Align overhaul#13
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btmonier
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smm477
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May 13, 2026
| * reference FASTA is filtered out if it accidentally appears in the list | ||
| * (PHGv2 warns against including the reference here). | ||
| */ | ||
| private fun writeAssemblyFileList(fastaFiles: List<Path>, baseOutputDir: Path): Path { |
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Is this the same as in AlignAssemblies? Can some of that code just be reused here?
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Yeh. I should make this more "DRY" since I will need to reuse this stuff for v2.
smm477
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May 13, 2026
aberthel
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May 13, 2026
zrm22
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May 15, 2026
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Summary
Rework
align-assembliesandalign-mutated-assembliesso they call PHGv2’s align-assemblies CLI (instead of orchestrating AnchorWave/minimap2 through Pixi)Features
phg align-assembliesBug Fixes
pixi run anchorwave/minimap2for these commands. A working PHGv2 installation wherevalidatePhgSetupexpects it is requiredBreaking Changes
Checklist
versioninbuild.gradle.kts(REQUIRED - see below)