Name Mode Size
..
align 040000
align_extend 040000
align_parallel 040000
align_profile 040000
align_split 040000
alignment_free 040000
arg_parse 040000
bam_io 040000
basic 040000
bed_io 040000
blast 040000
consensus 040000
file 040000
find 040000
gff_io 040000
graph_algorithms 040000
graph_align 040000
graph_msa 040000
graph_types 040000
index 040000
journaled_set 040000
journaled_string_tree 040000
map 040000
math 040000
misc 040000
modifier 040000
parallel 040000
parse_lm 040000
pipe 040000
random 040000
realign 040000
reduced_aminoacid 040000
rna_io 040000
roi_io 040000
score 040000
seeds 040000
seq_io 040000
sequence 040000
sequence_journaled 040000
simd 040000
simple_intervals_io 040000
statistics 040000
store 040000
stream 040000
system 040000
tabix_io 040000
translation 040000
ucsc_io 040000
vcf_io 040000
LICENSE 100644 2 kb
align.h 100644 10 kb
align_extend.h 100644 2 kb
align_parallel.h 100644 5 kb
align_profile.h 100644 3 kb
align_split.h 100644 3 kb
alignment_free.h 100644 3 kb
arg_parse.h 100644 3 kb
bam_io.h 100644 4 kb
basic.h 100644 4 kb
bed_io.h 100644 3 kb
blast.h 100644 3 kb
consensus.h 100644 3 kb
file.h 100644 4 kb
find.h 100644 4 kb
gff_io.h 100644 3 kb
graph_algorithms.h 100644 3 kb
graph_align.h 100644 3 kb
graph_msa.h 100644 3 kb
graph_types.h 100644 4 kb
index.h 100644 9 kb
journaled_set.h 100644 4 kb
journaled_string_tree.h 100644 4 kb
map.h 100644 3 kb
math.h 100644 3 kb
mman.h 100644 5 kb
modifier.h 100644 4 kb
parallel.h 100755 4 kb
parse_lm.h 100644 3 kb
pipe.h 100644 3 kb
platform.h 100644 18 kb
random.h 100644 3 kb
realign.h 100644 3 kb
reduced_aminoacid.h 100644 4 kb
rna_io.h 100644 3 kb
roi_io.h 100644 3 kb
score.h 100644 3 kb
seeds.h 100644 4 kb
seq_io.h 100644 3 kb
sequence.h 100644 6 kb
sequence_journaled.h 100644 3 kb
simd.h 100644 6 kb
simple_intervals_io.h 100644 3 kb
statistics.h 100644 2 kb
store.h 100644 3 kb
stream.h 100644 5 kb
system.h 100644 3 kb
tabix_io.h 100644 3 kb
translation.h 100644 2 kb
ucsc_io.h 100644 2 kb
vcf_io.h 100644 3 kb
version.h 100644 2 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