James Kane
@jameskane.blog
Software Engineer. Retro Computing. Genetic Genealogist. Fitness Enthusiast. TTRPG Gamer. Living the in the American Midwest.
Making 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.
November 20, 2025 at 2:31 AM
Making 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.
Updated 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 decoding-us.com/coverage-ben....
Next step is to add the JSON file into your PDS to participate in decoding-us.com/coverage-ben....
October 30, 2025 at 1:36 AM
Updated 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 decoding-us.com/coverage-ben....
Next step is to add the JSON file into your PDS to participate in decoding-us.com/coverage-ben....
Well 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.
October 20, 2025 at 5:38 PM
Well 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.
And 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.
October 7, 2025 at 1:30 PM
And 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.
First 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.
Headed to Nashville in two weeks to wrap up a Trifecta.
September 23, 2025 at 2:47 PM
First 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.
Headed to Nashville in two weeks to wrap up a Trifecta.
#SavageRace placing obstacles before the starting line. Had a great time near Chicago on Saturday. Signing up again for next year.
June 30, 2025 at 9:20 PM
#SavageRace placing obstacles before the starting line. Had a great time near Chicago on Saturday. Signing up again for next year.
Finished 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.
github.com/JamesKane/De...
github.com/JamesKane/De...
June 17, 2025 at 12:39 AM
Finished 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.
github.com/JamesKane/De...
github.com/JamesKane/De...
Added 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. #CitizenScience
June 4, 2025 at 9:49 PM
Added 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. #CitizenScience
Kickstarter rewards are in from @trolllordgames.bsky.social for use with their Siege Engine system.
April 21, 2025 at 5:28 PM
Kickstarter rewards are in from @trolllordgames.bsky.social for use with their Siege Engine system.
Picked up an #OrangePi RV2, since it has the RISC-V Vector extensions my JH7110-based VisionFive 2 board lacks.
Geekbench 6 Scores:
VF2 => 74 single core, 215 multi core
RV2 => 128 single core, 509 multi core
RK3588 OPi 5 Plus => 754 single core, 3028 multi core
Not terrible for $50.
Geekbench 6 Scores:
VF2 => 74 single core, 215 multi core
RV2 => 128 single core, 509 multi core
RK3588 OPi 5 Plus => 754 single core, 3028 multi core
Not terrible for $50.
April 21, 2025 at 1:03 PM
Picked up an #OrangePi RV2, since it has the RISC-V Vector extensions my JH7110-based VisionFive 2 board lacks.
Geekbench 6 Scores:
VF2 => 74 single core, 215 multi core
RV2 => 128 single core, 509 multi core
RK3588 OPi 5 Plus => 754 single core, 3028 multi core
Not terrible for $50.
Geekbench 6 Scores:
VF2 => 74 single core, 215 multi core
RV2 => 128 single core, 509 multi core
RK3588 OPi 5 Plus => 754 single core, 3028 multi core
Not terrible for $50.
New shiny backer copy of @koboldpress.com’s Dungeons & Ruins arrived today. Will need to make some time to read it this week.
February 3, 2025 at 10:11 PM
New shiny backer copy of @koboldpress.com’s Dungeons & Ruins arrived today. Will need to make some time to read it this week.
Easing back into outdoor activities. 25 lb plate in the ruck and generally a pace to stick to zone 2 for about two and a half miles. Quite chilly out this afternoon.
February 1, 2025 at 10:53 PM
Easing back into outdoor activities. 25 lb plate in the ruck and generally a pace to stick to zone 2 for about two and a half miles. Quite chilly out this afternoon.
This may actually be running acceptably on the overgrown cell phone aka small Graviton EC2 instance running the DB. Once I have the caching setup, it'll get added in the Studies view.
The end-point is being built to easily embed in a self-hosted page or just use the internal.
The end-point is being built to easily embed in a self-hosted page or just use the internal.
December 29, 2024 at 10:58 PM
This may actually be running acceptably on the overgrown cell phone aka small Graviton EC2 instance running the DB. Once I have the caching setup, it'll get added in the Studies view.
The end-point is being built to easily embed in a self-hosted page or just use the internal.
The end-point is being built to easily embed in a self-hosted page or just use the internal.
Pulled the first 48Gbase of @pacbio.bsky.social Revio reads for HG00117. The Y callable loci on hs1 is nice and clean. I will need to go back and get the full file to play with the sub-sampling locally to find an optimal amount for future plans on the other 135 of them.
