore::alignment > > | |
| shore::mapping_pair_finder_pipe | Collect concordant or unique pairings from position-sorted and PE corrected map.lists |
| shore::pipe_facade< mapping_pair_joiner_pipe, std::vector< shore::alignment >, shore::alignment > | |
| shore::mapping_pair_joiner_pipe | Join paired alignments into one |
| shore::pipe_facade< multiplexer, append_type, current_type, true > | |
| shore::pipe_facade< sff_flatten_pipe, sff_read, read > | |
| shore::sff_flatten_pipe | Convert SFF file records obtained from sff_reader into regular raw read records |
| shore::pipe_facade< shore::flatten_alignment_pipe, shore::alignment, shore::read > | |
| shore::flatten_alignment_pipe | Extract the read information from alignments |
| shore::pipe_facade< shore::hits_correction_single_pipe, shore::alignment, shore::alignment > | |
| shore::hits_correction_single_pipe | Set the number of hits to the number of entries in the alignment file |
| shore::pipe_facade< splitter< shore::shore::alignment >, shore::shore::alignment, shore::shore::alignment > | |
| shore::pipe_facade< splitter< T >, T, T > | |
| shore::splitter< T > | Takes up functors for filtering items from a pipeline |
| shore::pipe_facade< thread, append_type, current_type, true > | |
| shore::pipe_facade< thru< shore::shore::alignment, shore::shore::alignment >, shore::shore::alignment, shore::shore::alignment > | |
| shore::pipe_facade< thru< shore::shore::read, shore::shore::read >, shore::shore::read, shore::shore::read > | |
| shore::pipe_facade< thru< T, U >, T, U > | |
| shore::thru< T, U > | Simply pass the data on, optionally perform a type cast |
| shore::pipe_facade< track, append_type, current_type, true > | |
| shore::pipeline_core_access | Grants the pipeline system access to private methods |
| shore::plugin< T > | Plugin interface for use with data source objects that manage internal buffers by inheriting from buffer_chain, e.g. monolithic |
| shore::sorting_check< T, Cmp > | Plugin to check that a dataset is sorted according to a comparator |
| shore::plugin< current_type > | |
| shore::plugin< dp_trace > | |
| shore::plugin< typename source_traits< basic_line_reader >::current_type > | |
| shore::sorting_check< typename source_traits< basic_line_reader >::current_type, bool(*)(const typename source_traits< basic_line_reader >::current_type &, const typename source_traits< basic_line_reader >::current_type &) > | |
| shore::poisson | Poisson distribution |
| shore::poissonifier | Adaptive duplicate read filtering |
| shore::program | Program base class |
| shore::psl_reader | Reader for BLAT PSL / PSLX files |
| shore::ptrkeeper | Clean up heap allocated objects |
| shore::qual_writer | .qual file writer |
| shore::qualvar_reader | Quality_variant file reader |
| shore::read | Short read data type |
| shore::read_reader | File format independent short read file reader |
| shore::sff_read::readdata | SFF (Standard Flowgram Format) Read Data Section as documented in the GS FLX documentation |
| shore::sff_read::readhead | SFF (Standard Flowgram Format) Read Header Section as documented in the GS FLX documentation |
| shore::refcore_base | Helper for implementing intpack::iterator / intpack::reference |
| shore::refcore< NBIT > | Helper for implementing intpack::iterator / intpack::reference |
| shore::refcore< 0 > | Helper for implementing intpack::iterator / intpack::reference |
| shore::refcore< 3 > | Helper for implementing intpack::iterator / intpack::reference |
| shore::refcore< 64 > | Helper for implementing intpack::iterator / intpack::reference |
| shore::refcore< 8 > | Helper for implementing intpack::iterator / intpack::reference |
| shore::refdict_entry | Entry in a reference sequence dictionary |
| shore::intpack::reference | Reference proxy class |
| shore::refseq_coor | Reference sequence coordinates |
