René's URL Explorer Experiment


Title: Add benchmark and validate script by bmesuere · Pull Request #17 · unipept/FragGeneScanRs · GitHub

Open Graph Title: Add benchmark and validate script by bmesuere · Pull Request #17 · unipept/FragGeneScanRs

X Title: Add benchmark and validate script by bmesuere · Pull Request #17 · unipept/FragGeneScanRs

Description: Better and faster Rust implementation of the FragGeneScan gene prediction model for short and error-prone reads. - Add benchmark and validate script by bmesuere · Pull Request #17 · unipept/FragGeneScanRs

Open Graph Description: This PR prepares for a set of potential performance improvements by adding a validation and benchmark script. Both scripts run on the 3 files in the examples directory. Performance baseline on my m...

X Description: This PR prepares for a set of potential performance improvements by adding a validation and benchmark script. Both scripts run on the 3 files in the examples directory. Performance baseline on my m...

Opengraph URL: https://github.com/unipept/FragGeneScanRs/pull/17

X: @github

direct link

Domain: patch-diff.githubusercontent.com

route-pattern/_view_fragments/voltron/pull_requests/show/:user_id/:repository/:id/pull_request_layout(.:format)
route-controllervoltron_pull_requests_fragments
route-actionpull_request_layout
fetch-noncev2:fd20f8b1-5850-0597-aae0-8529be331133
current-catalog-service-hashae870bc5e265a340912cde392f23dad3671a0a881730ffdadd82f2f57d81641b
request-id9E26:87780:16FDA92:1FB5C36:698F5341
html-safe-nonce8182f86adbc9389b0b58266e8dd99b0f784d7e83fb1f9a585b10a1c154b88e11
visitor-payloadeyJyZWZlcnJlciI6IiIsInJlcXVlc3RfaWQiOiI5RTI2Ojg3NzgwOjE2RkRBOTI6MUZCNUMzNjo2OThGNTM0MSIsInZpc2l0b3JfaWQiOiI1MTk3MjA0NzM4MjY5OTkxNzQ1IiwicmVnaW9uX2VkZ2UiOiJpYWQiLCJyZWdpb25fcmVuZGVyIjoiaWFkIn0=
visitor-hmac15f915eb332b4a09c089aad8b813f6cdf28db5c2993ea7b4bd496c71b64805d2
hovercard-subject-tagpull_request:3236240563
github-keyboard-shortcutsrepository,pull-request-list,pull-request-conversation,pull-request-files-changed,copilot
google-site-verificationApib7-x98H0j5cPqHWwSMm6dNU4GmODRoqxLiDzdx9I
octolytics-urlhttps://collector.github.com/github/collect
analytics-location///voltron/pull_requests_fragments/pull_request_layout
fb:app_id1401488693436528
apple-itunes-appapp-id=1477376905, app-argument=https://github.com/_view_fragments/voltron/pull_requests/show/unipept/FragGeneScanRs/17/pull_request_layout
twitter:imagehttps://opengraph.githubassets.com/ce847088ce77c6d48413bb9113dc6e69ce5d851b25bf00705cac24140f0453a5/unipept/FragGeneScanRs/pull/17
twitter:cardsummary_large_image
og:imagehttps://opengraph.githubassets.com/ce847088ce77c6d48413bb9113dc6e69ce5d851b25bf00705cac24140f0453a5/unipept/FragGeneScanRs/pull/17
og:image:altThis PR prepares for a set of potential performance improvements by adding a validation and benchmark script. Both scripts run on the 3 files in the examples directory. Performance baseline on my m...
og:image:width1200
og:image:height600
og:site_nameGitHub
og:typeobject
og:author:usernamebmesuere
hostnamegithub.com
expected-hostnamegithub.com
None56b76ab55fc1aaa874bbbc88f5793e7d72ba4b8f5d8181d7ee2475ab4eddf816
turbo-cache-controlno-cache
go-importgithub.com/unipept/FragGeneScanRs git https://github.com/unipept/FragGeneScanRs.git
octolytics-dimension-user_id7722082
octolytics-dimension-user_loginunipept
octolytics-dimension-repository_id381984303
octolytics-dimension-repository_nwounipept/FragGeneScanRs
octolytics-dimension-repository_publictrue
octolytics-dimension-repository_is_forkfalse
octolytics-dimension-repository_network_root_id381984303
octolytics-dimension-repository_network_root_nwounipept/FragGeneScanRs
turbo-body-classeslogged-out env-production page-responsive
disable-turbofalse
browser-stats-urlhttps://api.github.com/_private/browser/stats
browser-errors-urlhttps://api.github.com/_private/browser/errors
releasecd0835cb24dcc013b26bf23ea516b18c66e9faa1
ui-targetfull
theme-color#1e2327
color-schemelight dark

