Iterate FASTA/FASTQ batches without R sequence materialization

mb_fastx_iter() opens one FASTA/FASTQ file, or two mate files, using the vendored minibwa reader. mb_fastx_next() returns a native FASTX batch, and mb_map_fastx_batch() maps that batch directly from native sequence buffers.

Usage

mb_fastx_iter(
  path,
  paired = c("auto", "none", "by_name", "two_file"),
  batch_bases = 100000000L,
  max_batch_bases = batch_bases,
  with_qual = FALSE,
  with_comment = FALSE
)

mb_fastx_next(iter)

mb_fastx_n(batch)

mb_map_fastx_batch(batch, index, opt = mb_opts())

Arguments

path: One FASTA/FASTQ path, or two paths for paired = "two_file".
paired: Pairing mode.
batch_bases: Approximate number of sequence bases to read per batch.
max_batch_bases: Maximum bases to read when extending a batch to keep a short paired fragment together.
with_qual, with_comment: Preserve qualities/comments in the native batch.
iter: Native FASTX iterator returned by mb_fastx_iter().
batch: Native FASTX batch returned by mb_fastx_next().
index: Index handle returned by mb_index_load().
opt: Options list from mb_opts().

Value

mb_fastx_iter() returns a native iterator. mb_fastx_next() returns a native FASTX batch or NULL at EOF. mb_fastx_n() returns the number of records in a FASTX batch. mb_map_fastx_batch() returns a native alignment batch.

Details

Pairing modes follow the CLI reader shape: "none" treats each record as a fragment, "by_name" groups adjacent records in one file with matching query names, and "two_file" reads one record from each of two files per fragment. "auto" selects "two_file" for two paths and "none" for one path.