SHORE core API. More...

Classes
class	size_iterator
	Proxy iterator over a sequence of indeces. More...

struct	blockcmp_pos
	Comparator that compares the start positions of blocks (used with d2tree) More...

struct	blockcmp_end
	Comparator that compares the end positions of blocks (used with d2tree) More...

struct	blockcmp_posend
	Comparator that compares the start position of a block with the end position of another block (used with d2tree) More...

class	twodex
	Range index class. More...

class	dp_alignment_matrix
	Matrix representation of an alignment. More...

struct	dp_traits
	Dynamic programming type traits. More...

struct	dp_traits< shore::nuc::base, shore::nuc::base >
	Dynamic programming type traits for shore::nuc::base. More...

struct	dp_alignment
	Representation of a dynamic programming alignment. More...

struct	dp_aligner_config
	Configuration for dp_aligner_pipe. More...

class	dp_aligner_pipe
	Dynamic programming aligner. More...

class	dp_multialigner_pipe
	Dynamic programming aligner (multiple reference sequences). More...

struct	dp_trace
	Dynamic programming alignment backtrace. More...

struct	dp_backtracer_config
	Dynamic programming alignment backtracer configuration. More...

class	dp_backtracer_pipe
	Dynamic programming alignment backtracer class. More...

class	d2tree
	2d-tree: index-sort containers of 2-dimensional data for range queries More...

class	cmp_tokens
	General purpose line comparator. More...

class	line_sorter
	ASCII text file sorting. More...

class	suffix_index
	On disk DNA suffix array and hash. More...

class	incremental_mean_var
	Online calculation of mean, variance and standard deviation. More...

struct	index_generator
	A generator that increments its value after each call. More...

struct	index_comparator
	Compare indexes referring to another data structure. More...

struct	index_comparator< DataIter, void >
	Compare indexes referring to another data structure. More...

struct	relabs
	Class that represents a value that may be either absolute or relative to another value. More...

class	ptrkeeper
	Clean up heap allocated objects. More...

class	mmapping
	Memory mapped file handling. More...

class	md5_sum
	MD5 checksum calculation. More...

struct	iless
	A case insensitive string comparator. More...

class	tok_occurrence
	Tokenizer for strings and other containers. Splits at delimiter occurences. More...

class	tok_occurrences
	Tokenizer for strings and other containers. Splits at delimiter occurences and allows multiple alternative delimiters. More...

class	tok_transition
	Tokenizer for strings and other containers. Splits at no-delimiter-delimiter transitions (and vice versa). More...

class	tok_transitions
	Tokenizer for strings and other containers. Splits at no-delimiter-delimiter transitions (and vice versa) and allows multiple alternative delimiters. More...

class	ltok_occurrence
	Tokenizer for strings and other containers. Splits at delimiter occurences, where the delimiter consists of multiple characters/items. More...

class	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. More...

class	valterm_iterator
	A forward iterator over null-terminated character arrays or other value-terminated arrays. More...

class	chartable
	String conversion tables. More...

struct	manipd
	Class that associates values with stream manipulators and formatting. More...

class	umask_ts
	Thread safe wrapper for umask. More...

class	timer
	Simple timer class. More...

class	frag_vector
	Pseudo container combining a set of iterator ranges. More...

class	intpack
	Vector for dynamic bit-width integer storage. More...

struct	refcore_base
	Helper for implementing intpack::iterator / intpack::reference. More...

struct	refcore
	Helper for implementing intpack::iterator / intpack::reference. More...

struct	refcore< 0 >
	Helper for implementing intpack::iterator / intpack::reference. More...

struct	refcore< 3 >
	Helper for implementing intpack::iterator / intpack::reference. More...

struct	refcore< 8 >
	Helper for implementing intpack::iterator / intpack::reference. More...

struct	refcore< 64 >
	Helper for implementing intpack::iterator / intpack::reference. More...

class	rle_queue
	Queue container that run length encodes its contents. More...

class	alignment_queue
	Read alignment storage queue. More...

class	alignment_3px
	Move the 3' end of alignments, but keep them sorted by position. More...

class	poissonifier
	Adaptive duplicate read filtering. More...

class	seqid_translator
	Transpose reference sequence IDs, e.g. for re-alignment in mapflowcell. More...

class	besthit_filter
	Discards redundant or suboptimal alignments. More...

class	alignment_statistic
	Collect statistics on alignments. More...

class	hits_correction_single_pipe
	Set the number of hits to the number of entries in the alignment file. More...

class	flatten_alignment_pipe
	Extract the read information from alignments. More...

class	mapping_pair_finder_pipe
	Collect concordant or unique pairings from position-sorted and PE corrected map.lists. More...

class	mapping_pair_joiner_pipe
	Join paired alignments into one. More...

class	alignment_trimmer_pipe
	Trim alignments that overlap range boundaries. More...

class	alignment_filter_pipe
	Combines various alignment filters. More...

class	alignment_condenser_pipe
	Replaces 'match' streches in the alignment string with their length, and reduces their quality resolution. More...

class	alignment_token
	Stretch of an alignment that corresponds to a single AlignmentOperation. More...

class	alignment_tokenizer
	Tokenize an alignment string into alignment_tokens. More...

class	alignment_builder
	Build an alignment string base by base. More...

class	alignment_helper
	Alignment string utilities. More...

class	aa
	Amino acid symbols. More...

struct	refseq_coor
	Reference sequence coordinates. More...

struct	refseq_region
	Range on a reference sequence with start and end on the same chromosome. More...

struct	refseq_range
	Range on a reference sequence where start and end may be on different chromosomes. More...

struct	genomic_coor
	Genomic coordinates. More...

struct	genomic_region
	Range on a genomic sequence with start and end on the same chromosome. More...

struct	genomic_range
	Range on a genomic sequence where start and end may be on different chromosomes. More...

struct	read
	Short read data type. More...

struct	alignment
	Alignment, e.g. map.list file entry. More...

class	sequence_record
	Record type for potentially long sequences, e.g. fasta entries. More...

struct	sff_read
	SFF (Standard Flowgram Format) read record. More...

struct	annotation_entry
	GFF3 annotation entry. More...

struct	delta_record
	NUCMER or PROMER alignment record. More...

struct	coverage
	Record representing a segment of constant coverage. More...

struct	refdict_entry
	Entry in a reference sequence dictionary. More...

struct	local_variant
	quality_variant.txt file record. More...

class	conversion_proxy
	Proxy iterator that converts the referenced values using a user-defined functor / function. More...

struct	conv_base_compl
	Conversion functor for use with conversion_proxy. More...

struct	conv_packed_compl
	Conversion functor for use with conversion_proxy. More...

struct	conv_char_compl
	Conversion functor for use with conversion_proxy. More...

struct	conv_int2base
	Conversion functor for use with conversion_proxy. More...

struct	conv_int2base_compl
	Conversion functor for use with conversion_proxy. More...

struct	conv_int2packed
	Conversion functor for use with conversion_proxy. More...

struct	conv_int2packed_compl
	Conversion functor for use with conversion_proxy. More...

struct	conv_int2char
	Conversion functor for use with conversion_proxy. More...

struct	conv_int2char_compl
	Conversion functor for use with conversion_proxy. More...

struct	conv_char2base
	Conversion functor for use with conversion_proxy. More...

struct	conv_char2base_compl
	Conversion functor for use with conversion_proxy. More...

struct	conv_char2packed
	Conversion functor for use with conversion_proxy. More...

struct	conv_char2packed_compl
	Conversion functor for use with conversion_proxy. More...

struct	conv_base2char
	Conversion functor for use with conversion_proxy. More...

struct	conv_base2char_compl
	Conversion functor for use with conversion_proxy. More...

struct	conv_base2packed
	Conversion functor for use with conversion_proxy. More...

struct	conv_base2packed_compl
	Conversion functor for use with conversion_proxy. More...

struct	conv_packed2char
	Conversion functor for use with conversion_proxy. More...

