Fix madc2vcf_all() "invalid substring arguments" error on off-target alleles#65
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Updated funding source and note about BIGr development.
CRAN 7.2 submission
…atches
When add_others = TRUE, compare() computed other_ref_base/other_alt_base with
substring() before checking that any mismatch positions remained. If an off-target
("Other") allele aligns to the reference with its only mismatch at the target SNP
position, that position is removed and pos_ref_idx/pos_alt_idx become integer(0),
so substring() errors with "invalid substring arguments" and the whole run aborts.
Move the two substring() calls inside the existing 'if (length(pos_ref_idx) > 0)'
guard, mirroring how the off-target Match alleles are already handled. Behavior is
unchanged when mismatch positions remain; existing madc2vcf_all tests still pass.
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Hi @shbrainard! Good to have codes from you. Thank you for your contribution, we will take a look and let you know :) |
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Summary
madc2vcf_all(..., add_others = TRUE)aborts withError: ... invalid substring argumentson some DArTag datasets.Root cause
In
compare()(R/madc2vcf_all.R), the off-target ("Other") branch computesother_ref_base/other_alt_basewithsubstring()before the existingif (length(pos_ref_idx) > 0)check. When an "Other" allele aligns to the reference with its only mismatch at the target SNP position, that index is removed, leavingpos_ref_idx/pos_alt_idxasinteger(0).substring(x, integer(0), integer(0))errors with "invalid substring arguments", and aborts the run.The off-target Match branch already protects its
substring()calls with the samelength(pos_ref_idx) > 0check; the Other branch applies this check too late.Fix
Move the two
substring()calls inside the existingif (length(pos_ref_idx) > 0)block, mirroring the Match branch. No behavior change when mismatch positions remain.Verification
add_others = TRUEpipeline completes.tests/testthat/test-madc2vcf_all.Rsuite passes.