| shore::refseq_range | Range on a reference sequence where start and end may be on different chromosomes |
| shore::refseq_region | Range on a reference sequence with start and end on the same chromosome |
| shore::coverage | Record representing a segment of constant coverage |
| shore::relabs< Abs_t > | Class that represents a value that may be either absolute or relative to another value |
| shore::rle_queue< T > | Queue container that run length encodes its contents |
| shore::row_reader | Read tab delimited entries from plain text files |
| shore::sam_base | Shared functionality for sam_reader and bam_reader |
| shore::bam_reader | Reader for BAM alignment files |
| shore::sam_reader | Reader for SAM alignment files |
| shore::sam_writer | Writer for SAM alignment files |
| shore::segment_reader | Reader for genomic segments in various file formats |
| shore::segment_writer | Writer for genomic segment data |
| shore::seqid_translator | Transpose reference sequence IDs, e.g. for re-alignment in mapflowcell |
| shore::sequence_record | Record type for potentially long sequences, e.g. fasta entries |
| shore::serial< T > | Serial part of a pipeline. Prevents instantiation and use of the |
| shore::serial< U > | |
| shore::serialization_core_access | Serialization access for classes with private data |
| shore::sff_read | SFF (Standard Flowgram Format) read record |
| shore::sig_spec< T > | Helper for signal / slot |
| shore::sig_spec< const append_type & > | |
| shore::sig_spec< const current_type & > | |
| shore::sig_spec< const dp_alignment< RefIter, QryIter, Scoring > & > | |
| shore::sig_spec< const dp_alignment< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type > & > | |
| shore::sig_spec< const dp_mapping & > | |
| shore::sig_spec< const dp_sequence< QryIter > & > | |
| shore::sig_spec< const dp_sequence< shore::shore::dna_iterator > & > | |
| shore::sig_spec< const dp_trace & > | |
| shore::sig_spec< const InputType & > | |
| shore::sig_spec< const OutputType & > | |
| shore::sig_spec< const read & > | |
| shore::sig_spec< const sff_read & > | |
| shore::sig_spec< const shore::alignment & > | |
| shore::sig_spec< const shore::read & > | |
| shore::sig_spec< const shore::shore::alignment & > | |
| shore::sig_spec< const shore::shore::read & > | |
| shore::sig_spec< const std::string & > | |
| shore::sig_spec< const std::vector< shore::alignment > & > | |
| shore::sig_spec< const T & > | |
| shore::sig_spec< const U & > | |
| shore::sig_spec< int > | |
| shore::sig_spec< void > | Helper for signal / slot |
| shore::signal< T > | Signal |
| shore::signal< const current_type & > | |
| shore::signal< const dp_alignment< RefIter, QryIter, Scoring > & > | |
| shore::signal< const dp_alignment< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type > & > | |
| shore::signal< const dp_mapping & > | |
| shore::signal< const dp_trace & > | |
| shore::signal< const OutputType & > | |
| shore::signal< const read & > | |
| shore::signal< const shore::alignment & > | |
| shore::signal< const shore::read & > | |
| shore::signal< const shore::shore::alignment & > | |
| shore::signal< const shore::shore::read & > | |
| shore::signal< const std::string & > | |
| shore::signal< const std::vector< shore::alignment > & > | |
| shore::signal< const T & > | |
| shore::signal< const U & > | |
| shore::signal< int > | |
| shore::signal< void > | |
| shore::sink< S, T > | Template for turning a class into a pipeline sink |
| shore::sink< channel, shore::shore::read > | |
| shore::sink< channel, T > | |
| shore::sink< rawsink, S > | |
| shore::sink< rawsink, shore::dp_trace > | |
| shore::sink< rawsink, shore::shore::alignment > | |
| shore::sink< rawsink, T > | |
| shore::sink< samheader, std::string > | |
| shore::sink< shore::flatread_writer > | |
