Expand description
brrrr
brrrr
and in particular, brrrr_lib
, is a library for supporting writing genomics file
formats in file formats that are usable by general-purpose analytics infrastructure, e.g.
Spark.
Quick Start
For example, to write a FASTA file to the stdout.
use std::io::stdout;
use brrrr_lib::json_writer::fa2jsonl;
fn main() {
let example_input = b">A\nATCG\n>B\nGCTA" as &[u8];
fa2jsonl(example_input, &mut stdout()).expect("Error... :(");
}
fa2jsonl
relies on JsonRecordWriter
, which knows how to parse the input fasta bytes and
write them to objects that implement Write
.
If you’re interested in the CLI, see: https://github.com/tshauck/brrrr/releases/latest
Modules
csv_writer holds a writer, and outputs FASTA and GFF records as csv.
Custom brrrr errors.
json_writer holds a writer, and outputs FASTA and GFF records as newline delimited json.
parquet_reader is like parquet_writer, but for reading parquet in.
parquet_writer holds a writer, and outputs FASTA and GFF records as parquet.
Types used within the library.
Interface for the generic writer object.