Convert `Number=A` to `Number=1` when creating an `ExpandedVCF`

Tái hiện vấn đề với extdata/ex2.vcf bằng readVcf(), expand(), writeVcf() và một readVcf() roundtrip. Bắt đầu bằng cách lần theo expand() và siêu dữ liệu header VCF cho trường AF INFO. Công việc được xem là hoàn tất khi các trường INFO được mở rộng theo từng allele vẫn giữ siêu dữ liệu tương thích, để giá trị AF không trở thành NumericList sau roundtrip.

It seems reasonable that per-allele ##INFO fields should be converted from Number=A to Number=1 when expand() is called, given that the 1:many relationship between rows and allelic values is now flattened into a 1:1 mapping.

This has practical consequences, too, as we can see:

fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")

library(VariantAnnotation)
out <- tempfile()
first <- readVcf(fl)
first <- expand(first)

writeVcf(first, out)
roundtrip <- readVcf(out, row.names=FALSE)
roundtrip <- expand(roundtrip)

all.equal(first, roundtrip)
## [1] "Attributes: < Component “assays”: Attributes: < Component “data”: Attributes: < Component “listData”: Component “GT”: Attributes: < Length mismatch: comparison on first 1 components > > > >"
## [2] "Attributes: < Component “assays”: Attributes: < Component “data”: Attributes: < Component “listData”: Component “GQ”: Attributes: < Length mismatch: comparison on first 1 components > > > >"
## [3] "Attributes: < Component “assays”: Attributes: < Component “data”: Attributes: < Component “listData”: Component “DP”: Attributes: < Length mismatch: comparison on first 1 components > > > >"
## [4] "Attributes: < Component “assays”: Attributes: < Component “data”: Attributes: < Component “listData”: Component “HQ”: Attributes: < Length mismatch: comparison on first 1 components > > > >"
## [5] "Attributes: < Component “info”: Attributes: < Component “listData”: Component “AF”: Modes: numeric, S4 > >"
## [6] "Attributes: < Component “info”: Attributes: < Component “listData”: Component “AF”: Attributes: < target is NULL, current is list > > >"
## [7] "Attributes: < Component “info”: Attributes: < Component “listData”: Component “AF”: target is numeric, current is CompressedNumericList > >"
## [8] "Attributes: < Component “metadata”: Component “header”: Attributes: < Component “header”: Attributes: < Component “listData”: Component “fileDate”: Attributes: < Component “listData”: Component “Value”: 1 string mismatch > > > >"

We can ignore mismatches 1-4, as these are inconsequential to most end-users (albeit annoying to developers, see #78). We can also ignore mismatch 8, which is discussed in #78. The interesting discrepancies are that of 5-7, where AF becomes a NumericList after a roundtrip through the VCF file. This is because its ##info is still registering Number=A but should really be Number=1 to match the fact that it's already been flattened by the expand() call to generate first.

R Under development (unstable) (2023-11-29 r85646)
Platform: aarch64-apple-darwin22.5.0
Running under: macOS Ventura 13.6.1

Matrix products: default
BLAS:   /Users/luna/Software/R/trunk/lib/libRblas.dylib
LAPACK: /Users/luna/Software/R/trunk/lib/libRlapack.dylib;  LAPACK version 3.11.0

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 utils     datasets  methods
[8] base

other attached packages:
 [1] VariantAnnotation_1.49.2    Rsamtools_2.19.2
 [3] Biostrings_2.71.1           XVector_0.43.0
 [5] SummarizedExperiment_1.33.1 Biobase_2.63.0
 [7] GenomicRanges_1.55.1        GenomeInfoDb_1.39.5
 [9] IRanges_2.37.0              S4Vectors_0.41.3
[11] MatrixGenerics_1.15.0       matrixStats_1.2.0
[13] BiocGenerics_0.49.1

loaded via a namespace (and not attached):
 [1] KEGGREST_1.43.0          rjson_0.2.21             lattice_0.22-5
 [4] vctrs_0.6.5              tools_4.4.0              bitops_1.0-7
 [7] generics_0.1.3           curl_5.2.0               parallel_4.4.0
[10] tibble_3.2.1             fansi_1.0.6              AnnotationDbi_1.65.2
[13] RSQLite_2.3.4            blob_1.2.4               pkgconfig_2.0.3
[16] Matrix_1.6-4             BSgenome_1.71.1          dbplyr_2.4.0
[19] lifecycle_1.0.4          GenomeInfoDbData_1.2.11  compiler_4.4.0
[22] stringr_1.5.1            progress_1.2.3           codetools_0.2-19
[25] yaml_2.3.8               RCurl_1.98-1.13          pillar_1.9.0
[28] crayon_1.5.2             BiocParallel_1.37.0      DelayedArray_0.29.0
[31] cachem_1.0.8             abind_1.4-5              tidyselect_1.2.0
[34] digest_0.6.33            stringi_1.8.3            restfulr_0.0.15
[37] dplyr_1.1.4              biomaRt_2.59.0           fastmap_1.1.1
[40] grid_4.4.0               cli_3.6.2                SparseArray_1.3.2
[43] magrittr_2.0.3           S4Arrays_1.3.1           GenomicFeatures_1.55.1
[46] XML_3.99-0.16            utf8_1.2.4               rappdirs_0.3.3
[49] filelock_1.0.3           prettyunits_1.2.0        bit64_4.0.5
[52] httr_1.4.7               bit_4.0.5                png_0.1-8
[55] hms_1.1.3                memoise_2.0.1            BiocIO_1.13.0
[58] BiocFileCache_2.11.1     rtracklayer_1.63.0       rlang_1.1.2
[61] glue_1.6.2               DBI_1.2.0                xml2_1.3.6
[64] R6_2.5.1                 GenomicAlignments_1.39.0 zlibbioc_1.49.0