possible problem parsing INFO description field #89
Description
An INFO record like
##INFO=<ID=VRS_Allele_IDs,Number=R,Type=String,Description="The computed identifiers for the GA4GH VRS Alleles corresponding to the GT indexes of the REF and ALT alleles [VRS version=2.0.1;VRS-Python version=2.1.1]">
is processed to
> vh@header@listData$INFO$Description[93]
[1] "The computed identifiers for the GA4GH VRS Alleles corresponding to the GT indexes of the REF and ALT alleles [VRS version"
Something about the equals sign causes truncation of string?
sessionInfo()
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] VariantAnnotation_1.52.0 Rsamtools_2.22.0 Biostrings_2.74.0
[4] XVector_0.46.0 SummarizedExperiment_1.36.0 Biobase_2.66.0
[7] GenomicRanges_1.58.0 GenomeInfoDb_1.42.1 IRanges_2.40.1
[10] S4Vectors_0.44.0 MatrixGenerics_1.18.0 matrixStats_1.4.1
[13] BiocGenerics_0.52.0 DT_0.33 AnVILGCP_1.0.0
[16] AnVIL_1.18.5 AnVILBase_1.0.0 dplyr_1.1.4
loaded via a namespace (and not attached):
[1] tidyselect_1.2.1 blob_1.2.4 bitops_1.0-9 RCurl_1.98-1.16
[5] fastmap_1.2.0 GenomicAlignments_1.42.0 promises_1.3.0 XML_3.99-0.17
[9] digest_0.6.37 mime_0.12 lifecycle_1.0.4 KEGGREST_1.46.0
[13] RSQLite_2.3.7 magrittr_2.0.3 compiler_4.4.2 rlang_1.1.4
[17] sass_0.4.9 tools_4.4.2 utf8_1.2.4 yaml_2.3.10
[21] rtracklayer_1.66.0 lambda.r_1.2.4 S4Arrays_1.6.0 htmlwidgets_1.6.4
[25] bit_4.5.0 curl_6.0.1 DelayedArray_0.32.0 pkgload_1.4.0
[29] abind_1.4-8 BiocParallel_1.40.0 miniUI_0.1.1.1 purrr_1.0.2
[33] grid_4.4.2 fansi_1.0.6 xtable_1.8-4 rapiclient_0.1.8
[37] cli_3.6.3 crayon_1.5.3 generics_0.1.3 rstudioapi_0.17.1
[41] rjson_0.2.23 httr_1.4.7 BiocBaseUtils_1.8.0 DBI_1.2.3
[45] cachem_1.1.0 zlibbioc_1.52.0 parallel_4.4.2 AnnotationDbi_1.68.0
[49] restfulr_0.0.15 formatR_1.14 vctrs_0.6.5 Matrix_1.7-1
[53] jsonlite_1.8.9 bit64_4.5.2 GenomicFeatures_1.58.0 crosstalk_1.2.1
[57] tidyr_1.3.1 jquerylib_0.1.4 glue_1.8.0 codetools_0.2-20
[61] futile.logger_1.4.3 later_1.3.2 BiocIO_1.16.0 UCSC.utils_1.2.0
[65] tibble_3.2.1 pillar_1.9.0 rappdirs_0.3.3 htmltools_0.5.8.1
[69] BSgenome_1.74.0 GenomeInfoDbData_1.2.13 R6_2.5.1 httr2_1.0.5
[73] shiny_1.9.1 lattice_0.22-6 futile.options_1.0.1 png_0.1-8
[77] memoise_2.0.1 httpuv_1.6.15 bslib_0.8.0 Rcpp_1.0.13-1
[81] SparseArray_1.6.0 pkgconfig_2.0.3