James Bonfield
@jbonfield.bsky.social
Walker, archer, and volunteer woodland warden by weekend, and bioinformatics software engineer and general geek by weekday.
My favourite prime is 15551, my favourite colour is, obviously, octarine, and I love nothing more than being immersed in nature.
My favourite prime is 15551, my favourite colour is, obviously, octarine, and I love nothing more than being immersed in nature.
Reposted by James Bonfield
I am delighted to announce the release of my latest project:
Fully documented source code for The Sentinel, Geoff Crammond’s 1986 masterpiece.
Here’s the repository; deep dives coming soon.
See thread for details.
1/9
github.com/markmoxon/th...
#retrocomputing #retrogaming #bbcmicro #c64 #8bit
Fully documented source code for The Sentinel, Geoff Crammond’s 1986 masterpiece.
Here’s the repository; deep dives coming soon.
See thread for details.
1/9
github.com/markmoxon/th...
#retrocomputing #retrogaming #bbcmicro #c64 #8bit
GitHub - markmoxon/the-sentinel-source-code-bbc-micro: Fully documented and annotated source code for The Sentinel on the BBC Micro
Fully documented and annotated source code for The Sentinel on the BBC Micro - markmoxon/the-sentinel-source-code-bbc-micro
github.com
January 2, 2026 at 4:29 PM
I am delighted to announce the release of my latest project:
Fully documented source code for The Sentinel, Geoff Crammond’s 1986 masterpiece.
Here’s the repository; deep dives coming soon.
See thread for details.
1/9
github.com/markmoxon/th...
#retrocomputing #retrogaming #bbcmicro #c64 #8bit
Fully documented source code for The Sentinel, Geoff Crammond’s 1986 masterpiece.
Here’s the repository; deep dives coming soon.
See thread for details.
1/9
github.com/markmoxon/th...
#retrocomputing #retrogaming #bbcmicro #c64 #8bit
Happy New Year Kavey
December 31, 2025 at 5:52 PM
Happy New Year Kavey
Reposted by James Bonfield
How about we get rid of political donors all together?
Ban the wealthy elite from owning UK politicians.
Ban the wealthy elite from owning UK politicians.
UK ministers urged to cap political donations to ‘rebuild voter confidence’
Letter from 19 organisations says a cap would help to protect democracy, weeks after £9m donation to Reform UK
www.theguardian.com
December 26, 2025 at 10:00 AM
How about we get rid of political donors all together?
Ban the wealthy elite from owning UK politicians.
Ban the wealthy elite from owning UK politicians.
Reposted by James Bonfield
@funranium.bsky.social
Always be stealing Dune memes!
Always be stealing Dune memes!
December 24, 2025 at 3:42 PM
@funranium.bsky.social
Always be stealing Dune memes!
Always be stealing Dune memes!
SAMtools / HTSLib / BCFTools 1.23 has been released. See the releasenotes on GitHub and www.htslib.org for details.
Samtools
Samtools
www.htslib.org
December 16, 2025 at 3:33 PM
SAMtools / HTSLib / BCFTools 1.23 has been released. See the releasenotes on GitHub and www.htslib.org for details.
The usual process ofbuilding modern C++ packages from GitHub...
Step 1: download and build yet another new version of cmake.
Bah Humbug. (I tried edited it and no, it did indeed need some new feature. Sigh) I miss the old ways.
Step 1: download and build yet another new version of cmake.
Bah Humbug. (I tried edited it and no, it did indeed need some new feature. Sigh) I miss the old ways.
November 25, 2025 at 4:16 PM
The usual process ofbuilding modern C++ packages from GitHub...
Step 1: download and build yet another new version of cmake.
Bah Humbug. (I tried edited it and no, it did indeed need some new feature. Sigh) I miss the old ways.
Step 1: download and build yet another new version of cmake.
Bah Humbug. (I tried edited it and no, it did indeed need some new feature. Sigh) I miss the old ways.
