Conversation
Owner
Author
|
There are a few things I really want to implement:
|
* Add FragmentWithBreak to interrupt a gene across assemblies
Adds fragment_with_break to both the Lua (src/fragment.tl) and Go
(go/lib/synthesis/fragment) implementations. It forces a single fragment
junction into a given window, splitting a sequence into "before" and
"after" halves whose overhangs never collide. This supports interrupting
a selection marker (e.g. kanR) across two assemblies so it is only
reconstituted in a later GoldenGate.
The break overhang is the most efficient non-palindromic 4bp overhang in
the window; each half is then fragmented independently, with the
after-break fragmentation excluding the before-break overhangs.
Includes matching tests/examples on both sides: a window/junction/
collision/round-trip test and a recursion-down example that fragments the
~1kbp chunks into 151-176bp pieces.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
* ci: bump test-lib/test-external Go toolchain to 1.24.x
The macos-latest runner's dyld now requires an LC_UUID load command,
which the Go 1.22.x linker omitted, causing bio.test to abort at load
("missing LC_UUID load command", signal: abort trap). Bumping the Go
toolchain to 1.24.x emits LC_UUID and fixes the macOS job. Both modules
declare go 1.22.0, so the newer toolchain is backward compatible.
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
---------
Co-authored-by: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
this integrates lua as a native language for dnadesign.