fix(solo): --soloBarcodeMate 1 requires clipping the barcode off that mate - #240
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fix(solo): --soloBarcodeMate 1 requires clipping the barcode off that mate#240BenjaminDEMAILLE wants to merge 1 commit into
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… mate STAR refuses the combination (ParametersSolo.cpp:145-150) because the barcode region is not cDNA and nothing else says how long it is. Here it ran to completion with the CB+UMI prefix aligned as sequence: 28 bases for 10x v3, with no error at any point in the run. Validation only, with the message pointing at --clip5pNbases / --clip3pNbases as STAR's does. A clip on either end of mate 1 satisfies it; a clip that only covers mate 2 does not. Closes #227.
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Closes #227.
--soloBarcodeMate 1says the CB+UMI sits inside mate 1. Nothing else in the parameter set says how many bases that is, which is why STAR refuses the run unless that mate is clipped (ParametersSolo.cpp:145-150).Here the combination ran to completion: the barcode prefix was handed to the aligner as if it were cDNA (28 bases of it for 10x v3), and no output said so. Best case the aligner soft-clipped it and the effective mate got shorter; worse, it dragged the alignment start.
Validation only. The message names the fix the way STAR's does, and a clip on either end of mate 1 satisfies it, including the single-value form that applies to both mates. A clip that covers only mate 2 does not.
Tests: the existing
solo_barcode_mate_validationnow supplies a clip (it was relying on the combination being accepted), plus a new test for each arm of the rule.cargo test,cargo clippy --all-targets -- -D warningson a cold cache, andcargo fmt --checkare green.🤖 Generated with Claude Code