[Bug] Promoter intervals exceed chromosome boundaries on chrM (hg38)

[XinzeWu]

version

GenomicFeatures_1.58.0

Description

Generated promoter intervals include coordinates outside chromosome boundaries. For example, on hg38 chrM (length = 16,569 bp):

chrM   -924   1076
chrM   -853   1147
chrM  15523  17523

The first two have negative starts, and the last exceeds the chromosome length.

Expected

All BED intervals should satisfy:
0 <= start < end <= chromSize.

Suggestion

When extending TSS to promoters, clip intervals to chromosome sizes (e.g. with bedtools slop -g hg38.sizes or GenomicRanges::trim() in R). Add validation or warnings for out-of-bound coordinates.

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