fix: locateVariants no longer silently drops intronic variants (#87)

[jmg421]

Summary

Fixes #87 (and the earlier #76).

locateVariants() silently returned 0 hits for variants that overlap intronic regions when the TxDb contains transcripts with empty feature sets (e.g., single-exon non-coding RNAs with no intron records).

Root Cause

All six internal cache-population sites in methods-locateVariants.R stored the raw GRangesList from cdsBy(), intronsByTranscript(), etc. without filtering out empty list elements. mapToTranscripts() (via findOverlaps(type="within")) behaves unexpectedly when the subject contains empty elements — variants that should match are silently dropped.

Fix

Add z[lengths(z) > 0L] filtering at every cache-fill site:

• cdsbytx (CodingVariants)
• intbytx (IntronVariants, SpliceSiteVariants)
• threeUTRbytx (ThreeUTRVariants)
• fiveUTRbytx (FiveUTRVariants)
• txbygene (IntergenicVariants)
• UTR construction in the AllVariants method

Testing

• Added unit test test_locateVariants_emptyGRangesList_issue87 that creates a synthetic GRangesList with an empty element and verifies that variants in valid introns are still found.
• Also tests the exact reproducer from the issue (chr22 SNPs against TxDb.Hsapiens.UCSC.hg19.knownGene) when the annotation package is available.

What was verified

• Synthetic test passes locally
• Package loads and dispatches correctly with the fix
• This is the same workaround that users in locateVariant from VariantAnnotation returns wrong results #76 and locateVariants failing on intronic variants #87 found manually (pre-filtering the cache) — now applied at the source.

[vjcitn]

Thanks for this. Have you acknowledged which agentic systems were used for this PR? We are developing guidelines for this process. I think it would be good to have this information in the text of the PR commentary.

[jmg421]

Thanks Vince. Yes — this PR was produced with the assistance of two agentic CLI tools:

1. Kiro CLI (Amazon's AI coding agent) — used for code exploration, writing the fix, and composing the PR
2. Jarvis CLI — a custom agentic tool I built that identifies issues, reads codebases, and drafts fixes

In both cases I review the diffs, understand the reasoning behind each change, and verify correctness before submitting. Happy to include this disclosure in future PR descriptions as standard practice — let me know if you'd like a specific format.