James Kane
@jameskane.blog
Software Engineer. Retro Computing. Genetic Genealogist. Fitness Enthusiast. TTRPG Gamer. Living the in the American Midwest.
More 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
github.com/JamesKane/Fe...
Next up NEON optimization
github.com/JamesKane/Fe...
GitHub - JamesKane/FerrousAlign: A Rust port of bwa-mem2, the next-generation Burrows-Wheeler Aligner for aligning DNA sequencing reads against large reference genomes.
A Rust port of bwa-mem2, the next-generation Burrows-Wheeler Aligner for aligning DNA sequencing reads against large reference genomes. - JamesKane/FerrousAlign
github.com
November 27, 2025 at 8:05 PM
More 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
github.com/JamesKane/Fe...
Next up NEON optimization
github.com/JamesKane/Fe...
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....
Looks 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.
October 24, 2025 at 7:13 PM
Looks 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.
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.
Note: 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.
Hamstrings are wrecked after swings yesterday. So much that I am moving out today’s run to tomorrow.
August 25, 2025 at 2:04 AM
Note: 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.
Hamstrings are wrecked after swings yesterday. So much that I am moving out today’s run to tomorrow.
First 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.
July 20, 2025 at 10:17 PM
First 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.
Well 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.
July 20, 2025 at 12:47 AM
Well 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.
#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.
Pulled 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.
June 22, 2025 at 11:30 PM
Pulled 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.
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...
I 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.
jameskane.blog/genomics/202...
jameskane.blog/genomics/202...
Human Pangenome Reference Experiments
Human Pangenome Reference Experiments - Setup A Pipeline
jameskane.blog
June 8, 2025 at 8:12 PM
I 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.
jameskane.blog/genomics/202...
jameskane.blog/genomics/202...
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
Messing 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.
May 31, 2025 at 2:03 AM
Messing 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.
Piecing 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
decoding-us.com/references
References
decoding-us.com
May 26, 2025 at 8:36 PM
Piecing 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
decoding-us.com/references
Long 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
Then on to getting AT Protocol OAuth working, and publishing a few more APIs.
#GeneticGenealogy #CitizenScience #DecodingUs
Decoding Us
decoding-us.com
May 24, 2025 at 1:47 AM
Long 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
Then on to getting AT Protocol OAuth working, and publishing a few more APIs.
#GeneticGenealogy #CitizenScience #DecodingUs
Stupid Questions from Co-Workers:
Can't we just delete the Production Cloud Formation stack for an error that can simply be rolled back from?
Can't we just delete the Production Cloud Formation stack for an error that can simply be rolled back from?
May 18, 2025 at 6:09 AM
Stupid Questions from Co-Workers:
Can't we just delete the Production Cloud Formation stack for an error that can simply be rolled back from?
Can't we just delete the Production Cloud Formation stack for an error that can simply be rolled back from?
Annoyed as hell. I wanted to get a new web app deployed this weekend, but because #cellcom is basically down. I can't receive the SMS messages for the 2-factor auth to finish configuration of the domain name.
May 17, 2025 at 9:18 PM
Annoyed as hell. I wanted to get a new web app deployed this weekend, but because #cellcom is basically down. I can't receive the SMS messages for the 2-factor auth to finish configuration of the domain name.
Starting to extract tools that were part of YDNA Warehouse.
1) Coverage - a hybrid of samtools coverage and CallableLoci. Still need to add BED and histogram output.
2) mt and Y DNA haplogroup finder FTDNAs trees.
Should work with any hg38 aligned BAM.
github.com/JamesKane/De...
1) Coverage - a hybrid of samtools coverage and CallableLoci. Still need to add BED and histogram output.
2) mt and Y DNA haplogroup finder FTDNAs trees.
Should work with any hg38 aligned BAM.
github.com/JamesKane/De...
GitHub - JamesKane/DecodingUsTools: Various tools for BAM files
Various tools for BAM files. Contribute to JamesKane/DecodingUsTools development by creating an account on GitHub.
github.com
May 10, 2025 at 12:36 AM
Starting to extract tools that were part of YDNA Warehouse.
1) Coverage - a hybrid of samtools coverage and CallableLoci. Still need to add BED and histogram output.
2) mt and Y DNA haplogroup finder FTDNAs trees.
Should work with any hg38 aligned BAM.
github.com/JamesKane/De...
1) Coverage - a hybrid of samtools coverage and CallableLoci. Still need to add BED and histogram output.
2) mt and Y DNA haplogroup finder FTDNAs trees.
Should work with any hg38 aligned BAM.
github.com/JamesKane/De...
Those son of a bitches on Heard Island have been brought to heel.
May 8, 2025 at 1:56 AM
Those son of a bitches on Heard Island have been brought to heel.
So… OSRIC 3.
PROs: Split into two volumes and smyth-sewn unlike my hard copy of OSRIC.
CONS: Landscape and I have two copies of original AD&D.
Need to think about this one for a while. #OSR.
www.backerkit.com/c/projects/m...
PROs: Split into two volumes and smyth-sewn unlike my hard copy of OSRIC.
CONS: Landscape and I have two copies of original AD&D.
Need to think about this one for a while. #OSR.
www.backerkit.com/c/projects/m...
OSRIC 3
The 2006 retro-clone of first edition AD&D, rewritten and reorganized for 2025! OSRIC 3 is easier to learn, with more examples of play. This is the beginning of a new product line for Mythmere Games, ...
www.backerkit.com
May 6, 2025 at 9:26 PM
So… OSRIC 3.
PROs: Split into two volumes and smyth-sewn unlike my hard copy of OSRIC.
CONS: Landscape and I have two copies of original AD&D.
Need to think about this one for a while. #OSR.
www.backerkit.com/c/projects/m...
PROs: Split into two volumes and smyth-sewn unlike my hard copy of OSRIC.
CONS: Landscape and I have two copies of original AD&D.
Need to think about this one for a while. #OSR.
www.backerkit.com/c/projects/m...
A movie I've watched more than six times.
(Gifs only, with Hard mode: no Star Wars, Star Trek, or LOTR)
(Gifs only, with Hard mode: no Star Wars, Star Trek, or LOTR)
April 30, 2025 at 2:53 PM
A movie I've watched more than six times.
(Gifs only, with Hard mode: no Star Wars, Star Trek, or LOTR)
(Gifs only, with Hard mode: no Star Wars, Star Trek, or LOTR)
