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aggregate_concept.h 100644 5 kb
allocator_chunkpool.h 100644 9 kb
allocator_interface.h 100644 15 kb
allocator_multipool.h 100644 10 kb
allocator_simple.h 100644 8 kb
allocator_singlepool.h 100644 9 kb
allocator_to_std.h 100644 7 kb
alphabet_adapt_builtins.h 100644 8 kb
alphabet_bio.h 100644 4 kb
alphabet_concept.h 100644 19 kb
alphabet_math.h 100644 9 kb
alphabet_profile.h 100644 14 kb
alphabet_qualities.h 100644 5 kb
alphabet_residue.h 100644 35 kb
alphabet_residue_funcs.h 100644 3 kb
alphabet_residue_tabs.h 100644 20 kb
alphabet_simple_type.h 100644 38 kb
alphabet_storage.h 100644 9 kb
array_construct_destruct.h 100644 45 kb
basic_aggregate.h 100644 3 kb
basic_allocator.h 100644 3 kb
basic_alphabet.h 100644 4 kb
basic_concept.h 100644 3 kb
basic_container.h 100644 3 kb
basic_debug.h 100644 3 kb
basic_device.h 100644 5 kb
basic_exception.h 100644 12 kb
basic_functors.h 100644 6 kb
basic_fundamental.h 100644 4 kb
basic_iterator.h 100644 4 kb
basic_math.h 100644 3 kb
basic_metaprogramming.h 100644 3 kb
basic_parallelism.h 100644 3 kb
basic_proxy.h 100644 3 kb
basic_smart_pointer.h 100644 3 kb
basic_stream.h 100644 43 kb
basic_tangle.h 100644 6 kb
basic_type.h 100644 12 kb
basic_view.h 100644 6 kb
boost_preprocessor_subset.h 100644 306 kb
builtin_functions.h 100644 3 kb
concept_checking.h 100644 27 kb
container_concept.h 100644 21 kb
debug_helper.h 100644 7 kb
debug_test_system.h 100644 82 kb
fundamental_chunking.h 100644 5 kb
fundamental_comparison.h 100644 6 kb
fundamental_concepts.h 100644 28 kb
fundamental_conversion.h 100644 6 kb
fundamental_metafunctions.h 100644 10 kb
fundamental_tags.h 100644 19 kb
fundamental_transport.h 100644 7 kb
holder_base.h 100644 15 kb
holder_simple.h 100644 9 kb
holder_tristate.h 100644 26 kb
hosted_type_interface.h 100644 9 kb
iterator_adapt_pointer.h 100644 4 kb
iterator_adapt_std.h 100644 20 kb
iterator_adaptor.h 100644 27 kb
iterator_base.h 100644 12 kb
iterator_concept.h 100644 23 kb
iterator_counting.h 100644 14 kb
iterator_interface.h 100644 15 kb
iterator_position.h 100644 10 kb
iterator_range.h 100644 13 kb
iterator_zip.h 100644 25 kb
macro_deprecated.h 100644 3 kb
math_functions.h 100644 7 kb
math_log_space_value.h 100644 15 kb
metaprogramming_control.h 100644 9 kb
metaprogramming_enable_if.h 100644 15 kb
metaprogramming_logic.h 100644 16 kb
metaprogramming_math.h 100644 7 kb
metaprogramming_type.h 100644 11 kb
metaprogramming_type_algebra.h 100644 11 kb
pair_base.h 100644 15 kb
pair_bit_compressed.h 100644 7 kb
pair_packed.h 100644 7 kb
profiling.h 100644 20 kb
property_map_concept.h 100644 6 kb
proxy_base.h 100644 15 kb
proxy_iterator.h 100644 11 kb
test_system.h 100644 19 kb
triple_base.h 100644 16 kb
triple_packed.h 100644 7 kb
tuple_base.h 100644 20 kb
tuple_bit_compressed.h 100644 19 kb
volatile_ptr.h 100644 7 kb
README.md
# RSeqAn SeqAn Headers for R [![Build Status](https://travis-ci.org/compbiocore/RSeqAn.svg?branch=master)](https://travis-ci.org/compbiocore/RSeqAn) [![codecov](https://codecov.io/gh/compbiocore/RSeqAn/branch/master/graph/badge.svg)](https://codecov.io/gh/compbiocore/RSeqAn) [![License](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause) [![Docs](https://img.shields.io/badge/docs-stable-steelblue.svg?style=flat-square)](https://compbiocore.github.io/RSeqAn) [![DOI](http://joss.theoj.org/papers/10.21105/joss.01160/status.svg)](https://doi.org/10.21105/joss.01160) ## Overview This package provides R with access to [SeqAn v2.4](http://www.seqan.de/) header files. SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. ## Usage RSeqAn can be used via the `LinkingTo:` field in the `DESCRIPTION` field of an R package. Note that the compiler will need to compile as C++14. This can be done in R as `Sys.setenv("PKG_CXXFLAGS"="-std=c++14")`. For a quick example, see our [introductory vignette](https://compbiocore.github.io/RSeqAn/first_example/). Alternatively you can run the C++ code from the vignette directly by entering ```r Rcpp::sourceCpp(system.file("extdata","first_example.cpp",package="RSeqAn")) pattern_search("This is an awesome tutorial to get to know SeqAn!", "tutorial") ``` Don't forget to set the C++14 compiler flags if you do this! ## Installation * We recommend installing the release version [through Bioconductor](https://bioconductor.org/packages/release/bioc/html/RSeqAn.html), especially if you are running R on Windows. Instructions are provided on their page. * Version 1.3.1 can also be installed [through Bioconductor](http://bioconductor.org/packages/devel/bioc/html/RSeqAn.html) (for now, Bioconductor has a separate release cycle), downloaded as [a tagged release](https://github.com/compbiocore/RSeqAn/releases/tag/v1.3.1), or installed with `devtools` by running: ```r devtools::install_github("compbiocore/RSeqAn", ref="v1.3.1") ``` This version contains `Rcpp::as` and `Rcpp::wrap` functions for `CharString` and is the one submitted to the [Journal of Open Source Software](https://joss.theoj.org/). * The development version can be installed with `devtools` by running: ```r devtools::install_github("compbiocore/RSeqAn", ref="devel") ``` This version contains additional wrappers, though we cannot guarantee that they will work for you. ## Author August Guang ## Release history See [`NEWS`](/inst/NEWS) for release history. ## Citation If you use this package in your work, even if only in auxiliary tools or pipelines please cite: Guang, (2019). RSeqAn: Headers and wrappers for the SeqAn library in R. Journal of Open Source Software, 4(34), 1160, https://doi.org/10.21105/joss.01160 Please do not forget to cite SeqAn as well: Reinert, K., Dadi, T. H., Ehrhardt, M., Hauswedell, H., Mehringer, S., Rahn, R., … Weese, D. (2017). The SeqAn C++ template library for efficient sequence analysis: A resource for programmers. Journal of Biotechnology. https://doi.org/10.1016/j.jbiotec.2017.07.017