December 28, 2024 at 5:32 PM
Pulled the first 48Gbase of @pacbio.bsky.social Revio reads for HG00117. The Y callable loci on hs1 is nice and clean. I will need to go back and get the full file to play with the sub-sampling locally to find an optimal amount for future plans on the other 135 of them.
The MVP of YDNA Study groups is live at ydna-warehouse.org/study/15103f.... Mix and match STR panels in the chart. Mostly just UX and report refinement planned for the next iteration.
December 26, 2024 at 10:59 PM
The MVP of YDNA Study groups is live at ydna-warehouse.org/study/15103f.... Mix and match STR panels in the chart. Mostly just UX and report refinement planned for the next iteration.
The evil black lines across the bottom 1/3 of the display are gone after its trip to California. Now I can get some work done.
December 26, 2024 at 8:41 PM
The evil black lines across the bottom 1/3 of the display are gone after its trip to California. Now I can get some work done.
Feature #6 - The SNP and STR matching tools now have contact buttons. No more bugging the site administration to put you in touch with them!
Keep in mind the STR matches are often more distant than you think. Check the SNP match list for the last 20 generations.
Keep in mind the STR matches are often more distant than you think. Check the SNP match list for the last 20 generations.
December 14, 2024 at 8:05 PM
Feature #6 - The SNP and STR matching tools now have contact buttons. No more bugging the site administration to put you in touch with them!
Keep in mind the STR matches are often more distant than you think. Check the SNP match list for the last 20 generations.
Keep in mind the STR matches are often more distant than you think. Check the SNP match list for the last 20 generations.
Feature #5 - My Studies page added to the tester profile. You can manage your display preferences for public projects and be notified of new studies that you match the recruitment targets.
December 14, 2024 at 8:05 PM
Feature #5 - My Studies page added to the tester profile. You can manage your display preferences for public projects and be notified of new studies that you match the recruitment targets.
Feature #4 - Studies are moving from Alpha to Beta for STR comparison and adding a browsing list for public facing ones. e.g. you don't need to be logged in to view the pages. The "Investigator Options" allows the investigators to contact members for clarifying details if needed. More planned here.
December 14, 2024 at 8:05 PM
Feature #4 - Studies are moving from Alpha to Beta for STR comparison and adding a browsing list for public facing ones. e.g. you don't need to be logged in to view the pages. The "Investigator Options" allows the investigators to contact members for clarifying details if needed. More planned here.
Feature #2 - Enable activation of 2-Factor Authentication
Feature #3 - Remove those pests you blocked should the need arise later.
Feature #3 - Remove those pests you blocked should the need arise later.
December 14, 2024 at 8:05 PM
Feature #2 - Enable activation of 2-Factor Authentication
Feature #3 - Remove those pests you blocked should the need arise later.
Feature #3 - Remove those pests you blocked should the need arise later.
Starting to wrap up backend work and transitioning to UI in the last release for YDNA Warehouse for 2024.
#1 new feature with preliminary UI - internal messaging to communicate with recent matches.
#1 new feature with preliminary UI - internal messaging to communicate with recent matches.
December 14, 2024 at 8:05 PM
Starting to wrap up backend work and transitioning to UI in the last release for YDNA Warehouse for 2024.
#1 new feature with preliminary UI - internal messaging to communicate with recent matches.
#1 new feature with preliminary UI - internal messaging to communicate with recent matches.
The top ten music artists from my 2024. Not exactly sure how Billy or Sammy made it to the top.
December 5, 2024 at 1:46 AM
The top ten music artists from my 2024. Not exactly sure how Billy or Sammy made it to the top.
I paid for all the cores... I will use all the cores.
Realigning a few dozen R1b-CTS4466 Big Y BAMs this weekend.
Realigning a few dozen R1b-CTS4466 Big Y BAMs this weekend.
December 1, 2024 at 2:27 AM
I paid for all the cores... I will use all the cores.
Realigning a few dozen R1b-CTS4466 Big Y BAMs this weekend.
Realigning a few dozen R1b-CTS4466 Big Y BAMs this weekend.
I guess I will be slumming it on single display for a few weeks. This thing needs to go in for repair but fortunately still under warranty.
November 25, 2024 at 12:52 PM
I guess I will be slumming it on single display for a few weeks. This thing needs to go in for repair but fortunately still under warranty.