hisat2_build: Generate HISAT2 index

In Rhisat2: R Wrapper for HISAT2 Aligner

Description

This function can be used to call the hisat2-build binary.

Usage

hisat2_build(
  references,
  outdir,
  ...,
  prefix = "index",
  force = FALSE,
  strict = TRUE,
  execute = TRUE
)

Arguments

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 force=TRUE.
...	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 outdir.
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.

Details

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.

Value

If execute is TRUE, the output generated by calling the hisat2-build binary. If execute is FALSE, the hisat2-build command.

Author(s)

Charlotte Soneson, based on code from Florian Hahne.

References

Kim D, Langmead B and Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods 12:357-360 (2015).

Examples

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"))

Rhisat2 documentation built on Nov. 8, 2020, 5:49 p.m.