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Rhisat2

R build status Code coverage

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

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'

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R wrapper around the hisat2 aligner.

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