SHORE API
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File List
Here is a list of all documented files with brief descriptions:
[detail level 123]
\-shore
 o-algo
 |o*2dex.hppCreate and query range index files
 |o*align.hppSimple dynamic programming alignment
 |o*d2tree.hpp2-dimensional kd-tree
 |o*sort_file.hppLow level text file sorting and merging functions
 |o*suffix.hppSuffix array algorithms
 |\*suffix_index.hppSuffix array on disk
 o-base
 |o*mathops.hppMiscellaneous math functions
 |o*memops.hppMiscellaneous helpers dealing with memmory access and allocation
 |o*pathops.hppHelpers dealing with file system paths
 |o*stringops.hppString conversion and manipulation
 |o*umask.hpp
 |\*util.hppMiscellaneous system utilities and other small helper functions
 o-container
 |o*frag_vector.hppPseudo container combining a set of iterator ranges
 |o*helpers.hppContainer-related helper functions
 |o*intpack.hppUnaligned integer storage
 |\*rle_queue.hppRun length encoded deque
 o-datatype
 |o*alignment_processing.hppRead alignment processing elements
 |o*alignment_string_ops.hppSHORE alignment string handling facilites
 |o*aminoacid.hppAmino acids
 |o*coor.hppReference sequence coordinates
 |o*datatypes.hppSHORE data records
 |o*dna_iterator.hppIterate over DNA sequences in different encodings
 |o*nucleotide.hppNucleotides
 |o*read_processing.hppRaw read processing elements
 |\*serialization.hppLibboost_serialization compliant serialization functions for libshore datatypes
 o-fmtio
 |o*alignment.hppFile format independent short read alignment reader
 |o*aln.hppCisgenome ALN file IO
 |o*bed.hppBED file IO
 |o*eland.hppELAND alignment file IO
 |o*fasta.hppFastA file IO
 |o*fastq.hppFastQ file IO
 |o*flatread.hppSHORE FlatRead format file IO
 |o*gff.hppGFF file IO
 |o*maplist.hppSHORE MapList file IO
 |o*mummer.hppMUMmer delta file IO
 |o*psl.hppBLAT PSL / PSLX file IO
 |o*qseq.hppIllumina QSEQ read file format IO
 |o*read.hppFile format independent short read file reader
 |o*refdict.hpp
 |o*sam.hppSAM/BAM file IO
 |o*segment.hppRead genomic segments in various file formats
 |o*sff.hpp454 SFF file IO
 |o*text.hppASCII plain text file IO
 |\*vcf.hppCurrently just quality_variant -> VCF conversion
 o-parallel
 |o*message_passing.hppInterface to the Message Passing Interface
 |o*message_passing_proxy.hppMessage passing interface parallelization proxy
 |o*parallel.hppMemory sharing agnostic parallelization system
 |o*parallel_log.hppMutually exclusive log file access
 |o*thread.hppThread class
 |\*thread_index.hppThread ID management
 o-processing
 |o*buffer_chain.hppIntegrate plain data sources with an internal buffer
 |o*extractor.hppRetrieve data from a pipeline
 |o*feed.hppFeed data to a pipeline
 |o*filter.hppConnect file readers, writers and processing steps through a signal/slot pipeline system
 |o*merge.hppMerge data from multiple pipeline inputs
 |o*method_check.hppCheck for presence of the optional pipeline methods flush(), next(), prepare()
 |o*monolithic_source.hppIntegrate plain data sources with an internal buffer
 |o*pipe_box.hppTemplate for transforming pipe elements for stand-alone use
 |o*pipeline.hppConnect file readers, writers and processing steps through a signal/slot pipeline system
 |o*plugin.hppIntegrate plain data sources with an internal buffer
 |\*signalslot.hppSignal/slot system
 o-program
 |o*av_parser.hppCommand line option parser
 |o*program.hppProgram base class file
 |\*uncaught_handler.hppHandle program exceptions
 o-statistics
 |o*berry.hppFinding the optimal log-transformation constant for ANOVA-type models uing the method proposed by Berry
 |o*binomial.hppBinomial distribution
 |o*chisquare.hppChi square distribution
 |o*exponential.hppExponential distribution
 |o*geometric.hppGeometric distribution
 |o*glm.hppGeneral Linear Model and linear hypothesis test
 |o*mtc.hppImplements the multiple testing correction methods of R's multtest package
 |\*poisson.hppPoisson distribution
 \-stream
  o*fileext.hppHelpers dealing with compression-related file extensions
  o*gzx.hppBlock-wise compression in gzip format
  o*stream_slicer.hppChop a file or input stream into slices
  o*streams.hppStream classes
  o*transpose.hpp
  \*xzx.hppBlock-wise compression in xz/lzma2 format