Add MODOMICS modification annotation support

[jayhesselberth]

Summary

Add functionality to fetch tRNA modification annotations from the MODOMICS database, align them to reference tRNA sequences, and integrate into the clover data model.

Context

read_mod_annotations() exists but is a minimal TSV reader with no way to generate annotation data. We need a way to programmatically download known tRNA modifications from MODOMICS and map them onto our reference sequences.

Proposed Approach

New file: R/modomics.R

Exported function: fetch_modomics_mods(fasta, organism, cache_dir = NULL, min_identity = 0.7)

1. Fetch MODOMICS modification dictionary (maps unicode chars → mod names) via /api/modifications?format=json
2. Fetch tRNA sequences for organism via /api/sequences?RNAtype=tRNA&organism={org}&format=json
3. Strip modification codes to get alignable RNA sequences
4. Align to reference FASTA using Biostrings::pairwiseAlignment(type = "local")
5. Transfer modification positions through the alignment
6. Return tibble with columns ref, pos, mod_full, mod1 (compatible with read_mod_annotations())

Internal helpers: .fetch_modomics_modifications(), .fetch_modomics_sequences(), .strip_modifications(), .extract_mod_positions(), .align_modomics_to_ref(), .match_modomics_to_refs(), .load_or_fetch() (cache helper)

Other changes

• R/clover-se.R: Update read_mod_annotations() to also accept a tibble (not just file path)
• DESCRIPTION: Add httr2 and jsonlite to Suggests
• R/globals.R: Add new global variables
• tests/testthat/test-modomics.R: Unit tests (mock data) + integration test (skip_if_offline())

Design Decisions

• Local alignment handles different 5'/3' ends and CCA tails between MODOMICS and reference
• Pre-filter candidates by amino acid before alignment to reduce cost
• httr2/jsonlite as Suggests (gated by rlang::check_installed())
• Optional cache_dir for offline use via saveRDS()/readRDS()

Organisms

S. cerevisiae, E. coli, H. sapiens, M. musculus initially (any MODOMICS organism supported)

Verification

fa <- clover_example("yeast/trna-ref.fa.gz")
mods <- fetch_modomics_mods(fa, "Saccharomyces cerevisiae")
mods