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Single nucleotide duplications are not parsed correctly #2

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selkamand opened this issue Jun 8, 2023 · 0 comments
Open

Single nucleotide duplications are not parsed correctly #2

selkamand opened this issue Jun 8, 2023 · 0 comments

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@selkamand
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selkamand commented Jun 8, 2023

Thanks so much for your work on this package. Just wanted to report hgvs style single nucleotide duplications aren't considered valid by the parser at the moment:

library(hgvsParseR)

# [FAILS] Single Nucleotide Dup (genomic space)
parseHGVS('g.33229410dup')
#>            hgvs subject    type
#> 1 g.33229410dup genomic invalid

# [FAILS] Single Nucleotide Dup (coding space)
parseHGVS('c.20dup')
#>      hgvs subject    type
#> 1 c.20dup  coding invalid


# [WORKS] Mutli Nucleotide Dup (correctly parsed)
parseHGVS('c.20_23dup')
#>         hgvs subject        type start end
#> 1 c.20_23dup  coding duplication    20  23
sessionInfo()
#> R version 4.2.3 (2023-03-15)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Big Sur ... 10.16
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
#> 
#> locale:
#> [1] en_AU.UTF-8/en_AU.UTF-8/en_AU.UTF-8/C/en_AU.UTF-8/en_AU.UTF-8
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] hgvsParseR_0.2.0.9000
#> 
#> loaded via a namespace (and not attached):
#>  [1] rstudioapi_0.13   knitr_1.42        magrittr_2.0.3    R.cache_0.15.0   
#>  [5] rlang_1.0.6       fastmap_1.1.1     fansi_1.0.4       styler_1.7.0     
#>  [9] tools_4.2.3       xfun_0.37         R.oo_1.25.0       utf8_1.2.3       
#> [13] cli_3.6.0         withr_2.5.0       htmltools_0.5.4   yaml_2.3.7       
#> [17] digest_0.6.31     tibble_3.2.0      lifecycle_1.0.3   purrr_1.0.1      
#> [21] vctrs_0.5.2       R.utils_2.11.0    fs_1.6.1          glue_1.6.2       
#> [25] evaluate_0.20     rmarkdown_2.20    reprex_2.0.1      compiler_4.2.3   
#> [29] pillar_1.8.1      R.methodsS3_1.8.2 pkgconfig_2.0.3

Created on 2023-06-08 by the reprex package (v2.0.1)

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