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'