zaeleus
commented
4 months ago Since you're manipulating the record, you won't have access to the raw record line. You have to use record buffers (vcf::variant::RecordBuf) and reserialize, e.g.,
main.rs
```rust
// cargo add noodles@0.68.0 --features vcf
use std::io;
use noodles::vcf::{
self,
variant::{io::Write, record::info::field::key, record_buf::info::field::Value},
};
static DATA: &[u8] = b"##fileformat=VCFv4.4
#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO
sq0\t1\t.\tA\t.\t.\tPASS\t.
";
fn main() -> io::Result<()> {
let mut reader = vcf::io::Reader::new(DATA);
let header = reader.read_header()?;
let stdout = io::stdout().lock();
let mut writer = vcf::io::Writer::new(stdout);
writer.write_header(&header)?;
for result in reader.record_bufs(&header) {
let mut record = result?;
record
.info_mut()
.insert(key::SAMPLES_WITH_DATA_COUNT.into(), Some(Value::from(1)));
writer.write_variant_record(&header, &record)?;
}
// => ##fileformat=VCFv4.4
// #CHROM POS ID REF ALT QUAL FILTER INFO
// sq0 1 . A . . PASS NS=1
Ok(())
}
```
If you want to manipulate raw strings, you can get the underlying reader after reading the header and read lines from there, e.g.,
let mut reader = vcf::io::Reader::new(DATA);
let header = reader.read_header()?;
for result in reader.get_mut().lines() {
let line = result?;
// ...
}
rkimoakbioinformatics
Hi, I'm developing a program which reads each record, add some INFO fields to it, and write the record to a file. As it will write The original record line plus some, I need the original record line. Is there a way to access the raw record lines through lazy::Record?