John Marshall
@johnm.bsky.social
Bioinformatics tools developer at Australia’s Centre for Population Genomics. Will edit GA4GH specifications for food. New Zealander fairly recently returned after a decade in the U.K.
Reasons to test on obscure platforms, part 87: I don't test pysam on 32-bit i386, but Debian do. Four years ago they patched their package to disable a `samtools calmd` test that fails on i386.
Turns out to be due to pysamised calmd writing to a garbage filename instead of the specified file. 🧵 1/2
Turns out to be due to pysamised calmd writing to a garbage filename instead of the specified file. 🧵 1/2
November 17, 2025 at 7:38 AM
Reasons to test on obscure platforms, part 87: I don't test pysam on 32-bit i386, but Debian do. Four years ago they patched their package to disable a `samtools calmd` test that fails on i386.
Turns out to be due to pysamised calmd writing to a garbage filename instead of the specified file. 🧵 1/2
Turns out to be due to pysamised calmd writing to a garbage filename instead of the specified file. 🧵 1/2
Reposted by John Marshall
Doctor says, 'Dont worry, parser design is simple. Great programmer Kate Compton has written the parser you seek’
November 16, 2025 at 2:44 PM
Doctor says, 'Dont worry, parser design is simple. Great programmer Kate Compton has written the parser you seek’
Reposted by John Marshall
When you think the cloud looks low because of the horizon but then: Sky Tower
November 6, 2025 at 5:32 PM
When you think the cloud looks low because of the horizon but then: Sky Tower
Reposted by John Marshall
VG will soon start adding headers to the GAF files it generates. The specifics are still uncertain, but if you maintain a GAF parser, it may be a good idea to skip lines starting with "@". Here is a draft specification for the vg flavor of GAF.
github.com
October 31, 2025 at 3:27 AM
VG will soon start adding headers to the GAF files it generates. The specifics are still uncertain, but if you maintain a GAF parser, it may be a good idea to skip lines starting with "@". Here is a draft specification for the vg flavor of GAF.
Reposted by John Marshall
October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Index zone by BenLangmead
benlangmead.github.io
October 30, 2025 at 6:11 PM
October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
BTW @jbonfield.bsky.social someone edited Wikipedia's CRAM page a while back to add the unreferenced claim that it stands for Compressed Reference-oriented Alignment Map. Citation needed! As I recall, it officially doesn't stand for anything but is merely reminiscent of compression and references…
CRAM (file format): Difference between revisions - Wikipedia
en.wikipedia.org
October 29, 2025 at 8:15 PM
BTW @jbonfield.bsky.social someone edited Wikipedia's CRAM page a while back to add the unreferenced claim that it stands for Compressed Reference-oriented Alignment Map. Citation needed! As I recall, it officially doesn't stand for anything but is merely reminiscent of compression and references…
Reposted by John Marshall
Okay, for the folks who asked: here's the majority AI view, writing up the reasonable, thoughtful view on AI that the vast majority of people in tech hold, that gets overshadowed by the bluster and hype of the tycoons trying to shill their nonsense. anildash.com/2025/10/17/t... Please share!
The Majority AI View - Anil Dash
A blog about making culture. Since 1999.
anildash.com
October 17, 2025 at 7:29 PM
Okay, for the folks who asked: here's the majority AI view, writing up the reasonable, thoughtful view on AI that the vast majority of people in tech hold, that gets overshadowed by the bluster and hype of the tycoons trying to shill their nonsense. anildash.com/2025/10/17/t... Please share!
Hard to believe how much damage SemVer has done to people’s brains.
October 10, 2025 at 1:49 PM
Hard to believe how much damage SemVer has done to people’s brains.
A file format specification (hopefully!) spells out what's valid and invalid. Implementations have choices for how they deal with variously out-of-spec files:
• reject with error message
• reject mysteriously
• accept as an extension, with a well-defined meaning
• accept mysteriously
• crash
• …
• reject with error message
• reject mysteriously
• accept as an extension, with a well-defined meaning
• accept mysteriously
• crash
• …
October 10, 2025 at 11:58 AM
A file format specification (hopefully!) spells out what's valid and invalid. Implementations have choices for how they deal with variously out-of-spec files:
• reject with error message
• reject mysteriously
• accept as an extension, with a well-defined meaning
• accept mysteriously
• crash
• …
• reject with error message
• reject mysteriously
• accept as an extension, with a well-defined meaning
• accept mysteriously
• crash
• …
Reposted by John Marshall
If you ever submit on bills, read legislation on legislation.govt.nz or use its RSS feeds to keep track of new bills, please tell the Parliamentary Counsel Office to make sure the new site keeps RSS. We shouldn't need to have an API key.
