Create a chunked FASTA/FASTQ iterator — sassy_fastx

sassy_fastx_iter() opens a FASTA or FASTQ file and returns an iterator that yields record-count-bounded batches. Parsing is performed by the vendored Rust needletail parser. Sequence and quality data in each batch are exposed as read-only raw ALTREP slices over immutable native batch buffers; they are not eagerly materialized as R strings.

Usage

sassy_fastx_iter(path, batch_records = 100000L, include_qual = TRUE)

Arguments

path: Path to a FASTA/FASTQ file. Gzip-compressed input is supported by the vendored needletail gzip backend.
batch_records: Maximum number of records returned by each sassy_fastx_next() call.
include_qual: If TRUE, FASTQ qualities are included as batch$qual. If FALSE, or for FASTA input, batch$qual is NULL.

Value

An external pointer with class sassy_fastx_iter.

Examples

fq <- tempfile(fileext = ".fastq")
writeLines(c("@r1", "ACGT", "+", "!!!!"), fq, useBytes = TRUE)
it <- sassy_fastx_iter(fq, batch_records = 1)
batch <- sassy_fastx_next(it)
rawToChar(batch$seq[[1]])
#> [1] "ACGT"