struct	conv_packed2char_compl
	Conversion functor for use with conversion_proxy. More...

struct	conv_packed2base
	Conversion functor for use with conversion_proxy. More...

struct	conv_packed2base_compl
	Conversion functor for use with conversion_proxy. More...

class	base_compl_iterator
	Conversion iterator. More...

class	packed_compl_iterator
	Conversion iterator. More...

class	char_compl_iterator
	Conversion iterator. More...

class	int2base_iterator
	Conversion iterator. More...

class	int2packed_iterator
	Conversion iterator. More...

class	int2char_iterator
	Conversion iterator. More...

class	int2base_compl_iterator
	Conversion iterator. More...

class	int2packed_compl_iterator
	Conversion iterator. More...

class	int2char_compl_iterator
	Conversion iterator. More...

class	base2packed_iterator
	Conversion iterator. More...

class	base2char_iterator
	Conversion iterator. More...

class	base2packed_compl_iterator
	Conversion iterator. More...

class	base2char_compl_iterator
	Conversion iterator. More...

class	packed2base_iterator
	Conversion iterator. More...

class	packed2char_iterator
	Conversion iterator. More...

class	packed2base_compl_iterator
	Conversion iterator. More...

class	packed2char_compl_iterator
	Conversion iterator. More...

class	char2base_iterator
	Conversion iterator. More...

class	char2packed_iterator
	Conversion iterator. More...

class	char2base_compl_iterator
	Conversion iterator. More...

class	char2packed_compl_iterator
	Conversion iterator. More...

class	dna_iterator
	Iterate over DNA sequences in different encodings. More...

class	packeddna_iterator
	Iterate over DNA sequences in different encodings. More...

class	chardna_iterator
	Iterate over DNA sequences in different encodings. More...

class	nuc
	Base symbol conversions. More...

class	color2seq
	Converts raw read sequences from SOLiD color space to sequence space. More...

class	pefilter
	Filter element for selecting reads with a certain paired end index. More...

class	serialization_core_access
	Serialization access for classes with private data. More...

class	alignment_reader
	Merged read of alignment files in various formats. More...

class	aln_writer
	Writes alignments in cisgenome ALN format. More...

class	bed_writer
	Writer for BED formatted files. More...

class	bedgraph_writer
	Writer for BEDGraph formatted files. More...

class	eland_reader
	Reader for Illumina ELAND alignment files. More...

class	fasta_reader
	FastA file reader. More...

class	fasta_writer
	Writer for FastA files. More...

class	basic_fastq_reader
	Fastq file reader (basic interface). More...

class	fastq_writer
	FastQ file writer. More...

class	qual_writer
	.qual file writer. More...

class	flatread_tags_parser
	Parser for SHORE FlatRead tags. More...

class	basic_flatread_reader
	Reader for SHORE FlatRead files (basic interface). More...

class	flatread_writer
	Writer for SHORE FlatRead files. More...

class	gff_reader
	Read genomic features from a GFF files. More...

class	gff_writer
	Write genomic features to a gff file. More...

class	maplist_tags_parser
	Parser class for MapList tags. More...

class	basic_maplist_reader
	Reader for SHORE MapList files (basic interface). More...

class	maplist_reader
	Reader for SHORE MapList files (monolithic interface). More...

class	maplist_writer
	Writer for SHORE MapList files. More...

class	delta_reader
	Reader for NUCMER / PROMER delta files. More...

class	psl_reader
	Reader for BLAT PSL / PSLX files. More...

class	basic_qseq_reader
	Reader for Illumina QSEQ files. More...

class	read_reader
	File format independent short read file reader. More...

class	basic_refdict_reader
	Reads reference sequence dictionary files. More...

class	sam_base
	Shared functionality for sam_reader and bam_reader. More...

class	sam_reader
	Reader for SAM alignment files. More...

class	bam_reader
	Reader for BAM alignment files. More...

class	sam_writer
	Writer for SAM alignment files. More...

class	segment_reader
	Reader for genomic segments in various file formats. More...

class	segment_writer
	Writer for genomic segment data. More...

class	basic_sff_reader
	454 SFF (Standard Flowgram Format) file reader. More...

class	sff_flatten_pipe
	Convert SFF file records obtained from sff_reader into regular raw read records. More...

class	basic_line_reader
	Read plain text files line by line (basic interface). More...

class	line_reader
	Read plain text files line by line (monolithic interface). More...

class	line_writer
	Plain text file writer. More...

class	row_reader
	Read tab delimited entries from plain text files. More...

class	vcf_writer
	Writes quality_variant entries in Variant Call Format (VCF). More...

class	qualvar_reader
	quality_variant file reader. More...

class	mpi
	Interface to the Message Passing Interface. More...

class	serial
	Serial part of a pipeline. Prevents instantiation and use of the. More...

class	parallel
	Parallel part of a pipeline. More...

class	sync
	Synchronization of parallel pipelines. More...

class	desync
	Gathers the data generated by the serial processing steps and multiplexes it to downstream after the mutex is unlocked. More...

class	parallelizer
	Pipeline parallelization. More...

class	parallel_log
	Logging for parallel operations. More...

class	thread
	Uncaught exception handling for threads. More...

class	thread_index
	Stores an enumerated ID for each thread number/process rank combination. More...

class	buffer_chain
	Base class for data sources that support adding plugin objects. More...

class	extractor
	Manually get data from the end of a pipeline. More...

class	feed
	Manually append data to the start of a pipeline. More...

class	thru
	Simply pass the data on, optionally perform a type cast. More...

struct	conversion
	Specializable assignment functor for use with conversion_pipe. More...

class	conversion_pipe
	Simply pass the data on, but perform a type conversion. More...

class	filter
	Takes up functors for filtering items from a pipeline. More...

class	splitter
	Takes up functors for filtering items from a pipeline. More...

class	merge
	Merge sorted data from multiple inputs. More...

class	monolithic
	Turns a data source without an internal buffer into one with an internal buffer. More...

struct	source_traits
	Specifies the data type a source provides through its current() method. More...

class	pipeline_core_access
	Grants the pipeline system access to private methods. More...

class	source
	Template for turning a class into a pipeline source. More...

class	sink
	Template for turning a class into a pipeline sink. More...

class	pipe
	Template for turning a class into a pipe element. More...

class	pipe_facade
	Template to aid implementing pipe elements. More...

class	plugin
	Plugin interface for use with data source objects that manage internal buffers by inheriting from buffer_chain, e.g. monolithic. More...

class	sorting_check
	Plugin to check that a dataset is sorted according to a comparator. More...

class	signal
	Signal. More...

class	slot
	Slot. More...

struct	sig_spec
	Helper for signal / slot. More...

struct	sig_spec< void >
	Helper for signal / slot. More...

struct	opt_base
	Helper for av_parser. More...

struct	opt_base1
	Helper for av_parser. More...

struct	opt_base2
	Helper for av_parser. More...

struct	av_option
	Helper for av_parser. More...

class	av_parser
	Command line option parser. More...

struct	av_option< std::pair< T, U > >
	Helper for av_parser. More...

struct	av_option< std::vector< T > >
	Helper for av_parser. More...

struct	av_option< std::set< T > >
	Helper for av_parser. More...

struct	av_option< std::vector< std::vector< T > > >
	Helper for av_parser. More...

struct	av_option< bool >
	Helper for av_parser. More...

struct	av_option< unary >
	Helper for av_parser. More...

class	program
	Program base class. More...

class	uncaught_handler
	Reporting uncaught program exceptions. More...

class	berry
	Class for finding the optimal log-transformation constant for ANOVA-type models uing the method proposed by Berry. More...

class	binomial
	Binomial distribution. More...

class	chisquare
	Chi square distribution. More...

class	exponential
	Exponential distribution. More...

class	geometric
	Geometric distribution. More...

class	glm
	General Linear Model. More...

class	glht
	Linear hypothesis test. More...

class	mtc
	Multiple testing correction. More...

class	poisson
	Poisson distribution. More...