Fill in the survey: www.legislation.govt.nz/news.aspx#rs...
Fill in the survey: www.legislation.govt.nz/news.aspx#rs...
I'm a bit sad to see the PCO is going to end the Legislation.govt.nz RSS feeds, replacing them with an authenticated API.
www.legislation.govt.nz/news.aspx#rs...
APIs are great, but RSS is widely supported and unauthenticated - a much lower barrier to use than having to develop a custom API client.
www.legislation.govt.nz/news.aspx#rs...
APIs are great, but RSS is widely supported and unauthenticated - a much lower barrier to use than having to develop a custom API client.
October 1, 2025 at 10:50 PM
If you ever submit on bills, read legislation on legislation.govt.nz or use its RSS feeds to keep track of new bills, please tell the Parliamentary Counsel Office to make sure the new site keeps RSS. We shouldn't need to have an API key.
Fill in the survey: www.legislation.govt.nz/news.aspx#rs...
Fill in the survey: www.legislation.govt.nz/news.aspx#rs...
Reposted by John Marshall
Genomics for Aotearoa New Zealand - Public Webinar 14th October
@nicrawlencenz.bsky.social will be giving a public webinar on myth busting de-exctinction.
The webinar will run from 11:00 am to 12:30 pm including time for questions.
Please boost this to help reach a broad audience. 🙏
@nicrawlencenz.bsky.social will be giving a public webinar on myth busting de-exctinction.
The webinar will run from 11:00 am to 12:30 pm including time for questions.
Please boost this to help reach a broad audience. 🙏
Public Webinar - Myth Busting De-Exctinction - Genomics for Aotearoa New Zealand
Myth busting de-extinction to sort fact from fiction. In this public talk, Associate Professor Nic Rawlence will provide a New Zealand perspective around claims of de-extinction.
genomics.nz
October 1, 2025 at 2:37 AM
Genomics for Aotearoa New Zealand - Public Webinar 14th October
@nicrawlencenz.bsky.social will be giving a public webinar on myth busting de-exctinction.
The webinar will run from 11:00 am to 12:30 pm including time for questions.
Please boost this to help reach a broad audience. 🙏
@nicrawlencenz.bsky.social will be giving a public webinar on myth busting de-exctinction.
The webinar will run from 11:00 am to 12:30 pm including time for questions.
Please boost this to help reach a broad audience. 🙏
Reposted by John Marshall
Wonderful news. A salutary reminder of the absolute benefits of scientific progress, and the absolute evil of conspiracist bollocks.
Huntington's disease successfully treated for first time www.bbc.com/news/article...
Huntington's disease successfully treated for first time www.bbc.com/news/article...
Huntington's disease successfully treated for first time
One of the most devastating diseases finally has a treatment that could transform lives, tearful doctors tell BBC
www.bbc.com
September 24, 2025 at 12:20 PM
Wonderful news. A salutary reminder of the absolute benefits of scientific progress, and the absolute evil of conspiracist bollocks.
Huntington's disease successfully treated for first time www.bbc.com/news/article...
Huntington's disease successfully treated for first time www.bbc.com/news/article...
Reposted by John Marshall
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.
A modest proposal: Unsuccessful InternetNZ electoral candidates should post to NetHub only in proportion to the percentage of votes they received.
September 16, 2025 at 9:16 PM
A modest proposal: Unsuccessful InternetNZ electoral candidates should post to NetHub only in proportion to the percentage of votes they received.
Reposted by John Marshall
Is there anyone here at one of the universities in Wellington, NZ, who would want to host me to give a talk around November 10th?
September 15, 2025 at 11:34 PM
Is there anyone here at one of the universities in Wellington, NZ, who would want to host me to give a talk around November 10th?
Reposted by John Marshall
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
Submitted on the Electoral Amendment Bill with 3 minutes to spare! Was reminded at the last minute that this bill has another go at disenfranchising prisoners (as has been shot down in the courts repeatedly)… so forgot to say that the deadline change likely won't speed up getting results anyway. 🫠
September 11, 2025 at 1:08 AM
Submitted on the Electoral Amendment Bill with 3 minutes to spare! Was reminded at the last minute that this bill has another go at disenfranchising prisoners (as has been shot down in the courts repeatedly)… so forgot to say that the deadline change likely won't speed up getting results anyway. 🫠
Reposted by John Marshall
Watching talks on CMake while working out. I truly appreciate the work folks put in to keep trying to explain the "modern" CMake way. But in every case, I quit watching in disgust. CMake is an example of how to do everything wrong, and when cutting your losses is the best course of action.
September 10, 2025 at 3:07 AM
Watching talks on CMake while working out. I truly appreciate the work folks put in to keep trying to explain the "modern" CMake way. But in every case, I quit watching in disgust. CMake is an example of how to do everything wrong, and when cutting your losses is the best course of action.