Links:

Skip to contenthttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17#start-of-content
https://patch-diff.githubusercontent.com/
Sign in https://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2Funipept%2FFragGeneScanRs%2Fpull%2F17
GitHub CopilotWrite better code with AIhttps://github.com/features/copilot
GitHub SparkBuild and deploy intelligent appshttps://github.com/features/spark
GitHub ModelsManage and compare promptshttps://github.com/features/models
MCP RegistryNewIntegrate external toolshttps://github.com/mcp
ActionsAutomate any workflowhttps://github.com/features/actions
CodespacesInstant dev environmentshttps://github.com/features/codespaces
IssuesPlan and track workhttps://github.com/features/issues
Code ReviewManage code changeshttps://github.com/features/code-review
GitHub Advanced SecurityFind and fix vulnerabilitieshttps://github.com/security/advanced-security
Code securitySecure your code as you buildhttps://github.com/security/advanced-security/code-security
Secret protectionStop leaks before they starthttps://github.com/security/advanced-security/secret-protection
Why GitHubhttps://github.com/why-github
Documentationhttps://docs.github.com
Bloghttps://github.blog
Changeloghttps://github.blog/changelog
Marketplacehttps://github.com/marketplace
View all featureshttps://github.com/features
Enterpriseshttps://github.com/enterprise
Small and medium teamshttps://github.com/team
Startupshttps://github.com/enterprise/startups
Nonprofitshttps://github.com/solutions/industry/nonprofits
App Modernizationhttps://github.com/solutions/use-case/app-modernization
DevSecOpshttps://github.com/solutions/use-case/devsecops
DevOpshttps://github.com/solutions/use-case/devops
CI/CDhttps://github.com/solutions/use-case/ci-cd
View all use caseshttps://github.com/solutions/use-case
Healthcarehttps://github.com/solutions/industry/healthcare
Financial serviceshttps://github.com/solutions/industry/financial-services
Manufacturinghttps://github.com/solutions/industry/manufacturing
Governmenthttps://github.com/solutions/industry/government
View all industrieshttps://github.com/solutions/industry
View all solutionshttps://github.com/solutions
AIhttps://github.com/resources/articles?topic=ai
Software Developmenthttps://github.com/resources/articles?topic=software-development
DevOpshttps://github.com/resources/articles?topic=devops
Securityhttps://github.com/resources/articles?topic=security
View all topicshttps://github.com/resources/articles
Customer storieshttps://github.com/customer-stories
Events & webinarshttps://github.com/resources/events
Ebooks & reportshttps://github.com/resources/whitepapers
Business insightshttps://github.com/solutions/executive-insights
GitHub Skillshttps://skills.github.com
Documentationhttps://docs.github.com
Customer supporthttps://support.github.com
Community forumhttps://github.com/orgs/community/discussions
Trust centerhttps://github.com/trust-center
Partnershttps://github.com/partners
GitHub SponsorsFund open source developershttps://github.com/sponsors
Security Labhttps://securitylab.github.com
Maintainer Communityhttps://maintainers.github.com
Acceleratorhttps://github.com/accelerator
Archive Programhttps://archiveprogram.github.com
Topicshttps://github.com/topics
Trendinghttps://github.com/trending
Collectionshttps://github.com/collections
Enterprise platformAI-powered developer platformhttps://github.com/enterprise
GitHub Advanced SecurityEnterprise-grade security featureshttps://github.com/security/advanced-security
Copilot for BusinessEnterprise-grade AI featureshttps://github.com/features/copilot/copilot-business
Premium SupportEnterprise-grade 24/7 supporthttps://github.com/premium-support
Pricinghttps://github.com/pricing
Search syntax tipshttps://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
documentationhttps://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
Sign in https://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2Funipept%2FFragGeneScanRs%2Fpull%2F17
Sign up https://patch-diff.githubusercontent.com/signup?ref_cta=Sign+up&ref_loc=header+logged+out&ref_page=%2F%3Cuser-name%3E%2F%3Crepo-name%3E%2Fvoltron%2Fpull_requests_fragments%2Fpull_request_layout&source=header-repo&source_repo=unipept%2FFragGeneScanRs
Reloadhttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
Reloadhttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
Reloadhttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
unipept https://patch-diff.githubusercontent.com/unipept
FragGeneScanRshttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs
Notifications https://patch-diff.githubusercontent.com/login?return_to=%2Funipept%2FFragGeneScanRs
Fork 1 https://patch-diff.githubusercontent.com/login?return_to=%2Funipept%2FFragGeneScanRs
Star 30 https://patch-diff.githubusercontent.com/login?return_to=%2Funipept%2FFragGeneScanRs
Code https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs
Issues 5 https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/issues
Pull requests 5 https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pulls
Actions https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/actions
Projects 0 https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/projects
Security 0 https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/security
Insights https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pulse
Code https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs
Issues https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/issues
Pull requests https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pulls
Actions https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/actions
Projects https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/projects
Security https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/security
Insights https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pulse
bmesuerehttps://patch-diff.githubusercontent.com/bmesuere
mainhttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/tree/main
benchmark/0https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/tree/benchmark/0
Conversationhttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
Commits1 (1)https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17/commits
Checkshttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17/checks
Files changedhttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17/files
Add benchmark and validate scripthttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17#top
bmesuerehttps://patch-diff.githubusercontent.com/bmesuere
mainhttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/tree/main
benchmark/0https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/tree/benchmark/0
https://patch-diff.githubusercontent.com/bmesuere
bmesuerehttps://patch-diff.githubusercontent.com/bmesuere
Feb 2, 2026https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17#issue-3885560173
Please reload this pagehttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
#18https://github.com/unipept/FragGeneScanRs/pull/18
#19https://github.com/unipept/FragGeneScanRs/pull/19
#20https://github.com/unipept/FragGeneScanRs/pull/20
#21https://github.com/unipept/FragGeneScanRs/pull/21
replace manual vector initialization #19https://github.com/unipept/FragGeneScanRs/pull/19
@ninewisehttps://github.com/ninewise
replace manual vector initialization #19https://github.com/unipept/FragGeneScanRs/pull/19
Please reload this pagehttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
https://patch-diff.githubusercontent.com/bmesuere
add benchmark and validate scripthttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17/commits/67ae292ff6682d039d6a856a4f560321d70a9e29
67ae292https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17/commits/67ae292ff6682d039d6a856a4f560321d70a9e29
https://patch-diff.githubusercontent.com/bmesuere
bmesuerehttps://patch-diff.githubusercontent.com/bmesuere
Feb 2, 2026 https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17#ref-pullrequest-3885801955
replace manual vector initialization #19 https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/19
https://patch-diff.githubusercontent.com/ninewise
ninewisehttps://patch-diff.githubusercontent.com/ninewise
Feb 2, 2026 https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17#pullrequestreview-3741181680
View reviewed changes https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17/files/67ae292ff6682d039d6a856a4f560321d70a9e29
scripts/validate.shhttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17/files/67ae292ff6682d039d6a856a4f560321d70a9e29#diff-d9555f91ec2cf16d2b3d23115fe3cf6600fa8b42627de82a81da48191c54d99c