| shore::size_iterator | Proxy iterator over a sequence of indeces |
| shore::slot< T > | Slot |
| shore::slot< const append_type & > | |
| shore::slot< const current_type & > | |
| shore::slot< const dp_alignment< RefIter, QryIter, Scoring > & > | |
| shore::slot< const dp_alignment< shore::shore::dna_iterator, shore::shore::dna_iterator, typename dp_traits< typename std::iterator_traits< shore::shore::dna_iterator >::value_type, typename std::iterator_traits< shore::shore::dna_iterator >::value_type >::scoring_type > & > | |
| shore::slot< const dp_mapping & > | |
| shore::slot< const dp_sequence< QryIter > & > | |
| shore::slot< const dp_sequence< shore::shore::dna_iterator > & > | |
| shore::slot< const dp_trace & > | |
| shore::slot< const InputType & > | |
| shore::slot< const OutputType & > | |
| shore::slot< const read & > | |
| shore::slot< const sff_read & > | |
| shore::slot< const shore::alignment & > | |
| shore::slot< const shore::read & > | |
| shore::slot< const shore::shore::alignment & > | |
| shore::slot< const shore::shore::read & > | |
| shore::slot< const std::string & > | |
| shore::slot< const std::vector< shore::alignment > & > | |
| shore::slot< const T & > | |
| shore::slot< const U & > | |
| shore::slot< int > | |
| shore::slot< void > | |
| shore::source< S, T > | Template for turning a class into a pipeline source |
| shore::source< shore::shore::merge< shore::shore::alignment, cmp_type > > | |
| shore::source_traits< T > | Specifies the data type a source provides through its current() method |
| shore::source_traits< basic_line_reader > | |
| shore::stream_slicer | Chop a file or input stream into slices, using mmap when possible |
| shore::streams_base | Base class for istreams and ostreams |
| shore::istreams | Manages an array of input streams |
| shore::ostreams | Manages an array of output streams |
| shore::suffix_index | On disk DNA suffix array and hash |
| shore::sync< T > | Synchronization of parallel pipelines |
| shore::sync< U > | |
| shore::thread | Uncaught exception handling for threads |
| shore::thread_index | Stores an enumerated ID for each thread number/process rank combination |
| shore::timer | Simple timer class |
| shore::tok_occurrence< iter_type, delim_type > | Tokenizer for strings and other containers. Splits at delimiter occurences |
| shore::tok_occurrences< iter_type, delim_iter_type > | Tokenizer for strings and other containers. Splits at delimiter occurences and allows multiple alternative delimiters |
| shore::tok_transition< iter_type, delim_type > | Tokenizer for strings and other containers. Splits at no-delimiter-delimiter transitions (and vice versa) |
| shore::tok_transitions< iter_type, delim_iter_type > | Tokenizer for strings and other containers. Splits at no-delimiter-delimiter transitions (and vice versa) and allows multiple alternative delimiters |
| shore::twodex | Range index class |
| shore::umask_ts | Thread safe wrapper for umask |
| shore::uncaught_handler | Reporting uncaught program exceptions |
| shore::valterm_iterator< T, termval > | A forward iterator over null-terminated character arrays or other value-terminated arrays |
| shore::vcf_writer | Writes quality_variant entries in Variant Call Format (VCF) |
| shore::xz_istream | Istream wrapper for xz decompression |
| shore::xz_ostream | Block-wise XZ compressing ostream wrapper |
| shore::xzbase | Base for xz... classes |
| shore::xzdeflater | XZ compress a stream in blocks |
| shore::xzindex | Read and access the index of an xz file |
| shore::xzindex::iterator | Iterator over the blocks of the streams |
| shore::xzinflater | Decode and seek in an xz compressed stream |
| shore::xzdeflater_sink | Sink device for block-wise xz compression |
| shore::xzinflater_source | Source device for xz decompression |
1.8.4 
