mzML export

OpenARaw writes mzML via openmassspec_core::write_mzml, the same writer every reader in the OpenMassSpec stack uses, so output is consistent across vendors.

cargo run --release --example to_mzml -- path/to/sample.d output.mzML

Or from your own code:

use openaraw::reader::Reader;
use openmassspec_core::write_mzml;

let mut reader = Reader::open("sample.d")?;
let mut out = std::fs::File::create("output.mzML")?;
write_mzml(&mut reader, &mut out)?;

The writer stops at the first spectrum that fails to decode and returns its error. To write the decodable spectra of a damaged bundle instead, pass RecordErrorPolicy::Skip and check the returned summary:

use openmassspec_core::{write_mzml_with_options, RecordErrorPolicy, WriteOptions};

let opts = WriteOptions::new().with_record_error_policy(RecordErrorPolicy::Skip);
let summary = write_mzml_with_options(&mut reader, &mut out, &opts)?;
if summary.skipped() > 0 {
    eprintln!("{} spectra could not be decoded and were skipped", summary.skipped());
}

write_mzml iterates the reader's spectra via SpectrumSource (the same stream described in Reader and Scan data) and emits PSI-MS CV-annotated mzML - MS:1001509 (Agilent MassHunter format) as the source-file format term and MS:1001508 (Agilent MassHunter nativeID format) as the native ID format, with per-spectrum polarity, scan mode, analyzer, and precursor information carried through where the reader populated it.