Support for indels in vmatchPattern for XStringSets

[tomsing1]

I think vmatchPattern doesn't support indels for XStringObjects, yet, as reported in this support thread. Hervé suggested to file an issue here, to keep it on the radar. I haven't found a corresponding issue yet, so here it is! (Apologies if I overlooked an existing issue.)

Reproducible example:

library(Biostrings)

subject <- DNAStringSet(
  c("GCTCTCTGCTCCTCCTGTTCGACAG", 
    "TCAGCCGCATCTTCTTTTGCGTCG", 
    "CCAGGTGAAGACGGGCGGAGA"))
pattern =   "AGACGGCGG"  # one G deleted

# with with.indels = FALSE, indels, no hits are reported
lengths(vmatchPattern(pattern, subject, with.indels = FALSE, max.mismatch = 1)) # 0 0 0

# with with.indels = TRUE, an error is raised
vmatchPattern(pattern, subject, with.indels = TRUE, max.mismatch = 1)
# Error in .XStringSet.vmatchPattern(pattern, subject, max.mismatch, min.mismatch,  : 
#  vmatchPattern() does not support indels yet

Session information

R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.5

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/Los_Angeles
tzcode source: internal

attached base packages:
[1] stats4 stats graphics grDevices datasets utils methods base

other attached packages:
[1] Biostrings_2.76.0 GenomeInfoDb_1.44.1 XVector_0.48.0 IRanges_2.42.0 S4Vectors_0.46.0
[6] BiocGenerics_0.54.0 generics_0.1.4

loaded via a namespace (and not attached):
[1] R6_2.6.1 GenomeInfoDbData_1.2.14 UCSC.utils_1.4.0 renv_1.1.5
[5] compiler_4.5.1 httr_1.4.7 tools_4.5.1 BiocManager_1.30.26
[9] jsonlite_2.0.0 crayon_1.5.3