bcf::Writer::write_vcf_record writes wrong FORMAT/GT

[malthesr]

Consider the following code:

use std::io;

use bcf::header::StringMaps;
use noodles_bcf as bcf;

use noodles_vcf as vcf;
use vcf::header::{
    format::Key,
    record::value::{
        map::{Contig, Format},
        Map,
    },
};

fn main() -> Result<(), Box<dyn std::error::Error>> {
    let header = vcf::Header::builder()
        .add_contig(Map::<Contig>::new("sq0".parse()?))
        .add_sample_name("sample")
        .add_format(Map::<Format>::from(Key::Genotype))
        .add_format(Map::<Format>::from(Key::ConditionalGenotypeQuality))
        .build();

    let record: vcf::Record = "sq0\t1\t.\tA\t.\t.\t.\t.\tGT:GQ\t0|0:13".parse()?;

    // Write record as BCF: FORMAT/GT field is missing
    let mut writer = bcf::Writer::new(io::stdout());
    writer.write_file_format()?;
    writer.write_header(&header)?;
    writer.write_vcf_record(&header, &StringMaps::from(&header), &record)?;

    // Write record as VCF: Works fine
    // let mut writer = vcf::Writer::new(io::stdout());
    // writer.write_header(&header)?;
    // writer.write_record(&record)?;

    Ok(())
}

Running cargo run | bcftools view prints:

##fileformat=VCFv4.3
##FILTER=<ID=PASS,Description="All filters passed">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Conditional genotype quality">
##contig=<ID=sq0>
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample
sq0	1	.	A	.	.	.	.	GT:GQ	:13

Note the missing 0|0 genotype. bcftools also gives a warning [E::bcf_format_gt] Unexpected type 7.

noodles itself panics on trying to read the resulting BCF. For instance, running cargo run > $bcf and then running the bcf_view example on $bcf panics:

thread 'main' panicked at 'not yet implemented: unhandled type: Some(String(3))', noodles-bcf/src/reader/record/genotypes.rs:432:15
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Writing the record as VCF seems to work fine, so I'm guessing the problem lies somewhere in bcf::Writer::write_vcf_record?

[zaeleus]

Thanks for reporting and providing an example!

The BCF writer didn't have a FORMAT GT field encoder and was incorrectly writing string values instead. There is now support for this in 4c760ff.