class	gzxbase
	Base for gzx... classes. More...

class	gzxindex
	Read and access the index extension of a gzip file. More...

class	gzxdeflater
	GZIP compress a stream in blocks. More...

class	gzxdeflater_sink
	Sink device for GZIP block-wise compression. More...

class	gzx_ostream
	Block-wise GZIP compressing ostream wrapper. More...

class	gzxinflater
	Decode or seek in a GZIP compressed stream. More...

class	gzxinflater_source
	Source device for GZIP decompression. More...

class	gzx_istream
	istream wrapper for GZIP decompression. More...

class	stream_slicer
	Chop a file or input stream into slices, using mmap when possible. More...

class	streams_base
	Base class for istreams and ostreams. More...

class	istreams
	Manages an array of input streams. More...

class	ostreams
	Manages an array of output streams. More...

class	ipipe
	Stream source for an input pipe. More...

class	opipe
	Stream source for an output pipe. More...

class	mmapping_source
	Stream source that reads from an mmapped file. More...

class	mmapping_ifstream
	Stream that reads from an mmapped file. More...

class	xzbase
	Base for xz... classes. More...

class	xzdeflater
	XZ compress a stream in blocks. More...

class	xzdeflater_sink
	Sink device for block-wise xz compression. More...

class	xz_ostream
	Block-wise XZ compressing ostream wrapper. More...

class	xzindex
	Read and access the index of an xz file. More...

class	xzinflater
	Decode and seek in an xz compressed stream. More...

class	xzinflater_source
	Source device for xz decompression. More...

class	xz_istream
	istream wrapper for xz decompression. More...

Typedefs
typedef shore::pipe_box < dp_mapper_pipe >	dp_mapper

typedef shore::sink < dp_mapping_writer >	dp_mapping_sink

typedef boost::uint8_t	uint8_t

typedef boost::uint16_t	uint16_t

typedef boost::uint32_t	uint32_t

typedef boost::uint64_t	uint64_t

typedef shore::source < alignment_reader >	alignment_source

typedef shore::sink< aln_writer >	aln_sink
	ALN file pipeline sink.

typedef shore::sink< bed_writer >	bed_sink
	BED file pipeline sink.

typedef shore::sink < bedgraph_writer >	bedgraph_sink
	BEDGraph file pipeline sink.

typedef shore::source < eland_reader >	eland_source
	ELAND file pipeline source.

typedef shore::source < fasta_reader >	fasta_source
	Fasta file pipeline source.

typedef shore::sink< fasta_writer >	fasta_sink
	Fasta file pipeline sink.

typedef shore::sink < fasta_writer, shore::read >	fasta_read_sink
	Fasta file pipeline sink for read.

typedef shore::monolithic < basic_fastq_reader, shore::read, shore::read::compare_type >	fastq_reader
	Fastq file reader (monolithic interface).

typedef shore::source < fastq_reader >	fastq_source
	Fastq file pipeline source.

typedef shore::sink< fastq_writer >	fastq_sink
	Fastq file pipeline sink.

typedef shore::sink< qual_writer >	qual_sink
	.qual file pipeline sink.

typedef shore::monolithic < basic_flatread_reader, shore::read, shore::read::compare_type >	flatread_reader
	Reader for SHORE FlatRead files (monolithic interface).

typedef shore::source < flatread_reader >	flatread_source
	FlatRead file pipeline source.

typedef shore::sink < flatread_writer >	flatread_sink
	FlatRead file pipeline sink.

typedef shore::source< gff_reader >	gff_source
	GFF file pipeline source.

typedef shore::sink< gff_writer >	gff_sink
	GFF file pipeline sink.

typedef shore::source < maplist_reader >	maplist_source
	MapList file pipeline source.

typedef shore::sink < maplist_writer >	maplist_sink
	MapList file pipeline sink.

typedef shore::source < delta_reader >	delta_source
	Delta file pipeline source.

typedef shore::source< psl_reader >	psl_source
	BLAT-PSL file pipeline source.

typedef shore::monolithic < basic_qseq_reader, shore::read, shore::read::compare_type >	qseq_reader

typedef shore::source < qseq_reader >	qseq_source
	QSEQ file pipeline source.

typedef shore::source < read_reader >	read_source
	File format independent short read file pipeline source.

typedef shore::monolithic < basic_refdict_reader, refdict_entry >	refdict_reader

typedef shore::source < refdict_reader >	refdict_source

typedef shore::monolithic < basic_refdict_reader, shore::refseq_region >	refdict_region_reader
	Read reference sequence dictionary entries as shore::refseq_region.

typedef shore::source < refdict_region_reader >	refdict_region_source

typedef shore::source< sam_reader >	sam_source
	SAM file pipeline source.

typedef shore::source< bam_reader >	bam_source
	BAM file pipeline source.

typedef shore::sink< sam_writer >	sam_sink
	SAM file pipeline sink.

typedef shore::sink < sam_writer, shore::read >	sam_read_sink
	SAM file pipeline sink for unaligned reads.

typedef shore::source < segment_reader >	segment_source
	Pipeline source for genomic segments in various file formats.

typedef shore::sink < segment_writer >	segment_sink
	Pipeline sink for genomic segment data.

typedef shore::monolithic < basic_sff_reader, sff_read, sff_read::compare_type >	sff_reader

typedef shore::source< sff_reader >	sff_source
	SFF file pipeline source.

typedef shore::source < line_reader >	line_source
	Text file pipeline source.

typedef shore::sink< line_writer >	line_sink
	Text file pipeline sink.

typedef shore::source< row_reader >	row_source
	Tab delimited table file pipeline source.

typedef shore::sink< vcf_writer >	vcf_sink
	VCF file pipeline sink.

typedef shore::source < qualvar_reader >	qualvar_source
	quality_variant file pipeline source.

Enumerations
enum	AlignmentMode { ALN_NONE =-1, ALN_GLOBAL =0, ALN_DANGLING_REF =1, ALN_DANGLING_QRY =2, ALN_DANGLING_ANY =3, ALN_LOCAL =7 }
	Valid ways of aligning one end of the sequences.

enum	ExtendedFlag { XFLAG_NA =-1, XFLAG_FALSE =0, XFLAG_TRUE =1, XFLAG_IRRELEVANT =2 }
	Flag type with additional values 'NA' and 'IRRELEVANT'.

enum	AlignmentOperation { ALN_NOOP =0, ALN_MATCH =1, ALN_SUBST =2, ALN_INS =4, ALN_DEL =8, ALN_LONGDEL =16, ALN_FRAGMENT =32, ALN_SOFTCLIP =64, ALN_BISULFITE =128, ALN_GRAPH =256, ALN_INVERT =512 }
	Operations that may me encoded in an alignment string. More...

enum	Strand { STR_FWD =1, STR_REV =2 }
	Strand.

enum	OptionalStrand { STR_NA_OPT =0, STR_FWD_OPT =STR_FWD, STR_REV_OPT =STR_REV }
	Strand with an additional value NA.

enum	ExtendedStrand { STR_NA_EXT =STR_NA_OPT, STR_FWD_EXT =STR_FWD, STR_REV_EXT =STR_REV, STR_UNKNOWN_EXT =3 }
	As OptionalStrand, with additional value UNKNOWN (e.g. as in GFF). More...

enum	FastqQualType { FQ_QUAL_SANGER, FQ_QUAL_ILLUMINA, FQ_QUAL_SOLEXA }
	Different types of quality string encodings for FastQ files.

enum	SAMFlags { SAM_PE_PAIRED_END =0x001, SAM_PE_PROPER_PAIR =0x002, SAM_UNMAPPED_SELF =0x004, SAM_PE_UNMAPPED_MATE =0x008, SAM_REVERSE_SELF =0x010, SAM_REVERSE_MATE =0x020, SAM_PE_READ1 =0x040, SAM_PE_READ2 =0x080, SAM_NO_PRIMARY_ALIGNMENT =0x100, SAM_QUALITY_FILTERED =0x200, SAM_DUPLICATE_READ =0x400 }
	Enumeration of valid SAM flags (bitmask).

enum	OptionFlags { OPT_NOTSET, OPT_SET, OPT_AUTO, OPT_MANDATORY }
	Different types of command line options. More...

