https://github.com/csoneson/rhisat2

R interface to the hisat2 aligner
https://github.com/csoneson/rhisat2

Last synced: 1 day ago
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R interface to the hisat2 aligner

• Host: GitHub
• URL: https://github.com/csoneson/rhisat2
• Owner: csoneson
• License: gpl-3.0
• Created: 2018-10-17T13:29:01.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2019-01-17T13:44:50.000Z (almost 6 years ago)
• Last Synced: 2024-12-18T11:47:10.251Z (21 days ago)
• Language: C++
• Homepage:
• Size: 10.6 MB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: NEWS
  • License: LICENSE

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README

        
## Rhisat2

[![Build Status](https://travis-ci.com/csoneson/Rhisat2.svg?branch=master)](https://travis-ci.com/csoneson/Rhisat2)

[![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/csoneson/Rhisat2?branch=master&svg=true)](https://ci.appveyor.com/project/csoneson/Rhisat2)

[![Code coverage](https://codecov.io/github/csoneson/Rhisat2/coverage.svg?branch=master)](https://codecov.io/github/csoneson/Rhisat2)

The `Rhisat2` R package provides an R interface to the [`hisat2`](https://ccb.jhu.edu/software/hisat2/index.shtml) spliced short-read aligner by [Kim et al. (2015)](https://www.nature.com/articles/nmeth.3317). The package contains wrapper functions to create a genome index and to perform the read alignment to the generated index.

### Source code

The source code for hisat2 v2.1.0 was obtained from [https://ccb.jhu.edu/software/hisat2/index.shtml](https://ccb.jhu.edu/software/hisat2/index.shtml) on October 17, 2018.

Based on the discussion at [https://github.com/BenLangmead/bowtie2/issues/81](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'