handle false positive warning when expanding ranges

[kriemo]

These are false positives, as trim is called immediately. To silence, one option would be to check for these ivls before expanding to avoid the warning.
From here

raer/R/filter_rse.R

Line 222 in 2e41592

x_extend <- trim(x + variant_dist)

library(raer)
library(GenomicFeatures)
mock_txdb <- function() {

    # mock up a txdb with genes
    gr <- GRanges(c(
        "SPCS3:100-120:-",
        "SPCS3:325-350:-"
    ))
    gr$source <- "raer"
    gr$type <- "exon"
    gr$source <- NA
    gr$phase <- NA_integer_
    gr$gene_id <- c(1, 2)
    gr$transcript_id <- c("1.1", "2.1")
    txdb <- makeTxDbFromGRanges(gr)
    txdb
}
rse_adar_ifn <- mock_rse()
rse <- rse_adar_ifn[seqnames(rse_adar_ifn) == "SPCS3"]
txdb <- mock_txdb()

filter_clustered_variants(rse, txdb, variant_dist = 100)
#> Warning in valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE): GRanges object contains 1 out-of-bound range located on sequence SPCS3.
#>   Note that ranges located on a sequence whose length is unknown (NA) or
#>   on a circular sequence are not considered out-of-bound (use
#>   seqlengths() and isCircular() to get the lengths and circularity flags
#>   of the underlying sequences). You can use trim() to trim these ranges.
#>   See ?`trim,GenomicRanges-method` for more information.
#> ℹ `filter_clustered_variants()`: removed 7 sites from 8 (1 remain)
#> class: RangedSummarizedExperiment 
#> dim: 1 2 
#> metadata(0):
#> assays(7): ALT nRef ... nC nG
#> rownames(1): site_SPCS3_99_1
#> rowData names(4): REF rpbz vdb sor
#> colnames(2): wt adar1_ko
#> colData names(1): sample

^{Created on 2023-10-05 with reprex v2.0.2}