Software Engineer. Retro Computing. Genetic Genealogist. Fitness Enthusiast. TTRPG Gamer. Living the in the American Midwest.https://bsky.app/profile/jameskane.bloghttps://bsky.app/profile/jameskane.blog/post/3metbgtdxj22jWorking on a rewrite of bwa-mem2 in #Swift 6 with a Metal acceleration path on Apple Silicon. Using the techniques from "Accelerating BWA-MEM Read Mapping on GPUs". hps://dl.acm.org/doi/10.1145/3577193.3593703 Early benches show 4x faster than bwa-mem2 with NEON patching with 1/3 RAM usage!14 Feb 2026 14:50 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3metbgtdxj22jhttps://bsky.app/profile/jameskane.blog/post/3mek473y4cs22After no success in finding a complete Swift binding for htslib for another project I've been planning, I had Claude whip one up. The code is reasonable so it's on Github: https://github.com/JamesKane/swift-htslib Expect changes as I find and fix the clanker's bugs and omissions.10 Feb 2026 23:23 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mek473y4cs22https://bsky.app/profile/jameskane.blog/post/3me5tew3v4c2sOne of these years I will not take a layoff from running for 2 months after race season, but this was not that year. 45 minutes of absolute destruction on the treadmill in the books.06 Feb 2026 02:13 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3me5tew3v4c2shttps://bsky.app/profile/jameskane.blog/post/3me4qmohrxk2gAdded a forked version of bwa-mem2 to my GitHub page, which compiles on ARM with NEON. Mostly leveraging sse2neon, but also some optimizations on top. https://github.com/JamesKane/bwa-mem2 Timings done with chm13v2.0 as the reference for 2,000,000 150 base pair reads on Apple Silicon.05 Feb 2026 15:51 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3me4qmohrxk2ghttps://bsky.app/profile/jameskane.blog/post/3mcuv4kpa2s2xNew SBC day. On paper the 32GB OrangePi 6 Plus should be pretty capable. I will need to setup and do some benchmarks after work tonight.20 Jan 2026 19:25 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mcuv4kpa2s2xhttps://bsky.app/profile/jameskane.blog/post/3mamdwd2h5k2nResurrecting an old project is always interesting to see how much your style and habits have evolved. Trying to get this minimal OS from the PowerPC era running on a RISC-V dev board is coming along. Almost enough POSIX here to attempt the Clang port.22 Dec 2025 23:06 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mamdwd2h5k2nhttps://bsky.app/profile/jameskane.blog/post/3mab6qansrc2lPlaying with a new UI in the Alpha version of the Navigator. We'll see if the analysis is able to pick-up that Illumina iSeq result is really an FGC Y Elite.18 Dec 2025 12:33 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3mab6qansrc2lhttps://bsky.app/profile/jameskane.blog/post/3ma55x3su2c2aDeveloping a new Bulk Merge system for the #DecodingUs tree system. Tracks the source attributions in a hierarchy with a goal of replacement for the #ISOGG Y-DNA tree which is no longer being maintained. Working a few edge-cases on the forward-seeking in recursive descent and tree grafting.16 Dec 2025 22:09 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3ma55x3su2c2ahttps://bsky.app/profile/jameskane.blog/post/3m7on5lu3hc2wLast update to #DecodingUs for the year. Lot's of changes as I've rewritten all of the old site's systems on the new foundations. https://jameskane.blog/genomics/2025/12/10/DecodingUs-December-2025-Release.html Next up for 2026 is to work on the new Haplogroup Discover System. #genetic #genealogy11 Dec 2025 03:31 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m7on5lu3hc2whttps://bsky.app/profile/jameskane.blog/post/3m7kwlwkcn22kNew milestone for #DecodingUs. #ATProtocol identify login is complete, so I can use the Admin only tools for prelaunch stuff. More to follow when the Edge-compute companion is more than a buggy Alpha (also shown with some test data.)09 Dec 2025 16:09 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m7kwlwkcn22khttps://bsky.app/profile/jameskane.blog/post/3m7grwh6wts2mShipped new changes to the #DecodingUs App layer. Mostly small changes visible now: 1) Updated the FAQ. 2) Finally added a Search to the References/Papers in the curation portal. 3) Fixed a dumb bug when you share a link to a tree. Tons of enablers for connecting the Federation. decoding-us.com https://decoding-us.com08 Dec 2025 00:35 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m7grwh6wts2mhttps://bsky.app/profile/jameskane.blog/post/3m7dlrezmcc2xNew Blog Post up on what's coming in 2026 after spending a few months working on designs for Decoding Us. https://jameskane.blog/genomics/2025/12/06/crowdsourcing-the-haplogroup-tree.html06 Dec 2025 18:07 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m7dlrezmcc2xhttps://bsky.app/profile/jameskane.blog/post/3m6n65zbuus2sMore progress on my #rust-lang port of BWA-MEM2. Now with similar samstats as the C++ version and passing GATK's ValidateSamFile tool (with the same minor INVALID_TAG_NM percentages). Last time I checked the read locations were 99% concordant. Next up NEON optimization https://github.com/JamesKane/FerrousAlign27 Nov 2025 20:05 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m6n65zbuus2shttps://bsky.app/profile/jameskane.blog/post/3m5zpzet7vs2jMaking some good headway with Anthropic's CLI tool in a #rust-lang port of BWA-MEM2 over vacation. Still working towards alignment parity, so it would be a drop in replacement for my GATK workflow. Then planning to explore adding GPU acceleration.20 Nov 2025 02:31 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m5zpzet7vs2jhttps://bsky.app/profile/jameskane.blog/post/3m4et4gnxjs2jUpdated the coverage module in decoding-us-tools to replicate the old ydna-warehouse.org's coverage