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