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fix linter issues
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Koeng101 committed Aug 27, 2024
1 parent af684d6 commit f36d2cd
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -76,6 +76,7 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [Unreleased]
- Adds recursive fragmentation. [#92](https://github.com/Koeng101/dnadesign/pull/92)
- Updated megamash documentation to be more specific. [#91](https://github.com/Koeng101/dnadesign/pull/91)
- Adds automatic python documentation generation. [#88](https://github.com/Koeng101/dnadesign/pull/88)
- Adds genbank parsing to python package. Release version 0.1.5 of dnadesign python. [#87](https://github.com/Koeng101/dnadesign/pull/87)
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6 changes: 4 additions & 2 deletions lib/synthesis/fragment/fragment.go
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Expand Up @@ -217,6 +217,9 @@ sub-fragments, then re-assembled from there.
******************************************************************************/

// Assembly is a recursive fragmentation, where higher level assemblies are
// created from lower level assemblies, until you get to the foundation, which
// is a basic fragmentation.
type Assembly struct {
Sequence string
Fragments []string
Expand All @@ -235,10 +238,9 @@ type Assembly struct {
// The assemblyPattern should be for how the oligo should be fragmented up.
// For example: []int{5,4,4,5} is a very reasonable standard if you have
// oligos with a 1/2000 mutation rate that are approximately 174bp - you
// would assmeble ~870bp fragments, which should have a 64.72% success rate,
// would assemble ~870bp fragments, which should have a 64.72% success rate,
// or a ~95% success rate over 3 colonies.
func RecursiveFragment(sequence string, maxCodingSizeOligo int, assemblyPattern []int, excludeOverhangs []string, includeOverhangs []string) (Assembly, error) {

/*
Ok, so this is a note for you hackers out there: this algorithm can be
greatly improved. The optimal way to do this would be to do a continuous
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