histograms. The image is from one of DanteLab's HiFi 4x coverage WGS pilot. Next step is to add the JSON file into your PDS to participate in https://decoding-us.com/coverage-benchmarks.30 Oct 2025 01:35 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m4et4gnxjs2jhttps://bsky.app/profile/jameskane.blog/post/3m3xlfcp5g22dLooks like one of my four 32GB DDR4 DIMMs has decided it's going to become a flake after 4 years. Time to find out how good the Crucial "limited life-time" warranty is.24 Oct 2025 19:13 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m3xlfcp5g22dhttps://bsky.app/profile/jameskane.blog/post/3m3neaosqe22nWell since I can't get anything productive with work done, started feeding in the replacement drives to increase the size of my nearly full NAS. Should only take 5 days or so to double the size of the pool.20 Oct 2025 17:38 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m3neaosqe22nhttps://bsky.app/profile/jameskane.blog/post/3m2mac7remk26And that fire jump in Nashville brings the 2025 racing season to a close for me. Time for a de-load and work out new programming strategies for next year.07 Oct 2025 13:29 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3m2mac7remk26https://bsky.app/profile/jameskane.blog/post/3lzj6334jic2vFirst time seeing the chain carry on a #spartanrace this weekend at the Badlands in Attica. Beast is on the books for 2025. Headed to Nashville in two weeks to wrap up a Trifecta.23 Sep 2025 14:46 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3lzj6334jic2vhttps://bsky.app/profile/jameskane.blog/post/3lx6vwnz64225Note: Skipping warmup before a session of kettlebell training is not advised after 50. Hamstrings are wrecked after swings yesterday. So much that I am moving out today’s run to tomorrow.25 Aug 2025 02:04 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3lx6vwnz64225https://bsky.app/profile/jameskane.blog/post/3lugixecbjs2hFirst 3 week training block done for the Midwest Spartan Beast in September. Sore and slow compared to this time of year last year. The training plan calls for a rest day tomorrow fortunately.20 Jul 2025 22:17 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3lugixecbjs2hhttps://bsky.app/profile/jameskane.blog/post/3lueatsjwnc2bWell the GoRuck Mackall has the same problem as the Rough Runners with my feet. The heel just doesn’t lock in correctly. Back to other options for rucking.20 Jul 2025 00:47 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3lueatsjwnc2bhttps://bsky.app/profile/jameskane.blog/post/3lsu4gv5qts2n#SavageRace placing obstacles before the starting line. Had a great time near Chicago on Saturday. Signing up again for next year.30 Jun 2025 21:20 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3lsu4gv5qts2nhttps://bsky.app/profile/jameskane.blog/post/3lsa7xxgmgk2uPulled out the GoRuck Rough Runners for a short ruck session this afternoon. Now I remember why they were pulled from rotation. They are great except the heals have hot spots that blister my ankles after more than a few minutes.22 Jun 2025 23:30 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3lsa7xxgmgk2uhttps://bsky.app/profile/jameskane.blog/post/3lrrazd77hs2cFinished rewriting the old histogram generator for plotting callable regions in a BAM. Now to create a module to uniquely fingerprint the source file to allow uploading anonymous stats for comparison. https://github.com/JamesKane/DecodingUsTools17 Jun 2025 00:39 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3lrrazd77hs2chttps://bsky.app/profile/jameskane.blog/post/3lr4ofccu3c2sI collected some notes and early observations for aligning files to HPRC's 1.1 release of the human pan genome with vg giraffe. Mostly working on organizing a workflow for when someone with substantially more compute resources releases graphs based on Release 2. https://jameskane.blog/genomics/2025/06/08/Human-Pangenome-Reference-Experiments.html08 Jun 2025 20:12 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3lr4ofccu3c2shttps://bsky.app/profile/jameskane.blog/post/3lqsrwik7wqa2Added a population heat map to #Decoding-Us, which is starting to work as the scripts backfill the geo positions for the public samples in the References page. This will incorporate the D2C samples that get added to the planned federated network. #CitizenScience04 Jun 2025 21:49 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3lqsrwik7wqa2https://bsky.app/profile/jameskane.blog/post/3lqgnshknjc2aMessing around with vg giraffe and the older chm13+Y release. I think I have a viable workflow for short paired-end reads and projecting them back to a linear reference. Now to wait on the folks with the big iron to release a graph update that includes chm13v2.31 May 2025 02:03 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3lqgnshknjc2ahttps://bsky.app/profile/jameskane.blog/post/3lq3zmynefc2mPiecing together a collection of #GeneticGenealogy relevant publications with their Impact Metrics and samples in ENA. If I can find the projects in this deluge of meta-data, I should be able to get it fully automatic and open for others to add papers by their DOI. decoding-us.com/references https://decoding-us.com/references26 May 2025 20:36 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3lq3zmynefc2mhttps://bsky.app/profile/jameskane.blog/post/3lpuznbqr6c2mLong weekend means there’s some time to get the Y and mtDNA trees loaded @ decoding-us.com. The views are ready but working on converting the final tree from YDNA Warehouse. Then on to getting AT Protocol OAuth working, and publishing a few more APIs. #GeneticGenealogy #CitizenScience #DecodingUs https://decoding-us.com24 May 2025 01:47 +0000at://did:plc:ppu2lhasfnyb4dkenakta4sp/app.bsky.feed.post/3lpuznbqr6c2m