https://github.com/bioconductor-source/rhisat2
Science Score: 23.0%
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○CITATION.cff file
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✓codemeta.json file
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○.zenodo.json file
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○DOI references
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✓Academic publication links
Links to: nature.com -
○Academic email domains
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○Scientific vocabulary similarity
Low similarity (9.9%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: gpl-3.0
- Language: C++
- Default Branch: devel
- Size: 13.5 MB
Statistics
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
Rhisat2
The Rhisat2 R package provides an R interface to the hisat2 spliced short-read aligner by Kim et al. (2015). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.
Source code
Rhisat2 v1.19.1 and newer
To allow compilation also on Linux aarch64, the Makefile obtained from hisat2 was adapted to exclude unsupported flags (-m64 and -msse2) on this platform. In addition, the mask2iupac array was converted from a char to a signed char. See here for the precise changes.
Rhisat2 v1.13.1 and newer
In Rhisat2 v1.13.1 and onwards, hisat2 was updated to v2.2.1, which was obtained from https://github.com/DaehwanKimLab/hisat2/releases on July 27, 2022.
Furthermore, Rhisat2 now includes parts of the SIMD Everywhere header library (https://github.com/simd-everywhere/simde) to support compilation on arm64, based on the implementation by Michael R. Crusoe crusoe@debian.org for the hisat2 (2.2.1-3) debian package (simde patch in http://deb.debian.org/debian/pool/main/h/hisat2/hisat2_2.2.1-3.debian.tar.xz, also forwarded in https://github.com/DaehwanKimLab/hisat2/pull/251).
Rhisat2 versions up to v1.13.0
The source code for hisat2 v2.1.0 was obtained from https://ccb.jhu.edu/software/hisat2/index.shtml on October 17, 2018.
Based on the discussion at https://github.com/BenLangmead/bowtie2/issues/81, the following small modification was made to allow compilation:
In the file src/aligner_result.cpp, line 1267
flag > 0
was replaced by
flag[0] != '\0'
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
GitHub Events
Total
- Member event: 1
- Push event: 3
- Create event: 1
Last Year
- Member event: 1
- Push event: 3
- Create event: 1
Dependencies
- actions/cache v1 composite
- actions/checkout v3 composite
- actions/upload-artifact v3 composite
- actions/upload-artifact master composite
- grimbough/bioc-actions/build-install-check v1 composite
- grimbough/bioc-actions/run-BiocCheck v1 composite
- grimbough/bioc-actions/setup-bioc v1 composite
- r-lib/actions/setup-pandoc v2 composite
- R >= 4.4.0 depends
- GenomicRanges * imports
- SGSeq * imports
- methods * imports
- txdbmaker * imports
- utils * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests
- github-pages >= 0
- jekyll-feed >= 0
- jemoji >= 0