File List

Here is a list of all documented files with brief descriptions:

[detail level 123]

shore
algo
2dex.hpp	Create and query range index files
align.hpp	Simple dynamic programming alignment
d2tree.hpp	2-dimensional kd-tree
sort_file.hpp	Low level text file sorting and merging functions
suffix.hpp	Suffix array algorithms
suffix_index.hpp	Suffix array on disk
base
mathops.hpp	Miscellaneous math functions
memops.hpp	Miscellaneous helpers dealing with memmory access and allocation
pathops.hpp	Helpers dealing with file system paths
stringops.hpp	String conversion and manipulation
umask.hpp
util.hpp	Miscellaneous system utilities and other small helper functions
container
frag_vector.hpp	Pseudo container combining a set of iterator ranges
helpers.hpp	Container-related helper functions
intpack.hpp	Unaligned integer storage
rle_queue.hpp	Run length encoded deque
datatype
alignment_processing.hpp	Read alignment processing elements
alignment_string_ops.hpp	SHORE alignment string handling facilites
aminoacid.hpp	Amino acids
coor.hpp	Reference sequence coordinates
datatypes.hpp	SHORE data records
dna_iterator.hpp	Iterate over DNA sequences in different encodings
nucleotide.hpp	Nucleotides
read_processing.hpp	Raw read processing elements
serialization.hpp	Libboost_serialization compliant serialization functions for libshore datatypes
fmtio
alignment.hpp	File format independent short read alignment reader
aln.hpp	Cisgenome ALN file IO
bed.hpp	BED file IO
eland.hpp	ELAND alignment file IO
fasta.hpp	FastA file IO
fastq.hpp	FastQ file IO
flatread.hpp	SHORE FlatRead format file IO
gff.hpp	GFF file IO
maplist.hpp	SHORE MapList file IO
mummer.hpp	MUMmer delta file IO
psl.hpp	BLAT PSL / PSLX file IO
qseq.hpp	Illumina QSEQ read file format IO
read.hpp	File format independent short read file reader
refdict.hpp
sam.hpp	SAM/BAM file IO
segment.hpp	Read genomic segments in various file formats
sff.hpp	454 SFF file IO
text.hpp	ASCII plain text file IO
vcf.hpp	Currently just quality_variant -> VCF conversion
parallel
message_passing.hpp	Interface to the Message Passing Interface
message_passing_proxy.hpp	Message passing interface parallelization proxy
parallel.hpp	Memory sharing agnostic parallelization system
parallel_log.hpp	Mutually exclusive log file access
thread.hpp	Thread class
thread_index.hpp	Thread ID management
processing
buffer_chain.hpp	Integrate plain data sources with an internal buffer
extractor.hpp	Retrieve data from a pipeline
feed.hpp	Feed data to a pipeline
filter.hpp	Connect file readers, writers and processing steps through a signal/slot pipeline system
merge.hpp	Merge data from multiple pipeline inputs
method_check.hpp	Check for presence of the optional pipeline methods flush(), next(), prepare()
monolithic_source.hpp	Integrate plain data sources with an internal buffer
pipe_box.hpp	Template for transforming pipe elements for stand-alone use
pipeline.hpp	Connect file readers, writers and processing steps through a signal/slot pipeline system
plugin.hpp	Integrate plain data sources with an internal buffer
signalslot.hpp	Signal/slot system
program
av_parser.hpp	Command line option parser
program.hpp	Program base class file
uncaught_handler.hpp	Handle program exceptions
statistics
berry.hpp	Finding the optimal log-transformation constant for ANOVA-type models uing the method proposed by Berry
binomial.hpp	Binomial distribution
chisquare.hpp	Chi square distribution
exponential.hpp	Exponential distribution
geometric.hpp	Geometric distribution
glm.hpp	General Linear Model and linear hypothesis test
mtc.hpp	Implements the multiple testing correction methods of R's multtest package
poisson.hpp	Poisson distribution
stream
fileext.hpp	Helpers dealing with compression-related file extensions
gzx.hpp	Block-wise compression in gzip format
stream_slicer.hpp	Chop a file or input stream into slices
streams.hpp	Stream classes
transpose.hpp
xzx.hpp	Block-wise compression in xz/lzma2 format