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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 #### 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 []( on July 27, 2022. Furthermore, Rhisat2 now includes parts of the SIMD Everywhere header library ( to support compilation on arm64, based on the implementation by Michael R. Crusoe <> for the hisat2 (2.2.1-3) debian package (simde patch in, also forwarded in #### Rhisat2 versions up to v1.13.0 The source code for hisat2 v2.1.0 was obtained from []( on October 17, 2018. Based on the discussion at [](, 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'