Skip to content

Latest commit

 

History

History
116 lines (83 loc) · 5.35 KB

README.md

File metadata and controls

116 lines (83 loc) · 5.35 KB
Raw

htsget-search

MIT licensed Build Status

Creates URL tickets for htsget-rs by processing bioinformatics files. It:

  • Takes a htsget query and produces htsget URL tickets.
  • Uses noodles to process files.

Overview

This crate is the primary mechanism by which htsget-rs interacts with, and processes bioinformatics files. It does this by using noodles to query files and their indices. This crate contains abstractions that remove commonalities between file formats. Together with file format specific code, this defines an interface that handles the core logic of a htsget request.

File structure

This crate is responsible for handling bioinformatics file data. It supports BAM, CRAM, VCF and BCF files. For htsget-rs to function, files need to be organised in the following way:

  • Each file format is paired with an index. All files must have specific extensions.
    • BAM: File must end with .bam; paired with BAI index, which must end with .bam.bai.
    • CRAM: File must end with .cram; paired with CRAI index, which must end with .cram.crai.
    • VCF: File must end with .vcf.gz; paired with TBI index, which must end with .vcf.gz.tbi.
    • BCF: File must end with .bcf; paired with CSI index, which must end with .bcf.csi.
  • VCF files are assumed to be BGZF compressed.
  • BGZF compressed files (BAM, CRAM, VCF) can optionally also have a GZ index to make byte ranges smaller.

As a library

This crate has the following features:

  • The HtsGet trait represents an entity that can resolve queries according to the htsget spec. The htsget trait comes with a basic model to represent components needed to perform a search: Query, Format, Class, Tags, Headers, Url, Response. HtsGetFromStorage is the struct which is used to process requests.

Feature flags

This crate has the following features:

  • s3-storage: used to enable S3Storage functionality.
  • url-storage: used to enable UrlStorage functionality.
  • experimental: used to enable experimental features that aren't necessarily part of the htsget spec, such as Crypt4GH support through C4GHStorage.

Minimising Byte Ranges

One challenge involved with implementing htsget is minimising the size of byte ranges returned in response tickets. Since htsget is used to reduce the amount of data a client needs to fetch by querying specific parts of a file, the data returned by htsget should ideally be as minimal as possible. This is done by reading the index file or the underlying target file, to determine the required byte ranges.

For BGZF files, GZI files are supported, which enable the smallest possible byte ranges.

BGZF file example

For BGZF compressed files, htsget-rs needs to return compressed byte positions. Also, after concatenating data from URL tickets, the resulting file must be valid. This means that byte ranges must start and finish on BGZF blocks, otherwise the concatenation would not result in a valid file. Index files (BAI, TBI, CSI) do not contain all the information required to produce minimal byte ranges. For example, consider this file:

  • There are 14 BGZF blocks positions using all available data in the corresponding index file (chunk start positions, chunk end positions, linear index positions, and metadata positions):
    • 4668, 256721, 499249, 555224, 627987, 824361, 977196, 1065952, 1350270, 1454565, 1590681, 1912645, 2060795 and 2112141.
  • Using just this data, the following query with:
    • referenceName=11, start=5015000, and end=5050000
  • Would produce these byte ranges:
    • bytes=0-4667
    • bytes=256721-1065951
  • However, an equally valid response, with smaller byte ranges is:
    • bytes=0-4667
    • bytes=256721-647345
    • bytes=824361-842100
    • bytes=977196-996014

To produce the smallest byte ranges, htsget-rs needs can search through GZI files and regular index files. It does not read data from the underlying target file.

Benchmarks

Since this crate is used to query file data, it is the most performance critical component of htsget-rs. Benchmarks, using Criterion.rs are written to test performance. Run benchmarks by executing:

cargo bench -p htsget-search --all-features

Alternatively if you are using cargo-criterion and want a machine-readable JSON output, run:

cargo criterion --bench search-benchmarks --message-format=json -- LIGHT 1> search-benchmarks.json

License

This project is licensed under the MIT license.