Build a minibwa index with the native library

Builds index files at prefix using the vendored minibwa C library. The package is GPL, so the native build includes minibwa's GPL-compatible low-memory indexing path; low_memory = FALSE uses the default libsais path.

Usage

mb_index_build(fasta, prefix, meth = FALSE, threads = 1L, low_memory = FALSE)

Arguments

fasta

Reference FASTA path. Gzip-compressed input is supported by minibwa/zlib.

prefix

Output prefix for .l2b, .mbw, and optionally .meth.mbw.

meth

Build the directional methylation index as well.

threads

Number of index-build threads requested by minibwa.

low_memory

Use minibwa's low-memory BWT builder.

Value

prefix, invisibly.