|Posted by James Blachly||PermalinkReply|
I'm delighted to finally post an official announcement of our package for high-throughput sequencing (HTS), also called Next-generation sequencing (NGS): `dhtslib`. It's not a very clever name, and we are working on a new one. ;)
Once upon a time, BioD was fairly active, but I am afraid D is not heavily used in bioinformatics and computational biology, especially in high-throughput (genome) sequencing applications when compared to its peers. However, our group (cancer genomics) has found D an ideal language which is easy to pick up for Python programmers and yet retains powerful features for C/C++ programmers.
`dhtslib` began as a thin wrapper over the ubiquitous, but very low-level and hard to use `htslib` C library (https://github.com/samtools/htslib/). We use `dhtslib` extensively in both public and private projects for computational biology, and over the years it has grown from simply a (huge) set of `extern (C)` definitions to a fully featured, RAII-enabled genome sequencing focused bioinformatics package. If you are working in this field, or know someone open to D who works in this field, I strongly encourage you to point them at `dhtslib`!
* `htslib` namespace with complete bindings to htslib
* `dhtslib` namespace with high level object-oriented interfaces, many using underlying htslib calls for high performance, but via convenient and idiomatic D including RAII, Forward ranges, etc.
* htslib-backed read/write of SAM/BAM/CRAM, VCF/BCF
* Readers for BED and GFF3/GTF (not part of htslib)
* FASTQ streamer
* CIGAR manipulations
The next version, v0.13.0, adds a novel feature "Typesafe Coordinates", which I'll post about separately in a moment!
James S Blachly, MD
The Ohio State University
 Here is a contemporary example of D used in high-throughput sequencing: DENTIST by Arne Ludwig at Max Planck institute
https://github.com/a-ludi/dentist -- if you know of more, please let me know!