Functions
template<typename RefIter , typename QryIter , typename Scoring >
void	dp_align (dp_alignment_matrix &matrix, RefIter rbeg, const size_t rsize, QryIter qbeg, const size_t qsize, const Scoring scoring, const AlignmentMode left_ends, const AlignmentMode exclude_left=ALN_NONE, const AlignmentMode exclude_right=ALN_NONE)
	Perform dynamic programming alignment.

template<typename first_t , typename second_t >
bool	paircmpx (const std::pair< first_t, second_t > &p1, const std::pair< first_t, second_t > &p2)
	First d2tree comparator for std::pair.

template<typename first_t , typename second_t >
bool	paircmpy (const std::pair< first_t, second_t > &p1, const std::pair< first_t, second_t > &p2)
	Second d2tree comparator for std::pair.

template<typename first_t , typename second_t >
bool	paircmpxy (const std::pair< first_t, second_t > &p1, const std::pair< first_t, second_t > &p2)
	Third d2tree comparator for std::pair.

bool	cmp_field0 (const char const c0, const char const c1)
	Numerically compares the first tab-delimited text field of two lines (reads_0.fl comparator).

bool	scmp_field0 (const std::string &s0, const std::string &s1)
	Numerically compares the first tab-delimited text field of two lines (std::string version of the reads_0.fl comparator).

bool	cmp_field0_lex (const char const c0, const char const c1)
	Lexically compares the first tab-delimited text field of two lines.

bool	cmp_line (const char const c0, const char const c1)
	Compares two text lines.

bool	cmp_maplist (const char const c0, const char const c1)
	Compares two map.list lines by position (columns 1&2).

bool	cmp_maplist_readid (const char const c0, const char const c1)
	Compares two map.list lines by read id (column 4).

bool	cmp_sam (const char const c0, const char const c1)
	Compares two mapping lines in sam format.

template<int K>
bool	cmp_field (const char const c0, const char const c1)
	Numerically compares two lines by field K (offset 0).

template<int K>
bool	cmp_field_lex (const char const c0, const char const c1)
	Lexically compares two lines by field K (offset 0).

template<typename Iter , typename Oter >
void	count_elements (Iter ibeg, Iter iend, Oter obeg, Oter oend, bool initialize_counts=true, int shift=0)
	Count elements in a range. More...

template<typename Iter >
void	counts_to_intervals (Iter beg, Iter end)

template<typename Iter , typename Oter >
void	suffix_array (Iter ibeg, Iter iend, Oter obeg, bool initialize_sa=true, typename std::iterator_traits< Iter >::value_type imax=std::numeric_limits< typename std::iterator_traits< Iter >::value_type >::max())
	Construct suffix array; values in input range must not be negative. More...

template<typename Ater , typename Oter >
void	suffix_ranks (Ater abeg, Ater aend, Oter rbeg)

template<typename Ster , typename Ater >
std::pair< size_t, size_t >	suffix_lcpmax (Ster sbeg, Ster send, Ater abeg)
	Get the value and position of the maximal lcp for a suffix array.

template<typename Ster , typename Ater , typename Oter >
void	suffix_lcp (Ster sbeg, Ster send, Ater abeg, Oter obeg)
	Construct the lcp array for a suffix array.

template<typename Ster , typename Ater , typename Qter >
std::pair< Ater, Ater >	suffix_query (Ster sbeg, Ster send, Ater abeg, Ater aend, Qter qbeg, Qter qend)
	Binary search on a suffix array.

template<typename Ster , typename Ater , typename Qter >
suffix_query_result< Ater, Qter >	suffix_query_prefix (Ster sbeg, Ster send, Ater abeg, Ater aend, Qter qbeg, Qter qend)
	Binary search on a suffix array.

template<typename Ster , typename Ater , typename Query >
std::pair< Ater, Ater >	suffix_query_incremental (Ster sbeg, Ster send, Ater abeg, Ater aend, const Query q, const size_t ofs)
	Binary search on a suffix array. More...

template<typename Ster , typename Ater , typename Qter >
std::pair< Ater, Ater >	suffix_query (Ster sbeg, Ster send, Ater abeg, Qter qbeg, Qter qend)
	Binary search on a suffix array.

template<typename Ster , typename Ater , typename Qter >
suffix_query_result< Ater, Qter >	suffix_query_prefix (Ster sbeg, Ster send, Ater abeg, Qter qbeg, Qter qend)
	Binary search on a suffix array.

template<typename Ster , typename Ater >
std::ostream &	suffix_dump (std::ostream &os, Ster sbeg, Ster send, Ater abeg)

template<typename Ster , typename Ater >
bool	suffix_test (Ster sbeg, Ster send, Ater abeg)
	Test correctness of a suffix array (slow)

template<class U , class T >
U	round (T floatval)
	brief Round a floating point value.

double	log2 (const double val)
	Base two logarithm.

template<class Iter >
double	mean (const Iter begin, const Iter end)
	Calculate the arithmetic mean of the values in a range.

template<class Iter >
double	pairs_mean (Iter begin, const Iter end)
	Calculate the arithmetic mean of the values in a range of (value,count) pairs.

template<class Iter >
double	medianize (const Iter begin, const Iter end)
	Reorder the values in a range such that the median is in the center. More...

template<class Iter >
double	geometric_mean (const Iter begin, const Iter end, const bool skipZ=false)
	Calculate the geometric mean of the values in a range.

template<class Iter >
double	harmonic_mean (const Iter begin, const Iter end)
	Calculate the harmonic mean of the values in a range.

template<class Iter , class Oter >
void	skewness_kurtosis (Iter begin, Iter end, Oter dest, const bool var_n)
	Calculate skewness and kurtosis for the values in a range. More...

template<class Iter >
double	var (const Iter begin, const Iter end, const double mu, const bool var_n=false)
	Calculate the variance of the values in a range, utilizing the previously calculated mean.

template<class Iter >
double	pairs_var (const Iter begin, const Iter end, const double mu, const bool var_n=false)
	Calculate the variance of the values in a range of value->count pairs, utilizing the previously calculated mean.

template<class Iter >
double	var (const Iter begin, const Iter end, const bool var_n=false)
	Calculate the variance of the values in a range.

template<class Iter >
double	stddev (const Iter begin, const Iter end, const bool var_n=false)
	Calculate the standard deviation of the values in a range.

template<class Iter >
double	stddev (const Iter begin, const Iter end, const double mu, const bool var_n=false)
	Calculate the standard deviation of the values in a range, utilizing the previously calculated mean.

template<class Iter >
double	pairs_stddev (const Iter begin, const Iter end, const double mu, const bool var_n=false)
	Calculate the standard deviation of a range of value->count pairs, utilizing the previously calculated mean.

template<class Xter , class Yter >
std::pair< double, double >	polycog (Xter x_beg, Xter x_end, Yter y_beg, double *const ret_area2)
	Calculate the centre of gravity of a polygon.

template<class Xter , class Yter >
std::pair< double, double >	polycog (Xter x_beg, Xter x_end, Yter y_beg)
	Calculate the centre of gravity of a polygon.

template<class Iter >
void	mean_filter (Iter beg, Iter end, const size_t width)
	Applies mean filtering to the given sequence. More...

template<class T , class Iter >
void	seq (T lb, const T ub, const size_t len, Iter dest)
	Generate sequence of equidistant values, between (inclusive) lb & ub.

template<class IIter , class OIter , class Rng >
void	random_copy (IIter b, IIter e, OIter o, Rng &rng)
	Shuffle the values in a range.

template<typename IndexIter >
void	index_fill (IndexIter ib, IndexIter ie)
	Fill a range with consecutive values.

