Re: dmdtags 1.0.0: an accurate tag generator for D source code
On Fri, Aug 27, 2021 at 09:38:58PM +, Paul Backus via Digitalmars-d-announce wrote: > `dmdtags` is a tags file generator for D source code that uses the DMD > compiler frontend for accurate parsing. > > This release supports 100%-accurate parsing of arbitrary D code > (tested on DMD and Phobos sources), as well as the most commonly-used > command line options, `-R`, `-o`, and `-a`. The generated tags file > has been tested for compatibility with Vim and is compliant with the > [POSIX standard for `ctags`][posix], so any editor with `ctags` > support should be able to use it. This is AWESOME!!! Thanks a ton for this... I'll definitely be using this in the near future! [...] > [`universal-ctags`][uctags], the current most-popular and > best-maintained tags file generator, claims support for many > programming languages, including D. However, its D parser is not > well-maintained, and it often excludes large numbers of symbols from > its output due to parsing failures. > > Because `dmdtags` uses the DMD frontend for parsing, its results will > always be accurate and up-to-date. For pure D projects, it can be used > as a replacement for `universal-ctags`. For mixed-language projects, > it can be used together with other tag generators with the `--append` > option. Is there any hope of merging this back to upstream ctags? Regardless, this is awesome. T -- Long, long ago, the ancient Chinese invented a device that lets them see through walls. It was called the "window".
Re: SAOC 2021 Projects Summarized
On 8/30/21 5:47 AM, Mike Parker wrote: > Ahmet Sait KoC’ak Being a fellow Turkish, I am curios why his last name is spelled that way. Unless it was sepecially requested by him, I would use the following obviously correct spelling: Ahmet Sait Koçak Ali
dhtslib v0.12.0 (high-throughput sequencing library)
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. ;) https://github.com/blachlylab/dhtslib/ https://code.dlang.org/packages/dhtslib Once upon a time, BioD[1] 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.[2] 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! Kind regards James S Blachly, MD The Ohio State University [0] https://github.com/blachlylab/dhtslib/ https://code.dlang.org/packages/dhtslib [1] https://github.com/biod/BioD [2] 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!
Announcement and Request: Typesafe Coordinate Systems for High-Throughput Sequencing Applications
In another post, I've just announced our D-based high throughput sequencing library, dhtslib. One feature that is, AFAIK, novel in the field is leveraging the compiler's type system to enforce correctness regarding different genome/reference sequence coordinate systems. Clearly, the encoding of domain specific knowledge in a language's type system is nothing new, but it is surprising that this has not been done before in bioinformatics, and it is an idea that IMO is long overdue given the trainwreck of different coordinate systems in our field. You can find dhtslib's develop branch, with Typesafe Coordinates merged and ready to use, here: https://github.com/blachlylab/dhtslib/ **Now the request:** We've drafted a manuscript describing Typesafe Coordinates as a sort of low-key endorsement of the D language and our library package `dhtslib`. You can find the manuscript here: https://github.com/blachlylab/typesafe-coordinates/ We would be very grateful to those of you who would take the time to read the manuscript and post comments (publicly or privately), _especially if we have made any incorrect statements_ or our language regarding type systems is awkward or nonstandard. We did praise D, and gently criticized Rust and OCaml* somewhat as it appeared to me that they lacked the features required to implement Typesafe Coordinate Systems in as ergonomic a way as we could in D. However, being a true novice at both of these other languages there is the possibility that I've missed something significant, and that the Rust and OCaml implementations could be retooled to match the D implementation. I'd still be glad to hear it if that's the case. I plan to make a few minor cleanups and submit this to a preprint server as well as a scientific journal in the next week or so. Kind regards James S Blachly, MD The Ohio State University * as a side note, I actually find the OCaml code quite attractive in its terseness: `let j = cl_interval_of_ho (ob_interval_of_zb i)`
Re: SAOC 2021 Projects Summarized
On Wednesday, 1 September 2021 at 04:56:28 UTC, Ali Çehreli wrote: On 8/30/21 5:47 AM, Mike Parker wrote: > Ahmet Sait KoC’ak Being a fellow Turkish, I am curios why his last name is spelled that way. Unless it was sepecially requested by him, I would use the following obviously correct spelling: Ahmet Sait Koçak Ali That's how it was submitted in the application. I simply copy-pasted.