Reposted by James Bonfield
Never forget: At breakneck speed we are leaving the stable Holocene climate in which human society developed and thrived. Weather extremes are outside historical experience. Sea-level rise is accelerating. Dangerous tipping points are ahead.
Graph: ed-hawkins.github.io/climate-visu...
Graph: ed-hawkins.github.io/climate-visu...
November 13, 2025 at 11:52 AM
Never forget: At breakneck speed we are leaving the stable Holocene climate in which human society developed and thrived. Weather extremes are outside historical experience. Sea-level rise is accelerating. Dangerous tipping points are ahead.
Graph: ed-hawkins.github.io/climate-visu...
Graph: ed-hawkins.github.io/climate-visu...
Spot on with printers though. Satanic devices, and clearly the subject of Rage Against The Machine.
November 23, 2025 at 8:39 AM
Spot on with printers though. Satanic devices, and clearly the subject of Rage Against The Machine.
A feeling of dirtiness, a sense of horror, verging on revulsion. So maybe it's a perfect fit for VCF? 🤣
My gut feeling is we'd be better just having a JSON equivalent to VCF than JSON inside VCF. (Eg if we wanted JSON, then the whole of info should be json, not just each element.)
My gut feeling is we'd be better just having a JSON equivalent to VCF than JSON inside VCF. (Eg if we wanted JSON, then the whole of info should be json, not just each element.)
November 7, 2025 at 8:29 AM
A feeling of dirtiness, a sense of horror, verging on revulsion. So maybe it's a perfect fit for VCF? 🤣
My gut feeling is we'd be better just having a JSON equivalent to VCF than JSON inside VCF. (Eg if we wanted JSON, then the whole of info should be json, not just each element.)
My gut feeling is we'd be better just having a JSON equivalent to VCF than JSON inside VCF. (Eg if we wanted JSON, then the whole of info should be json, not just each element.)
I hear you wish -S. It's not so much that it's not needed, it doesn't harm, but that it's typically indicative of out of date information still doing the rounds/
My pet peeve is "samtools view -b foo.sam > foo.bam" instead of "-o". It causes lots of confusion with nohup and similar.
My pet peeve is "samtools view -b foo.sam > foo.bam" instead of "-o". It causes lots of confusion with nohup and similar.
October 30, 2025 at 1:44 PM
I hear you wish -S. It's not so much that it's not needed, it doesn't harm, but that it's typically indicative of out of date information still doing the rounds/
My pet peeve is "samtools view -b foo.sam > foo.bam" instead of "-o". It causes lots of confusion with nohup and similar.
My pet peeve is "samtools view -b foo.sam > foo.bam" instead of "-o". It causes lots of confusion with nohup and similar.
I've heard that before too, but the naming of it predates my involvement so I've no idea if it stood for anything. It's plausible, but *shrug*.
October 30, 2025 at 8:12 AM
I've heard that before too, but the naming of it predates my involvement so I've no idea if it stood for anything. It's plausible, but *shrug*.
It's curious to see grokipedia is up and has samtools, SAM and BAM pages all with a flurry of edits. Oddly, most of those edits are correcting minor edits in the Wikipedia pages it based its content on (presumably via some AI rewriting tool).
A shame the originals weren't edited too.
A shame the originals weren't edited too.
October 29, 2025 at 7:54 PM
It's curious to see grokipedia is up and has samtools, SAM and BAM pages all with a flurry of edits. Oddly, most of those edits are correcting minor edits in the Wikipedia pages it based its content on (presumably via some AI rewriting tool).
A shame the originals weren't edited too.
A shame the originals weren't edited too.
Reposted by James Bonfield
The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...
