hisat2_build {Rhisat2} | R Documentation |
This function can be used to call the hisat2-build
binary.
hisat2_build( references, outdir, ..., prefix = "index", force = FALSE, strict = TRUE, execute = TRUE )
references |
Character vector. The path to the files containing the reference sequences from which to build the HISAT2 index. |
outdir |
Character scalar. The path to the output directory in which to
store the HISAT2 index. If the directory already exists, the function will
throw an error, unless |
... |
Additional arguments passed to the binaries. |
prefix |
Character scalar. The prefix to use for the HISAT2 index files. |
force |
Logical scalar. Whether to force overwriting of |
strict |
Logical scalar. Whether strict checking of input arguments should be enforced. |
execute |
Logical scalar. Whether to execute the assembled shell command. If FALSE, return a string with the command. |
All additional arguments in ...
are interpreted as additional
arguments to the HISAT2 binaries. Any flags are supposed to be represented as
logical values (e.g., quiet=TRUE
will be translated into
--quiet
). Parameters with additional input are supposed to be
character or numeric vectors, and the individual elements are collapsed into
a single comma-separated string (e.g., k=2
is translated into -k
2
, bmax=100
into --bmax 100
). Some arguments to the HISAT2
binaries will be ignored if they are already handled as explicit function
arguments. See the output of hisat2_build_usage()
for details about
available parameters.
If execute
is TRUE, the output generated by calling the
hisat2-build
binary. If execute
is FALSE, the
hisat2-build
command.
Charlotte Soneson, based on code from Florian Hahne.
Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12:357-360 (2015).
tmp <- tempdir() refs <- list.files(system.file(package="Rhisat2", "extdata/refs"), full.names=TRUE, pattern="\\.fa$") x <- hisat2_build(references=refs, outdir=file.path(tmp, "index"), force=TRUE) head(x) list.files(file.path(tmp, "index"))