Module tbx

Module for working with tabix-indexed text files.

This module allows to read tabix-indexed text files (such as BED) in a convenient but in a line-based (and thus format-agnostic way). For accessing tabix-inxed VCF files, using the bcf module is probably a better choice as this module gives you lines from the text files which you then have to take care of parsing.

In general, for reading tabix-indexed files, first to open the file by creating a tbx::Reader objects, possibly translate the chromosome name to its numeric ID in the file, fetch the region of interest using fetch(), and finally iterate over the records using records().

Examples

use rust_htslib::tbx::{self, Read};

// Create a tabix reader for reading a tabix-indexed BED file.
let path_bed = "file.bed.gz";
let mut tbx_reader = tbx::Reader::from_path(&path_bed)
    .expect(&format!("Could not open {}", path_bed));

// Resolve chromosome name to numeric ID.
let tid = match tbx_reader.tid("chr1") {
    Ok(tid) => tid,
    Err(_) => panic!("Could not resolve 'chr1' to contig ID"),
};

// Set region to fetch.
tbx_reader
    .fetch(tid, 0, 100_000)
    .expect("Could not seek to chr1:1-100,000");

// Read through all records in region.
for record in tbx_reader.records() {
    // ... actually do some work
}

Structs

• Reader
  A Tabix file reader.
• Records
  Iterator over the lines of a tabix file.

Traits

• Read
  A trait for a Tabix reader with a read method.