template<typename DataIter , typename IndexIter >
void	index_sort (IndexIter ib, IndexIter ie, DataIter db)
	Sort indexes with reference to another data structure.

template<typename DataIter , typename IndexIter , typename Comparator >
void	index_sort (IndexIter ib, IndexIter ie, DataIter db, Comparator data_cmp)
	Sort indexes with reference to another data structure.

template<typename DataIter , typename OrderingIter , typename RankIter >
void	ranks (RankIter first, RankIter last, OrderingIter ob, DataIter db)
	Compute 0-based ranks given an ordering. Equal stretches share the same, highest rank value.

template<class Abs_t >
std::istream &	operator>> (std::istream &is, relabs< Abs_t > &dest)
	Parse a relabs object from a stream. A '' suffix indicates a relative value.

template<class Abs_t >
std::ostream &	operator<< (std::ostream &os, const relabs< Abs_t > &val)
	Write a relabs object to a stream. A '' suffix is used to indicate a relative value.

template<class T , int SZ>
size_t	size (T(&)[SZ])
	Get the size of a fixed size array.

template<class T , int SZ>
T *	end (T(&array)[SZ])
	Get the end pointer for a fixed size array.

std::ostream &	memdump (std::ostream &os, const void *src, size_t n)
	Write a bit-wise dump of a given memory location.

void *	bit_memcpy (void const dst, const void const src, const size_t nbits, const size_t dst_bitofs, const size_t src_bitofs=0)
	Perform a bit-aligned memcpy.

uint64_t	ntoh64 (const void *const netw64)
	Converts a 64 bit integer from network byte order to host byte order.

uint32_t	ntoh32 (const void *const netw32)
	Converts a 32 bit integer from network byte order to host byte order.

uint16_t	ntoh16 (const void *const netw16)
	Converts a 16 bit integer from network byte order to host byte order.

uint64_t	letoh64 (const void *const le64)
	Converts a 64 bit integer from little endian byte order to host byte order.

uint32_t	letoh32 (const void *const le32)
	Converts a 32 bit integer from little endian byte order to host byte order.

uint16_t	letoh16 (const void *const le16)
	Converts a 16 bit integer from little endian byte order to host byte order.

uint64_t	hton64 (const void *const host64)
	converts a 64 bit integer from host byte order to network byte order */

uint32_t	hton32 (const void *const host32)
	converts a 32 bit integer from host byte order to network byte order */

uint16_t	hton16 (const void *const host16)
	converts a 16 bit integer from host byte order to network byte order */

std::string	home ()
	Get the current user's home directory.

std::string	config_home ()
	Get the config file directory for the current user (usually ~/.config/).

std::string	expand_home (const std::string &path)
	Expand leading tilde '~' char into the current user's home directory.

std::string	path_parent (const std::string &path)
	Get the parent directory for a path.

std::string	path_leaf (const std::string &path)
	Get only the last element in a path.

std::string	path_trunk (const std::string &path)
	Get only the first element in a path.

std::string	path_clean (const std::string &path)
	Make a path absolute and remove "." and ".." nodes and multiple slashes.

std::string	path_enum (const std::string &path, const std::string &suffix, int &num_ofs, const char sep='_')
	Increment a counter until the file <path><sep><counter><suffix> does not exist.

std::string	path_enum (const std::string &path, const std::string &suffix=std::string())
	Increment a counter until the file <path>_<counter><suffix> does not exist.

bool	is_executable (const std::string &fn)
	Test if a path points to a file that we're permitted to execute.

std::string	mktempdir (const std::string &prefix)
	Create a temporary file directory with the given path prefix. More...

std::string	which_nofail (const std::string &command, const std::string &env=std::string())
	Equivalent to the shell command.

uint64_t	file_size (const std::string &fn)
	Get the size of a file.

void	toupper (std::string &str)
	In-place conversion to upper case.

template<class Ex >
std::string	which_fail (const std::string &command, const std::string &env=std::string())
	Equivalent to the shell command.

std::string	which (const std::string &command, const std::string &env=std::string())
	Equivalent to the shell command.

template<class Iter >
void	glob (Iter b, Iter e, std::vector< std::string > &ret)

template<class Iter >
std::vector< std::string >	glob (Iter b, Iter e)
	Find files matching the given glob pattern.

void	glob (const std::string &pattern, std::vector< std::string > &ret)
	Find files matching the given glob pattern.

std::vector< std::string >	glob (const std::string &pattern)
	Find files matching the given glob pattern.

uint64_t	get_mtime (const std::string &path)
	Get the modification time for a path.

bool	is_older (const std::string &path1, const std::string &path2)
	Test if path1 modification time is older than the one for path2.

void	tolower (std::string &str)
	In-place conversion to lower case.

template<typename Iter >
bool	is_numeric (Iter b, Iter e)
	Test if a range of characters contains only digits.

std::vector< std::string >	split (const std::string &s, const char delim='\t')
	Tokenize a string. Splits at delimiter occurences.

std::vector< std::string >	split (const std::string &s, const char *const delims)
	Tokenize a string. Splits at delimiter occurences and allows multiple alternative delimiters.

std::vector< std::string >	tsplit (const std::string &s, const char delim='\t')
	Tokenize a string. Splits at no-delimiter-delimiter transitions (and vice versa).

std::vector< std::string >	tsplit (const std::string &s, const char *const delims)
	Tokenize a string. Splits at no-delimiter-delimiter transitions (and vice versa) and allows multiple alternative delimiters.

std::vector< std::string >	lsplit (const std::string &s, const std::string &delim)
	Tokenize a string. Splits at delimiter occurences, where the delimiter consists of multiple characters.

std::vector< std::string >	ltsplit (const std::string &s, const std::string &delim)
	Tokenize a string. Splits at no-delimiter-delimiter transitions (and vice versa), where the delimiter consists of multiple characters/items.

template<class StringIterator >
size_t	split (const std::string &s, StringIterator destination, const char delim='\t', const size_t limit=std::numeric_limits< size_t >::max()-1)
	Tokenize a string into a container. More...

template<class StringIterator >
size_t	split (const std::string &s, StringIterator destination, const char *const delims, const size_t limit=std::numeric_limits< size_t >::max()-1)
	Tokenize a string into a container using multiple alternative delimiters. More...

template<class StringIterator >
size_t	tsplit (const std::string &s, StringIterator destination, const char delim='\t', const size_t limit=std::numeric_limits< size_t >::max()-1)
	Tokenize a into a container. Splits at no-delimiter-delimiter transitions (and vice versa). More...

template<class StringIterator >
size_t	tsplit (const std::string &s, StringIterator destination, const char *const delims, const size_t limit=std::numeric_limits< size_t >::max()-1)
	Tokenize a into a container using multiple alternative delimiters. Splits at no-delimiter-delimiter transitions (and vice versa). More...

template<typename T >
std::string	to_string (const T &value, const int prec)
	Format the given value as a string.

template<typename T , int precision>
std::string	to_string (const T &value)
	Format the given value as a string.

template<typename T >
std::string	to_string (const T &value)
	Format the given value as a string.

template<>
std::string	to_string< bool > (const bool &value)

template<>
std::string	to_string< std::ostringstream > (const std::ostringstream &str)
	Format the given value as a string (override the template for ostringstreams).

template<>
std::string	to_string< std::string > (const std::string &s)
	Format the given value as a string (override the template for strings).

template<class Iter >
std::string	join (Iter begin, Iter end, const std::string &delim)
	Join the values in a range into a string.

template<class Iter >
std::string	join (const Iter begin, const Iter end)
	Join the values in a range into a string, using TAB as delimiter.

template<typename T >
std::string	join (const std::vector< T > &sv, const std::string &delim)
	Join the values in a std::vector into a string.

template<typename T >
std::string	join (const std::vector< T > &sv)
	Join the values in a std::vector into a string, using TAB as delimiter.

template<class Iteriter >
std::string	ijoin (Iteriter begin, Iteriter end, const std::string &delim)
	Join the given range of string iterators into a string.