Efficient and accurate search in petabase-scale sequence repositories - Nature
MetaGraph enables scalable indexing of large sets of DNA, RNA or protein sequences using annotated de Bruijn graphs.
www.nature.com
October 9, 2025 at 2:40 PM
The Metagraph paper is out in Nature; it showed up in my feeds today! Congratulations to Mikhail Karasikov, @gxxxr.bsky.social, @akkah21.bsky.social and all of the other authors (whom I'd love to follow on Bluesky if I can find you ;P) www.nature.com/articles/s41...
You can't out reform Reform. They're loony conspiracy theory nutters - you shouldn't *want* to woo them!
We need parties that accept why the economy has tanked and will take steps to fix it. Leaving the ECM - Common Market - was the dumbiest idea ever (regardless of how you voted on Brexit).
We need parties that accept why the economy has tanked and will take steps to fix it. Leaving the ECM - Common Market - was the dumbiest idea ever (regardless of how you voted on Brexit).
October 9, 2025 at 4:47 PM
You can't out reform Reform. They're loony conspiracy theory nutters - you shouldn't *want* to woo them!
We need parties that accept why the economy has tanked and will take steps to fix it. Leaving the ECM - Common Market - was the dumbiest idea ever (regardless of how you voted on Brexit).
We need parties that accept why the economy has tanked and will take steps to fix it. Leaving the ECM - Common Market - was the dumbiest idea ever (regardless of how you voted on Brexit).
Reposted by James Bonfield
"OpenZL is our answer to the tension between the performance of format-specific compressors and the maintenance simplicity of a single executable binary."
engineering.fb.com/2025/10/06/d...
engineering.fb.com/2025/10/06/d...
October 6, 2025 at 8:58 PM
"OpenZL is our answer to the tension between the performance of format-specific compressors and the maintenance simplicity of a single executable binary."
engineering.fb.com/2025/10/06/d...
engineering.fb.com/2025/10/06/d...
Reposted by James Bonfield
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
A complete diploid human genome benchmark for personalized genomics
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and ...
www.biorxiv.org
September 22, 2025 at 5:01 PM
Delighted to finally announce a preprint describing the Q100 project! “A complete diploid human genome benchmark for personalized genomics” For which we finished HG002 to near-perfect accuracy: www.biorxiv.org/content/10.1... 🧵[1/14]
Note: OLD POST! (2023), but I just noticed it.
While it's nice to see comparisons, why compare an (at the time) 2 year old GATK against a 5 year old bcftools?
Since then both have come on a lot. It'd be interesting to see new independent comparisons. (Neither can hold up to deepvariant now.)
While it's nice to see comparisons, why compare an (at the time) 2 year old GATK against a 5 year old bcftools?
Since then both have come on a lot. It'd be interesting to see new independent comparisons. (Neither can hold up to deepvariant now.)
Important comparison of Bcftools and GTK in simulated Drosophila genomes: "by benchmark analyses with a simulated insect population...Bcftools mpileup performs better than GATK HaplotypeCaller in terms of recovery rate and accuracy regardless of mapping software."
The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species...
Scientific Reports - The evaluation of Bcftools mpileup and GATK HaplotypeCaller for variant calling in non-human species
www.nature.com
September 18, 2025 at 8:58 PM
Note: OLD POST! (2023), but I just noticed it.
While it's nice to see comparisons, why compare an (at the time) 2 year old GATK against a 5 year old bcftools?
Since then both have come on a lot. It'd be interesting to see new independent comparisons. (Neither can hold up to deepvariant now.)
While it's nice to see comparisons, why compare an (at the time) 2 year old GATK against a 5 year old bcftools?
Since then both have come on a lot. It'd be interesting to see new independent comparisons. (Neither can hold up to deepvariant now.)
I noted in their presentation they said that samtools mpileup didn't work. I think they're a bit out of date. Bcftools mpileup --poly-mqual can handle the qualities in homopolymers, plus other newer -X profiles.
I haven't tuned it yet though for SBX, but think it'll be OK in general. (To try!)
I haven't tuned it yet though for SBX, but think it'll be OK in general. (To try!)
