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.
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'