template<typename Iter >
std::string	ijoin (const std::vector< Iter > &sv, const std::string &delim)
	Join the given vector of string iterators into a string.

std::vector< std::string >	join2d (std::vector< std::vector< std::string > > &pv, const std::string &delim)
	Join a 2-dimensional std::vector into a one-dimensional std::vector<std::string> >.

template<typename T >
std::string	to_string (const std::vector< T > &v)
	Format the given value as a string (override the template for vector).

template<typename T >
std::string	to_string (const std::vector< std::vector< T > > &v)
	Format the given value as a string (override the template for vector).

template<typename conv_type , void()(conv_type const) initfunc>
const conv_type *	chartab ()
	String conversion tables.

void	ctabinit_digit (int *const table)
	String conversion tables.

template<int exp>
void	ctabinit_expdigit (int64_t *const table)
	String conversion tables.

void	ctabinit_base32hex (int *const table)
	String conversion tables.

template<typename iter_type >
uint64_t	parse_uint64 (iter_type beg, iter_type end)
	Parse an unsigned int from an iterator range.

template<typename iter_type >
int64_t	parse_int64 (iter_type beg, iter_type end)
	Parse a signed int from an iterator range.

template<typename T >
void	parse_value (T *dest, const std::string &str)
	Parse a value from a string. More...

template<>
void	parse_value< std::string > (std::string *dest, const std::string &str)
	Parse a value from a string (std::string specialization).

template<>
void	parse_value< bool > (bool *dest, const std::string &str)
	Parse a value from a string (bool specialization). More...

template<typename T >
T	parse_value (const std::string &str)
	Parse a value from a string.

template<>
double	parse_value< double > (const std::string &str)
	Parse a value from a string (speedup for double).

template<typename iter_type >
void	parse_value (std::string *const dest, iter_type beg, iter_type end)
	Parse a value from an iterator range.

template<typename iter_type >
void	parse_value (uint64_t *const dest, iter_type beg, iter_type end)
	Parse a value from an iterator range.

template<typename iter_type >
void	parse_value (int64_t *const dest, iter_type beg, iter_type end)
	Parse a value from an iterator range.

template<typename T , typename iter_type >
void	parse_value (T const dest, iter_type beg, iter_type end, typename boost::enable_if< boost::is_integral< T > >::type dummy_int=0, typename boost::enable_if< boost::is_signed< T > >::type *dummy_sign=0)
	Parse a value from an iterator range.

template<typename T , typename iter_type >
void	parse_value (T const dest, iter_type beg, iter_type end, typename boost::enable_if< boost::is_integral< T > >::type dummy_int=0, typename boost::disable_if< boost::is_signed< T > >::type *dummy_sign=0)
	Parse a value from an iterator range.

template<typename Dest , typename Default >
void	parse_envvar (Dest *const dest, const std::string &envvar, const Default &def)
	Stores the value of an environment variable into a variable, or or assigns the given default if the environment variable is not set.

template<typename Dest , typename Default >
Dest	parse_envvar (const std::string &envvar, const Default &def)
	Gets the value of an environment variable, or returns the given default if the environment variable is not set.

bool	charcmp_ci (const char a, const char b)
	Case insensitive char comparator function.

bool	charcmp_equal_ci (const char a, const char b)
	Case insensitive test if two chars are equal.

template<typename Iterator >
bool	equal_ci (const std::string &s, Iterator b, Iterator e)
	Case insensitive test if a string equals the character in a range.

bool	starts_with_cs (const std::string &s, const std::string &pref)
	Case sensitive test if a string starts with a given prefix.

bool	ends_with_cs (const std::string &s, const std::string &suff)
	Case sensitive test if a string ends with a given suffix.

bool	starts_with_ci (const std::string &s, const std::string &pref)
	Case insensitive test if a string starts with a given prefix.

bool	ends_with_ci (const std::string &s, const std::string &suff)
	Case insensitive test if a string ends with a given suffix.

std::string	toggle_suffix_cs (const std::string &s, const std::string &suff)
	Add or remove the given suffix to a string (case sensitive).

std::string	remove_suffix_cs (const std::string &s, const std::string &suff)
	Remove the given suffix from a string, should it exist (case sensitive).

std::string	toggle_suffix_ci (const std::string &s, const std::string &suff)
	Add or remove the given suffix to a string (case insensitive).

std::string	remove_suffix_ci (const std::string &s, const std::string &suff)
	Remove the given suffix from a string, should it exist (case insensitive).

template<class T >
std::string	lprefix (const T &what, const std::string &prefix)
	Add a prefix to each line in a string.

std::vector< std::string >	wrap_line (const std::string &line, const size_t maxlw)
	Wrap a line of text at white space positions.

void	expand_tabs (std::istream &in, std::ostream &out, const int colsep=4, const std::vector< size_t > &maxwidths=std::vector< size_t >(), const bool headings=true)
	Aligns all TAB positions in a text by converting them to spaces.

std::string	expand_tabs (const std::string &str, const int colsep=4, const std::vector< size_t > &maxwidths=std::vector< size_t >(), const bool headings=true)
	Aligns all TAB positions in a text by converting them to spaces.

template<class Iter >
std::string	expand_tabs (const std::string &str, const int colsep, Iter b_maxwidths, Iter e_maxwidths, const bool headings=true)
	Aligns all TAB positions in a text by converting them to spaces.

template<typename Iter >
std::pair< Iter, Iter >	trim (Iter beg, Iter end)
	Get a pair of iterators indicating the white space trimmed version of the given range.

template<class T >
std::ostream &	operator<< (std::ostream &os, const manipd< T > &mp)

template<class T >
std::istream &	operator>> (std::istream &is, manipd< T > &mp)

template<typename exception_type >
void	throw_exception (const std::string &msg)

template<>
void	throw_exception< void > (const std::string &msg)

template<class exception_type , class Iter >
Iter	match_arg (const std::string &arg, Iter beg, Iter end, const std::string &exlabel=std::string("match_arg"))
	Try to find a match for a string in a given set of possible values. More...

template<class Ex , class Iter >
size_t	match_arg_idx (const std::string &arg, Iter beg, Iter end, const std::string &exlabel=std::string("match_arg"))
	Version of match_arg() that returns an array index instead of an iterator.

template<typename Enum , typename Iter >
std::istream &	parse_enum (std::istream &in, Enum &dest, Iter beg, Iter end)
	Parse an enum value using match_arg().

template<typename Enum , int SZ>
std::istream &	parse_enum (std::istream &in, Enum &dest, const std::string(&templ)[SZ])
	Parse an enum value using match_arg().

template<typename Enum >
enum_traits< Enum >::istream_type &	operator>> (std::istream &in, Enum &en)
	Enum<-string conversion operator.

template<typename Enum >
enum_traits< Enum >::ostream_type &	operator<< (std::ostream &out, const Enum &en)
	Enum->string conversion operator.

template<typename T >
void	throw_exception (const T &ex)
	Throw an exception; if debugging is enabled, prints a message and optionally a backtrace when an exception is generated.

int	get_maxopenfiles (const bool hardlim=false)
	Get the maximal number of open files.

int	get_nopenfiles ()
	Get the number of files currently opened by the calling process.

std::string	timestr ()
	Get a string representation of the current time.

uint64_t	time_stamp ()
	Get a time stamp of the form yyyymmddhhmmss.

template<class T >
std::vector< typename T::key_type >	map_keys (const T &m)
	Get the keys in a std::map as a vector.

template<class T >
std::vector< typename T::mapped_type >	map_values (const T &m)
	Get the values in a std::map as a vector.