ninewisehttps://patch-diff.githubusercontent.com/ninewise
Feb 2, 2026https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17#discussion_r2755680580
Learn morehttps://docs.github.com/articles/managing-disruptive-comments/#hiding-a-comment
Please reload this pagehttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
scripts/validate.shhttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17/files/67ae292ff6682d039d6a856a4f560321d70a9e29#diff-d9555f91ec2cf16d2b3d23115fe3cf6600fa8b42627de82a81da48191c54d99c
ninewisehttps://patch-diff.githubusercontent.com/ninewise
Feb 2, 2026https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17#discussion_r2755684443
Learn morehttps://docs.github.com/articles/managing-disruptive-comments/#hiding-a-comment
Please reload this pagehttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
scripts/validate.shhttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17/files/67ae292ff6682d039d6a856a4f560321d70a9e29#diff-d9555f91ec2cf16d2b3d23115fe3cf6600fa8b42627de82a81da48191c54d99c
ninewisehttps://patch-diff.githubusercontent.com/ninewise
Feb 2, 2026https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17#discussion_r2755709385
Learn morehttps://docs.github.com/articles/managing-disruptive-comments/#hiding-a-comment
Please reload this pagehttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
scripts/benchmark.shhttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17/files/67ae292ff6682d039d6a856a4f560321d70a9e29#diff-5f6e359844c35a4a8756375deaf6ef2fb33f9c9a86caedf8b22fad670a1d445a
ninewisehttps://patch-diff.githubusercontent.com/ninewise
Feb 2, 2026https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17#discussion_r2755717054
Learn morehttps://docs.github.com/articles/managing-disruptive-comments/#hiding-a-comment
Please reload this pagehttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
scripts/validate.shhttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17/files/67ae292ff6682d039d6a856a4f560321d70a9e29#diff-d9555f91ec2cf16d2b3d23115fe3cf6600fa8b42627de82a81da48191c54d99c
ninewisehttps://patch-diff.githubusercontent.com/ninewise
Feb 2, 2026https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17#discussion_r2755724660
Learn morehttps://docs.github.com/articles/managing-disruptive-comments/#hiding-a-comment
Please reload this pagehttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
Replace string formatting and appending with write! #20 https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/20
Precompute deletion penalties and log values #21 https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/21
https://patch-diff.githubusercontent.com/bmesuere
bmesuerehttps://patch-diff.githubusercontent.com/bmesuere
Feb 3, 2026https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17#issuecomment-3842253056
@ninewisehttps://github.com/ninewise
Please reload this pagehttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
https://github.co/hiddenchars
https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/{{ revealButtonHref }}
Sign up for freehttps://patch-diff.githubusercontent.com/join?source=comment-repo
Sign in to commenthttps://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2Funipept%2FFragGeneScanRs%2Fpull%2F17
https://patch-diff.githubusercontent.com/ninewise
ninewise https://patch-diff.githubusercontent.com/ninewise
https://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17/files/67ae292ff6682d039d6a856a4f560321d70a9e29
Copilot code review https://patch-diff.githubusercontent.com/apps/copilot-pull-request-reviewer
Copilot https://patch-diff.githubusercontent.com/apps/copilot-pull-request-reviewer
Please reload this pagehttps://patch-diff.githubusercontent.com/unipept/FragGeneScanRs/pull/17
https://patch-diff.githubusercontent.com/bmesuere
https://patch-diff.githubusercontent.com/ninewise
https://github.com
Termshttps://docs.github.com/site-policy/github-terms/github-terms-of-service
Privacyhttps://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Securityhttps://github.com/security
Statushttps://www.githubstatus.com/
Communityhttps://github.community/
Docshttps://docs.github.com/
Contacthttps://support.github.com?tags=dotcom-footer

Viewport: width=device-width


URLs of crawlers that visited me.