Module variant 

VCF variant record representation and field access.

This module provides types and functions for working with VCF/BCF variant records. The Variant struct wraps a bcf::Record and provides convenient access to standard VCF fields (CHROM, POS, REF, ALT, etc.) as well as INFO and FORMAT data.

Value Types

• InfoValue: Represents INFO field values (scalar, array, flag, or absent)
• FormatValue: Represents FORMAT field values (per-sample data)

Standalone Functions

For cases where you have a borrowed bcf::Record reference (e.g., from a GcCell in V8 bindings), standalone helper functions are provided:

• record_info: Get INFO field from a borrowed record
• record_format: Get FORMAT field from a borrowed record
• record_sample: Get all FORMAT fields for a single sample
• record_samples: Get all FORMAT fields for multiple samples
• record_to_string: Format record as VCF line

Example

use htsvcf_core::variant::{Variant, InfoValue};
use htsvcf_core::header::Header;
use rust_htslib::bcf::{self, Read};

let mut reader = bcf::Reader::from_path("input.vcf.gz").unwrap();
let header = unsafe { Header::new(reader.header().inner) };

for result in reader.records() {
    let record = result.unwrap();
    let variant = Variant::from_record(record);

    println!("{}:{}", variant.chrom(), variant.pos());

    // Access INFO fields
    match variant.info(&header, "DP") {
        InfoValue::Int(dp) => println!("DP = {}", dp),
        InfoValue::Absent => println!("No DP"),
        _ => {}
    }
}

Structs

Variant

A VCF/BCF variant record with convenient field accessors.

Enums

FormatValue

Represents a value from a FORMAT field in a VCF record.

InfoValue

Represents a value from an INFO field in a VCF record.

Functions

format_float_missing

Get the missing value sentinel for FORMAT float fields.

format_int_missing

Get the missing value sentinel for FORMAT integer fields.

get_format_tag_names

Get the list of FORMAT tag names present in a record.

record_clear_format

Clear (remove) a FORMAT field from a record.

record_clear_info

Clear an INFO field from a record.

record_format

Get a FORMAT field value from a record (per-sample).

record_info

Get an INFO field value from a record.

record_sample

Get sample data from a record for a single sample by name.

record_samples

Get sample data from a record for all samples or a subset.

record_set_format_float

Set a FORMAT float field on a record.

record_set_format_integer

Set a FORMAT integer field on a record.

record_set_format_string

Set a FORMAT string field on a record.

record_set_info_flag

Set an INFO flag value on a record.

record_set_info_float

Set an INFO float value on a record.

record_set_info_integer

Set an INFO integer value on a record.

record_set_info_string

Set an INFO string value on a record.

record_to_string

Format a record as a VCF line string.