std::ostream &	operator<< (std::ostream &os, const poissonifier::pf_core::pos &p)

refseq_coor	operator+ (const refseq_coor &c0, const refseq_coor::diff_t d)

refseq_coor	operator- (const refseq_coor &c0, const refseq_coor::diff_t d)

refseq_coor::diff_t	operator- (const refseq_coor &c0, const refseq_coor &c1)

bool	operator< (const refseq_coor &gc1, const refseq_coor &gc2)

bool	operator> (const refseq_coor &gc1, const refseq_coor &gc2)

bool	operator<= (const refseq_coor &gc1, const refseq_coor &gc2)

bool	operator>= (const refseq_coor &gc1, const refseq_coor &gc2)

bool	operator== (const refseq_coor &gc1, const refseq_coor &gc2)

bool	operator!= (const refseq_coor &gc1, const refseq_coor &gc2)

std::ostream &	operator<< (std::ostream &os, const refseq_coor &gc)

std::istream &	operator>> (std::istream &is, refseq_coor &gc)

bool	operator== (const refseq_region &gc1, const refseq_region &gc2)

bool	operator!= (const refseq_region &gc1, const refseq_region &gc2)

bool	operator== (const refseq_range &gc1, const refseq_range &gc2)

bool	operator!= (const refseq_range &gc1, const refseq_range &gc2)

std::ostream &	operator<< (std::ostream &os, const refseq_range &gr)

std::istream &	operator>> (std::istream &is, refseq_range &gr)

std::istream &	operator>> (std::istream &in, Strand &s)
	Parse Strand.

std::ostream &	operator<< (std::ostream &out, const Strand &s)
	Print Strand.

Strand	other_strand (const Strand strand)
	Get the opposite strand.

std::istream &	operator>> (std::istream &in, OptionalStrand &s)
	Parse OptionalStrand.

std::ostream &	operator<< (std::ostream &out, const OptionalStrand &s)
	Print OptionalStrand.

OptionalStrand	other_strand (const OptionalStrand strand)
	Get the opposite strand.

std::istream &	operator>> (std::istream &in, ExtendedStrand &s)
	Parse ExtendedStrand.

std::ostream &	operator<< (std::ostream &out, const ExtendedStrand &s)
	Print ExtendedStrand.

ExtendedStrand	other_strand (const ExtendedStrand strand)
	Get the opposite strand.

std::istream &	operator>> (std::istream &is, genomic_range &gr)
	Parse genomic_range. More...

std::ostream &	operator<< (std::ostream &os, const genomic_range &gr)
	Print a genomic_range. More...

std::istream &	operator>> (std::istream &is, annotation_entry::Phase &phase)

std::ostream &	operator<< (std::ostream &os, const annotation_entry::Phase &phase)

std::ostream &	operator<< (std::ostream &os, const nuc::base b)

template<typename Archive >
void	serialize (Archive &ar, shore::refseq_coor &c, const unsigned int version)
	Serialization for shore::refseq_coor.

template<typename Archive >
void	serialize (Archive &ar, shore::refseq_region &c, const unsigned int version)
	Serialization for shore::refseq_region.

template<typename Archive >
void	serialize (Archive &ar, shore::refseq_range &c, const unsigned int version)
	Serialization for shore::refseq_range.

template<typename Archive >
void	serialize (Archive &ar, shore::genomic_coor &c, const unsigned int version)
	Serialization for shore::genomic_coor.

template<typename Archive >
void	serialize (Archive &ar, shore::genomic_region &c, const unsigned int version)
	Serialization for shore::genomic_region.

template<typename Archive >
void	serialize (Archive &ar, shore::genomic_range &c, const unsigned int version)
	Serialization for shore::genomic_range.

template<typename Archive >
void	serialize (Archive &ar, shore::read::accessory &r, const unsigned int version)

template<typename Archive >
void	serialize (Archive &ar, shore::read &r, const unsigned int version)

template<typename Archive >
void	serialize (Archive &ar, shore::alignment::accessory &a, const unsigned int version)

template<typename Archive >
void	serialize (Archive &ar, shore::alignment &a, const unsigned int version)

template<typename Archive >
void	serialize (Archive &ar, shore::dp_trace &t, const unsigned int version)

template<typename Archive >
void	serialize (Archive &ar, shore::dp_mapping &m, const unsigned int version)

template<typename Archive >
void	serialize (Archive &ar, shore::alignment_statistic &c, const unsigned int version)
	Serialization for shore::alignment_statistic.

std::ostream &	operator<< (std::ostream &out, const shore::read &e)
	Write a FlatRead formatted SHORE read entry.

std::ostream &	operator<< (std::ostream &os, const shore::alignment &en)
	Write an alignment struct to a MapList stream.

template<typename T >
std::istream &	read_bigendian (std::istream &in, T &value)

std::istream &	operator>> (std::istream &in, shore::local_variant &e)

template<typename T , typename U >
serial< U > &	operator\| (serial< T > &ser1, serial< U > &ser2)
	Connect two serial pipeline elements.

template<typename T , typename U >
parallel< U > &	operator\| (parallel< T > &par1, parallel< U > &par2)
	Connect two parallel pipeline elements.

template<typename T , typename U >
parallelizer< U > &	operator\| (serial< T > &ser, parallelizer< U > &paz)
	Connect a serial pipeline element to a parallelizer element.

template<typename T , typename U >
parallel< U > &	operator\| (parallelizer< T > &paz, parallel< U > &par)
	Connect a parallelizer to a parallel pipeline element.

template<typename T , typename U >
sync< U > &	operator\| (parallel< T > &par, sync< U > &syn)
	Connect a parallel pipeline element to a sync element.

template<typename T , typename U >
serial< U > &	operator\| (sync< T > &syn, serial< U > &ser)
	Connect a sync element to a serial pipeline element.

template<typename T , typename U >
desync< U > &	operator\| (serial< T > &ser, desync< U > &dsc)
	Connect a serial pipeline element to a desync element.

template<typename T , typename U >
parallel< U > &	operator\| (desync< T > &dsc, parallel< U > &par)
	Connect a desync element to a parallel pipeline element.

template<typename T >
void	dump (serial< T > &ser)

template<typename A , typename B >
B &	operator\| (A &a, B &b)
	Connect two pipeline elements.

template<typename Cmp >
bool	is_valid_comparator (const Cmp &cmp, typename boost::disable_if< boost::is_pointer< Cmp > >::type *=0)
	Check if cmp can be used for comparisons (always true for non function pointers).

template<typename Cmp >
bool	is_valid_comparator (const Cmp &cmp, typename boost::enable_if< boost::is_pointer< Cmp > >::type *=0)
	Check if cmp can be used for comparisons (for function pointers, check that non-null).

template<typename T >
std::string	typestr (const T const value, typename boost::disable_if< boost::is_integral< T > >::type dummy_int=0, typename boost::disable_if< boost::is_float< T > >::type *dummy_float=0)

template<typename T >
std::string	typestr (const T const value, typename boost::enable_if< boost::is_integral< T > >::type dummy_int=0)

template<typename T >
std::string	typestr (const T const value, typename boost::enable_if< boost::is_float< T > >::type dummy_float=0)

std::string	typestr (const char *value)

template<typename T >
std::string	typestr (const shore::relabs< T > *const value)

template<typename T >
std::string	typestr (const std::vector< T > *const value)

template<typename T >
std::string	typestr (const std::vector< std::vector< T > > *const value)

template<typename T >
std::string	typestr (const std::set< T > *const value)

std::string	path_compression (const std::string &path)
	Get only the compression suffix of a path name.

bool	path_remove_compression (std::string &path)
	Remove any compression suffix from a path name. More...

std::string	path_without_compression (const std::string &path)
	Get the path name with any compression suffix removed.

std::string	file_maybe_compressed (const std::string &fn, bool *exists=0)
	Append or remove compression suffixes from a path name, depending on which one exists. More...

bool	file_exists_compressed (const std::string &fn)
	Test if a file, or a compressed version, exists.

Variables
const int *const	ctab_digit

const int64_t *const	ctab_expdigit [21]

Detailed Description

SHORE core API.