September 18, 2025 at 8:47 PM
I noted in their presentation they said that samtools mpileup didn't work. I think they're a bit out of date. Bcftools mpileup --poly-mqual can handle the qualities in homopolymers, plus other newer -X profiles.
I haven't tuned it yet though for SBX, but think it'll be OK in general. (To try!)
I haven't tuned it yet though for SBX, but think it'll be OK in general. (To try!)
Reposted by James Bonfield
I'm sorry, worldwide, irrevocable, non-exclusive, transferable permission to my voice and likeness? For what now? In any manner for any purpose???
This is in academia/.edu's new ToS, which you're prompted to agree to on login. Anyway I'll be jumping ship. You can find my stuff at hcommons.org.
This is in academia/.edu's new ToS, which you're prompted to agree to on login. Anyway I'll be jumping ship. You can find my stuff at hcommons.org.
September 17, 2025 at 5:16 PM
I'm sorry, worldwide, irrevocable, non-exclusive, transferable permission to my voice and likeness? For what now? In any manner for any purpose???
This is in academia/.edu's new ToS, which you're prompted to agree to on login. Anyway I'll be jumping ship. You can find my stuff at hcommons.org.
This is in academia/.edu's new ToS, which you're prompted to agree to on login. Anyway I'll be jumping ship. You can find my stuff at hcommons.org.
Instagram is like facebork but even more annoying. I looked and I can't even find the equivalent post for you over there. It's just a hateful platform. Probably OK for doom scrolling on a phone, but that's about it.
September 16, 2025 at 8:01 AM
Instagram is like facebork but even more annoying. I looked and I can't even find the equivalent post for you over there. It's just a hateful platform. Probably OK for doom scrolling on a phone, but that's about it.
We ought to update htslib.org with more precise recipes, especially for things like conda where we know A) people make mistakes, often and B) it's used A LOT. We may be able to point to something like biocontainers too (or roll our own, but I'd rather not).
It's rarely built from source it seems.
It's rarely built from source it seems.
Samtools
Samtools
htslib.org
September 15, 2025 at 1:58 PM
We ought to update htslib.org with more precise recipes, especially for things like conda where we know A) people make mistakes, often and B) it's used A LOT. We may be able to point to something like biocontainers too (or roll our own, but I'd rather not).
It's rarely built from source it seems.
It's rarely built from source it seems.
Even more prolific is looking at their WhatsApp number from the minimap2 fake site, and associated email. So so many fake sites. Scary
(See 447950904740 phone number, and emmawatsofficial54 partial email search results).
(See 447950904740 phone number, and emmawatsofficial54 partial email search results).
September 15, 2025 at 9:06 AM
Even more prolific is looking at their WhatsApp number from the minimap2 fake site, and associated email. So so many fake sites. Scary
(See 447950904740 phone number, and emmawatsofficial54 partial email search results).
(See 447950904740 phone number, and emmawatsofficial54 partial email search results).
A google for the support phone number shows how many other phishing sites they have.
www.google.com/search?clien...
Most likely their "support" offering involves getting you to install some trojan.
www.google.com/search?clien...
Most likely their "support" offering involves getting you to install some trojan.
Google Search
www.google.com
September 15, 2025 at 8:53 AM
A google for the support phone number shows how many other phishing sites they have.
www.google.com/search?clien...
Most likely their "support" offering involves getting you to install some trojan.
www.google.com/search?clien...
Most likely their "support" offering involves getting you to install some trojan.
Reposted by James Bonfield
minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...
github.com/lh3/minimap2...
Phishing site : minimap2.com · Issue #1316 · lh3/minimap2
Not sure how to label this one, but I have come across a website minimap2.com which appears to be AI generated but is serving it's own copy of the Github repository. If you search the address or em...
github.com
September 9, 2025 at 3:40 PM
minimap2.com is potentially a phishing site. Please don't use anything from that website.
github.com/lh3/minimap2...
github.com/lh3/minimap2...