HTS.cr

HTS.cr provides Crystal bindings for HTSlib that allow you to read and write file formats commonly used in genomics, such as SAM, BAM, VCF, and BCF.

Requirements

Crystal
HTSlib
- Ubuntu : apt install libhts-dev
- macOS : brew install htslib
- Any OS : Build from source code
- Make sure that pkg-config can detect htslib: pkg-config --libs htslib

Installation

Add hts to your shard.yml:

dependencies:
  hts:
    github: bio-cr/hts.cr
    branch: develop

Run shards install

Usage

Read SAM / BAM / CRAM

require "hts/bam"

HTS::Bam.open(bam_path) do |bam|
  bam.each do |r|
    tags = r.aux

    p name: r.qname,
      chrom: r.chrom,
      start: r.pos + 1,
      cigar: r.cigar.to_s,
      seq: r.seq,
      qual: r.qual_string,
      nm: tags.get_int("NM"),
      mc: tags.get_string("MC")
  end
end

Read VCF / BCF

require "hts/bcf"

HTS::Bcf.open(bcf_path) do |bcf|
  bcf.each do |r|
    p chrom: r.chrom,
      pos: r.pos + 1,
      id: r.id,
      qual: r.qual,
      filter: r.filter,
      ref: r.ref,
      alt: r.alt,
      info_dp: r.info.get_int("DP"),
      genotypes: r.format.get_string("GT")
  end
end

API Overview

High level API - Classes include Bam, Bcf, Tabix, Faidx, etc.
LibHTS - Native C bindings to HTSLib
For more information, please see API documentation.

 ┌──────────────────── HTS ────────────────────┐
 │                                             │
 │ ┌─ Bam ────────┬─ Bcf ───────┬─ Tabix ────┐ │
 │ │ SAM BAM CRAM │ VCF BCF     │ TABIX      │ │
 │ └──────────────┴─────────────┴────────────┘ │
 │                     ┌─LibHTS2───────────┐   │
 │ ┌─LibHTS────────────┤ Macro functions   ├─┐ │
 │ │ Native C bindings └───────────────────┘ │ │
 │ └─────────────────────────────────────────┘ │
 └─────────────────────────────────────────────┘

LibHTS2: Since methods cannot be added to Lib in the Crystal language, macro functions are implemented in the LibHTS2 module. This is different from Ruby-htslib.

Looking for flexibility?

The Crystal language is suited for creating efficient command-line tools. The Ruby language, on the other hand, is suited for exploratory analysis.

ruby-htslib

Contributing

:rocket: Feel free to fork it!

git clone https://github.com/bio-cr/hts.cr
cd hts.cr
crystal spec

Bug reports and pull requests are welcome.

Benchmark

https://github.com/brentp/vcf-bench

code: https://github.com/kojix2/vcf-bench/blob/kojix2/crystal-htslib/read.cr