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      /                                \
   
   
         ALN                         BT
     1   global                      global
     2   local                       local
     3   dangling_ref/dangling_any   dangling_ref/dangling_any/dangling_same
     4   dangling_qry/dangling_any   dangling_qry/dangling_any/dangling_same
     5   dangling_ref/dangling_any   dangling_qry/dangling_any/dangling_other
     6   dangling_qry/dangling_any   dangling_ref/dangling_any/dangling_other
     7   dangling_ref/dangling_any   global
     8   dangling_qry/dangling_any   global
     9   global                      dangling_ref/dangling_any
    10   global                      dangling_qry/dangling_any
    11   local                       dangling_ref/dangling_any
    12   local                       dangling_qry/dangling_any
    13   dangling_ref/dangling_any   local
    14   dangling_qry/dangling_any   local
    15   local                       global
    16   global                      local

This file is part of SHORE.

SHORE is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

SHORE is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with SHORE. If not, see http://www.gnu.org/licenses/.

Enumeration Type Documentation

enum shore::AlignmentOperation

Operations that may me encoded in an alignment string.

Enumerator
ALN_MATCH	Alignment match, T.
ALN_SUBST	Alignment mismatch, [AT].
ALN_INS	Insertion, [-T].
ALN_DEL	Deletion, [T-].
ALN_LONGDEL	Long query gap, [L150].
ALN_FRAGMENT	Alignment region without sequence data of some (possibly estimated if at an end of an alignment) size, [F150], e.g. a result of paired-end read joining or 3' extension.
ALN_SOFTCLIP	Soft clip, <ACGATT>.
ALN_BISULFITE	Methyl mismatch, e.g. {CT}.
ALN_GRAPH	Sequence graph mismatch / indel, e.g. (A-).
ALN_INVERT	Modifier for ALN_FRAGMENT that reverses the strand, e.g.: [f150].

enum shore::ExtendedStrand

As OptionalStrand, with additional value UNKNOWN (e.g. as in GFF).

I.e. STR_NA_EXT="not stranded", STR_UNKNOWN_EXT="stranded, but strand unknown".

enum shore::OptionFlags

Different types of command line options.

Enumerator
OPT_NOTSET	Command line option without a default value.
OPT_SET	Command line option with a default value.
OPT_AUTO	Command line option whose default will vary depending on other factors.
OPT_MANDATORY	Mandatory command line option.

Function Documentation

template<typename Iter , typename Oter >

void shore::count_elements	(	Iter	ibeg,
		Iter	iend,
		Oter	obeg,
		Oter	oend,
		bool	initialize_counts = `true`,
		int	shift = `0`
	)

Count elements in a range.

Output range must be zero-initialized and have at least size max_element(ibeg,iend)+2

std::string shore::file_maybe_compressed	(	const std::string &	fn,
		bool *	exists = `0`
	)

Append or remove compression suffixes from a path name, depending on which one exists.

Returns: The modified file name and store a bool indicating if it exists.

template<class exception_type , class Iter >

Iter shore::match_arg	(	const std::string &	arg,
		Iter	beg,
		Iter	end,
		const std::string &	exlabel = `std::string("match_arg")`
	)

Try to find a match for a string in a given set of possible values.

First tries to find a perfect match. If a perfect match is not found, looks for a case insensitive complete match. If none is found, tries to find a matching prefix, first case sensitive, then case insensitive.

If no match, or multiple matches are found at the same stage of the lookup, an exception of the user-specified type is generated.

template<class Iter >

void shore::mean_filter	(	Iter	beg,
		Iter	end,
		const size_t	width
	)

Applies mean filtering to the given sequence.

Parameters

	begin	Begin of the sequence.
	end	End of the sequence.
[in]	width	Width of the sliding window, must be odd.

template<class Iter >

double shore::medianize	(	const Iter	begin,
		const Iter	end
	)

Reorder the values in a range such that the median is in the center.

Returns: The median of the values in the range.

std::string shore::mktempdir ( const std::string & prefix)

Create a temporary file directory with the given path prefix.

Returns: The name of the created directory.

std::ostream& shore::operator<<	(	std::ostream &	os,
		const genomic_range &	gr
	)

Print a genomic_range.

Format:

'SEQ1:POS..[SEQ2:]END';

'SEQ1:POS...XEND' if range size is zero;

END is inclusive, XEND exclusive

std::istream& shore::operator>>	(	std::istream &	is,
		genomic_range &	gr
	)

Parse genomic_range.

Formats:

'SEQ:POS..END', 'SEQ:POS~SIZE', 'SEQ1:POS..SEQ2:END';

'SEQ:POS...XEND', 'SEQ1:POS...SEQ2:XEND';

END is inclusive, XEND exclusive

template<typename T >

void shore::parse_value	(	T *	dest,
		const std::string &	str
	)

Parse a value from a string.

This one is required by av_parser.

template<>

void shore::parse_value< bool >	(	bool *	dest,
		const std::string &	str
	)

Parse a value from a string (bool specialization).

bool: Allow t[rue],f[alse],y[es],n[o] and 0,1.

bool shore::path_remove_compression ( std::string & path)

Remove any compression suffix from a path name.

Returns: True If the path name was altered.

template<class Iter , class Oter >

void shore::skewness_kurtosis	(	Iter	begin,
		Iter	end,
		Oter	dest,
		const bool	var_n
	)

Calculate skewness and kurtosis for the values in a range.

Parameters

[in]	begin	Begin of the input range.
[in]	end	End of the input range.
[out]	dest	Output location for skewness and kurtosis; must have size >=2.
[in]	var_n

template<class StringIterator >

size_t shore::split	(	const std::string &	s,
		StringIterator	destination,
		const char	delim = `'\t'`,
		const size_t	limit = `std::numeric_limits<size_t>::max()-1`
	)

Tokenize a string into a container.

Returns: Number of tokens, or (limit+1) if there are more tokens available than limit.

template<class StringIterator >

size_t shore::split	(	const std::string &	s,
		StringIterator	destination,
		const char *const	delims,
		const size_t	limit = `std::numeric_limits<size_t>::max()-1`
	)

Tokenize a string into a container using multiple alternative delimiters.

Returns: Number of tokens, or (limit+1) if there are more tokens available than limit.

template<typename Iter , typename Oter >

void shore::suffix_array	(	Iter	ibeg,
		Iter	iend,
		Oter	obeg,
		bool	initialize_sa = `true`,
		typename std::iterator_traits< Iter >::value_type	imax = `std::numeric_limits<typename std::iterator_traits<Iter>::value_type>::max()`
	)

Construct suffix array; values in input range must not be negative.

Parameters

ibeg	Iterator to the begin of the input sequence.
iend	Iterator to the end of the input sequence.
obeg	Iterator to the storage where the array is constructed.
initialize_sa	Initialize the output range to zero?
imax	Maximum value in the input range (size of the bucket array).

template<typename Ster , typename Ater , typename Query >

std::pair<Ater,Ater> shore::suffix_query_incremental	(	Ster	sbeg,
		Ster	send,
		Ater	abeg,
		Ater	aend,
		const Query	q,
		const size_t	ofs
	)

Binary search on a suffix array.

Parameters

sbeg	Start of the text.
send	End of the text.
abeg	Start of the suffix array range.
aend	End of the suffix array range.
q	Letter of the query.
ofs	Position of q in the query string.

template<class StringIterator >

size_t shore::tsplit	(	const std::string &	s,
		StringIterator	destination,
		const char	delim = `'\t'`,
		const size_t	limit = `std::numeric_limits<size_t>::max()-1`
	)

Tokenize a into a container. Splits at no-delimiter-delimiter transitions (and vice versa).

Returns: Number of tokens, or (limit+1) if there are more tokens available than limit.

template<class StringIterator >

size_t shore::tsplit	(	const std::string &	s,
		StringIterator	destination,
		const char *const	delims,
		const size_t	limit = `std::numeric_limits<size_t>::max()-1`
	)

Tokenize a into a container using multiple alternative delimiters. Splits at no-delimiter-delimiter transitions (and vice versa).

Returns: Number of tokens, or (limit+1) if there are more tokens available than limit.

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Enumeration Type Documentation

Function Documentation