ruby-htslib Interim report

ruby-htslib_Interim_report.md

ruby-htslib - High-throughput sequencing data manipulation for Ruby - Interim report

(Created by Google Translate)

2021-01-25 kojix2

Github: https://github.com/kojix2/ruby-htslib

Slack: https://sciruby.slack.com (Japanese)

Overview

Ruby-htslib is the Ruby bindings to HTSlib, a C library for processing high throughput sequencing (HTS) data. It will provide APIs to read and write file formats such as SAM/BAM and VCF/BCF.

In recent years, next-generation sequencing (NGS) technologies for reading DNA and RNA sequences have become popular in the life science field. We will provide a way to manipulate the HTS file formats from Ruby. We aim to improve the Ruby ecosystem in genomics.

Implementation

• Low level API

  • Added about 320 htslib functions to the HTS::FFI module.
  • Mainly regular expression replacement and manual additions.
  • Bit field is not supported.
  • Only few macros have been implemented.
  • Created an example to read a Bam file using low level API.

• High level API

  • Aim to implement hts-python/hts-nim compliant API.
    • https://github.com/quinlan-lab/hts-python
  • Not very advanced. I implemented a part of the Bam class and confirmed that it actually works.

Future plan

• Low level API

  • Improving reliability
    • Add tests little by little.
  • Support for bit fields, macro fuctions, constants, etc.
  • Automatic generation of the bindings
    • currently considering c2ffi.

• High level API

  • Currently working.

• Adding some advanced analysis workflow as an example.

Not-to-do

• Performance improvement.
• Integration with BioRuby API inside ruby-htslib
• Migration from FFI to Fiddle

Appendix

• Qiita article (japanese)