Hacker News: bede

New comment by bede in "An update on recent Claude Code quality reports"

bede — Fri, 24 Apr 2026 10:43:45 +0000

I too would far rather bear a token cost than have my sessions rot silently beneath my feet. I usually have ~5 running CC sessions, some of which I may leave for a week or two of inactivity at a time.

New comment by bede in "Backblaze has stopped backing up OneDrive and Dropbox folders and maybe others"

bede — Tue, 14 Apr 2026 16:47:09 +0000

Thanks for publicising. I recently decided not to renew my Backblaze in favour of 'self hosting' encrypted backups outside the US. But I was horrified to learn that my git repos may not have been backed up, nor my Dropbox, whose subscription I also recently cancelled. Good riddance.

My experience using restic has been excellent so far, snapshots take 5 mins rather than 30 mins with backblaze's Mac client. I just hope I can trust it…

New comment by bede in "I put my whole life into a single database"

bede — Tue, 10 Mar 2026 14:27:20 +0000

> Probably obvious for many, but I didn't realize ACs don't transport any air into the room, but just moves it around

I had the same epiphany as you days after acquiring a CO2 monitor. Most people notice poor indoor air quality from proxies such as humidity and temperature. AC (without ventilation) eliminates these and tricks our senses very effectively, giving us cool and fresh feeling indoor spaces full of CO2 and devoid of oxygen.

New comment by bede in "How London cracked mobile phone coverage on the Underground"

bede — Sun, 18 Jan 2026 08:36:31 +0000

> There’s another distance limit at work here, and that is the speed of light. It takes milliseconds for the signal in your phone to reach the hotel above ground and be handed over to the mobile network.

It takes roughly 100us for light to travel 30km – Can you explain how the speed of light is relevant here?

New comment by bede in "OpenZL: An open source format-aware compression framework"

bede — Mon, 06 Oct 2025 22:55:36 +0000

For BAM this could be a good place to start: https://www.htslib.org/benchmarks/CRAM.html

Happy to discuss further

New comment by bede in "OpenZL: An open source format-aware compression framework"

bede — Mon, 06 Oct 2025 20:46:37 +0000

Author of [0] here. Congratulations and well done for resisting. Eager to try it!

Edit: Have you any specific advice for training a fasta compressor beyond that given in e.g. "Using OpenZL" (https://openzl.org/getting-started/using-openzl/)

New comment by bede in "Removing newlines in FASTA file increases ZSTD compression ratio by 10x"

bede — Tue, 16 Sep 2025 08:22:04 +0000

A Zstd maintainer clarified this: https://news.ycombinator.com/item?id=45251544

> Ultimately, Zstd is a byte-oriented compressor that doesn't understand the semantics of the data it compresses

New comment by bede in "Removing newlines in FASTA file increases ZSTD compression ratio by 10x"

bede — Tue, 16 Sep 2025 08:19:29 +0000

Fascinating, thank you.

New comment by bede in "Removing newlines in FASTA file increases ZSTD compression ratio by 10x"

bede — Mon, 15 Sep 2025 15:01:01 +0000

Thanks for reminding me to benchmark this!

New comment by bede in "Removing newlines in FASTA file increases ZSTD compression ratio by 10x"

bede — Mon, 15 Sep 2025 13:05:44 +0000

Yes, when doing anything intensive with lots of sequences it generally makes sense to liberate them from FASTA as early as possible and index them somehow. But as an interchange format FASTA seems quite sticky. I find the pervasiveness of fastq.gz particularly unfortunate with Gzip being as slow as it is.

> Took me a while to realize that Grace Blackwell refers to a person and not an Nvidia chip :)

I even confused myself about this while writing :-)

New comment by bede in "Removing newlines in FASTA file increases ZSTD compression ratio by 10x"

bede — Mon, 15 Sep 2025 12:45:18 +0000

BAM format is widely used but assemblies still tend to be generated and exchanged in FASTA text. BAM is quite a big spec and I think it's fair to say that none of the simpler binary equivalents to FASTA and FASTQ have caught on yet (XKCD competing standards etc.)

e.g. https://github.com/ArcInstitute/binseq

New comment by bede in "Removing newlines in FASTA file increases ZSTD compression ratio by 10x"

bede — Mon, 15 Sep 2025 12:22:47 +0000

Thank you for clarifying this – yes the non-semantic nature of these particular line breaks is a key detail I omitted.

New comment by bede in "Removing newlines in FASTA file increases ZSTD compression ratio by 10x"

bede — Mon, 15 Sep 2025 11:03:44 +0000

Exactly. The line breaks break the runs of otherwise identical bits in identical sequences. Unless two identical subsequences are exactly in phase with respect to their line breaks, the hashes used for long range matching are different for otherwise identical subsequences.

New comment by bede in "Removing newlines in FASTA file increases ZSTD compression ratio by 10x"

bede — Mon, 15 Sep 2025 10:58:41 +0000

Yes I'd expect a dict-based approach to do better here. That's probably how it should be done. But --long is compelling for me because using it requires almost no effort, it's still very fast, and yet it can dramatically improve compression ratio.

New comment by bede in "Removing newlines in FASTA file increases ZSTD compression ratio by 10x"

bede — Sat, 13 Sep 2025 10:26:39 +0000

Yes, it sounds like 7-Zip/LZMA can do this using custom filters, among other more exotic (and slow) statistical compression approaches.

Removing newlines in FASTA file increases ZSTD compression ratio by 10x

bede — Fri, 12 Sep 2025 16:25:11 +0000

Article URL: https://log.bede.im/2025/09/12/zstandard-long-range-genomes.html

Comments URL: https://news.ycombinator.com/item?id=45223827

Points: 279

# Comments: 113

New comment by bede in "QuakeNotch: Quake Terminal on your MacBook's notch"

bede — Sun, 20 Jul 2025 20:21:17 +0000

Just watched my iPhone 15 battery drop 2% scrolling for <60s

New comment by bede in "FP8 is ~100 tflops faster when the kernel name has "cutlass" in it"

bede — Fri, 11 Jul 2025 11:15:15 +0000

Thank you, perhaps the parent can be edited to use this URL instead

New comment by bede in "Why Android can't use CDC Ethernet (2023)"

bede — Mon, 09 Jun 2025 05:52:32 +0000

I assumed that the article must be about a frustrated CDC employee just trying to get internet access at work.

New comment by bede in "Spotify will reduce total headcount by approximately 17%"

bede — Tue, 05 Dec 2023 12:16:57 +0000

I also lost faith in certain scientists (and many more politicians) during the pandemic. But be wary of generalising about a such a large and interdisciplinary group of people. Voices amplified by the media (indeed like Robert Malone on Rogan's podcast) often grossly misrepresent scientific consensus.