solo: --soloBarcodeMate does not require clipping the barcode off the mate, so the barcode bases stay in the aligned read

[BenjaminDEMAILLE]

Found while implementing the barcode SAM tags in #226, which touches this validation block but deliberately did not change it.

What STAR does

ParametersSolo.cpp:145-150: when --soloBarcodeMate puts the barcode inside a cDNA mate, STAR refuses the run unless that mate has clipping configured.

if ( pP->pClip.in[0].N[barcodeRead] == 0 && pP->pClip.in[1].N[barcodeRead] == 0 ){//clipping not specified for the mate with barcodes
    exitWithError("EXITING because of fatal PARAMETERS error: --soloBarcodeMate " + to_string(barcodeReadIn) +
                  " specifies that barcode sequence is a part of the mate " + to_string(barcodeReadIn) +
                  ", which requires clipping the barcode off this mate."
                  "\nSOLUTION: clip the barcode sequence from 5' or/and 3' with --clip5pNbases   or/and --clip3pNbases ."
                  " The values for mate1 and mate2 have to specified, specify 0 for no clipping.", ...);
};

The rule exists because the barcode region is not cDNA. STAR has no way to know how many bases to drop other than being told.

What rustar-aligner does

Parameters::validate checks --soloBarcodeMate 1 only for the solo type and the read-file count (src/params/mod.rs, the match params.solo_barcode_mate block). Nothing checks --clip5pNbases / --clip3pNbases.

So --soloBarcodeMate 1 without a clip runs to completion, and mate 1 is aligned with its CB+UMI prefix still attached: for 10x v3 geometry that is 28 bases of barcode in front of the cDNA. The read either soft-clips those bases (best case, a shorter effective mate) or drags the alignment start, and the run reports no error at any point.

Suggested fix

Extend the 1 => arm of the solo_barcode_mate match to require a non-zero clip5pNbases or clip3pNbases on the barcode mate, with STAR's message. It is a validation-only change, plus a test asserting that the combination is refused and that it is accepted once a clip is given.

Scope note

--soloBarcodeMate is 0 or 1 here; STAR also accepts 2 and 3, which rustar rejects with its own message. The check above applies to whichever mate is selected.