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

Reproduce el problema con extdata/ex2.vcf usando readVcf(), expand(), writeVcf() y un readVcf() de roundtrip. Empieza rastreando expand() y los metadatos del encabezado VCF para el campo AF INFO. La tarea está terminada cuando los campos INFO expandidos por alelo conservan metadatos compatibles, de modo que el valor AF no se convierta en una NumericList después del 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