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.
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.
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 [email protected] 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 DaehwanKimLab/hisat2#251).
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 BenLangmead/bowtie2#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'