Naively assumed that with the #InternetNZ election over, we wouldn't be hearing from the spaceman again. But I haven't been back there for long; perhaps he's been invested in spamming them with the same opinion over and over for longer than I realise…
September 9, 2025 at 1:16 AM
Naively assumed that with the #InternetNZ election over, we wouldn't be hearing from the spaceman again. But I haven't been back there for long; perhaps he's been invested in spamming them with the same opinion over and over for longer than I realise…
Reposted by John Marshall
We have endless browser and html extensions, but it maddens me that no one made a common ISP-level protocol to query datacaps that returns:
- Monthly quota (if any)
- Current usage (bytes used)
- Reset date/time
- Throttling policy (what happens when you hit the cap)
- Monthly quota (if any)
- Current usage (bytes used)
- Reset date/time
- Throttling policy (what happens when you hit the cap)
September 3, 2025 at 8:20 PM
We have endless browser and html extensions, but it maddens me that no one made a common ISP-level protocol to query datacaps that returns:
- Monthly quota (if any)
- Current usage (bytes used)
- Reset date/time
- Throttling policy (what happens when you hit the cap)
- Monthly quota (if any)
- Current usage (bytes used)
- Reset date/time
- Throttling policy (what happens when you hit the cap)
Reposted by John Marshall
Americans, I am once again begging you to consider that sometimes people aren't in America and may be discussing their own bad governments on the niche microblogging website. Please. I am begging.
September 3, 2025 at 3:49 PM
Americans, I am once again begging you to consider that sometimes people aren't in America and may be discussing their own bad governments on the niche microblogging website. Please. I am begging.
Pleased that Debian 13 "trixie" has now been released. Prior to this, by my reckoning Debian was the only remaining major platform that did not package Cython 3.x in its system package repositories.
With Cython 3 available everywhere, pysam can reasonably require it and simplify a few things.
With Cython 3 available everywhere, pysam can reasonably require it and simplify a few things.
August 10, 2025 at 12:12 AM
Pleased that Debian 13 "trixie" has now been released. Prior to this, by my reckoning Debian was the only remaining major platform that did not package Cython 3.x in its system package repositories.
With Cython 3 available everywhere, pysam can reasonably require it and simplify a few things.
With Cython 3 available everywhere, pysam can reasonably require it and simplify a few things.
“Why are you so mindbogglingly pedantic about not using identifiers in the compiler's reserved namespace, John?”
(Not sure how the reporter has managed to get the Linux kernel version of <ctype.h> though. Or some other header that similarly defines _P.)
(Not sure how the reporter has managed to get the Linux kernel version of <ctype.h> though. Or some other header that similarly defines _P.)
Makefile bam_consensus.o Error · Issue #2248 · samtools/samtools
Please help me ~~~~ Samtools (v.1.22/v.1.22.1) installation failed. An error occurred while compiling the 'bam_consensus.o' file during the make process. The error appears as follows: "bam_consensu...
github.com
August 8, 2025 at 12:32 PM
“Why are you so mindbogglingly pedantic about not using identifiers in the compiler's reserved namespace, John?”
(Not sure how the reporter has managed to get the Linux kernel version of <ctype.h> though. Or some other header that similarly defines _P.)
(Not sure how the reporter has managed to get the Linux kernel version of <ctype.h> though. Or some other header that similarly defines _P.)
You can lead an open-source maintainer to water (provide a minimal test file exhibiting your bug, already named according to the style of their existing test files), but you can't make them drink (incorporate the new test case into their test suite).
August 6, 2025 at 11:40 AM
You can lead an open-source maintainer to water (provide a minimal test file exhibiting your bug, already named according to the style of their existing test files), but you can't make them drink (incorporate the new test case into their test suite).
If someone wanted to pay me to give bioinformatics format specifications the time and attention they deserve, I would be very pleased.
Otherwise, the work occurs as academic generosity in odd hours by people who are already oversubscribed in their day jobs.
Otherwise, the work occurs as academic generosity in odd hours by people who are already oversubscribed in their day jobs.
I think that having a *well-specified* format is the most important part. Writing a binary parser is no harder than writing a text parser, as long as I know exactly what it is that I'm parsing (often it's much easier even). I agree regarding "official" parsers. One way to achieve that may be 1/2
August 5, 2025 at 11:24 PM
If someone wanted to pay me to give bioinformatics format specifications the time and attention they deserve, I would be very pleased.
Otherwise, the work occurs as academic generosity in odd hours by people who are already oversubscribed in their day jobs.
Otherwise, the work occurs as academic generosity in odd hours by people who are already oversubscribed in their day jobs.