Drop WT leak from "_wt" rows in parse_stripped_hgvs#34
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run_rosace.R:62 (and the mirrored helper at tests/r/testthat/ helper-functions.R:28) ran: WT <- substr(hgvs_string, 1, 1) ABOVE the "_wt" short-circuit. For wildtype rows this set WT to "_" before the function returned, leaving variant metadata with WT = "_" (the underscore from the sentinel string, not an amino acid). finalize_variants_in_rosace then propagated that into rosace_obj@var.data$wildtype, where it sat alongside real amino acid codes like "A", "M", etc. Every downstream regex branch (synonymous, missense, nonsense, deletion, insertion) sets WT from its own str_match capture group, so the pre-branch substr() was a redundant initial guess that got overwritten in every successful parse. Removing it makes _wt return with WT = "" (matches the function's default initializer above), which finalize_variants_in_rosace happily passes through. Side effect for malformed inputs that match no regex branch: WT changes from substr(hgvs, 1, 1) to "". The malformed-return case already has variant="", pos=-1, len=-1, mutation_type="" — adding WT="" to that list is more honest about "we couldn't parse this" than echoing back a stray first character. Tighten the existing _wt test to assert WT = "" explicitly. The old test asserted variant/pos/mutation_type but skipped WT, which is how this lived for so long. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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run_rosace.R:62 (and the mirrored helper at tests/r/testthat/ helper-functions.R:28) ran:
WT <- substr(hgvs_string, 1, 1)
ABOVE the "wt" short-circuit. For wildtype rows this set WT to "" before the function returned, leaving variant metadata with WT = "_" (the underscore from the sentinel string, not an amino acid). finalize_variants_in_rosace then propagated that into rosace_obj@var.data$wildtype, where it sat alongside real amino acid codes like "A", "M", etc.
Every downstream regex branch (synonymous, missense, nonsense, deletion, insertion) sets WT from its own str_match capture group, so the pre-branch substr() was a redundant initial guess that got overwritten in every successful parse. Removing it makes _wt return with WT = "" (matches the function's default initializer above), which finalize_variants_in_rosace happily passes through.
Side effect for malformed inputs that match no regex branch: WT changes from substr(hgvs, 1, 1) to "". The malformed-return case already has variant="", pos=-1, len=-1, mutation_type="" — adding WT="" to that list is more honest about "we couldn't parse this" than echoing back a stray first character.
Tighten the existing _wt test to assert WT = "" explicitly. The old test asserted variant/pos/mutation_type but skipped WT, which is how this lived for so long.