fix: locateVariants/predictCoding no longer silently drop large INDELs (#81)

[jmg421]

Summary

Large INDELs (e.g. 2542bp deletions from Sniffles2) that span multiple exons were silently dropped by locateVariants() and predictCoding() because the internal call to GenomicFeatures::mapToTranscripts() uses type='within' in findOverlaps(), which requires the variant to fit entirely within a single exon/CDS element.

Root Cause

mapToTranscripts(GenomicRanges, GRangesList) at line 209-210 of GenomicFeatures calls:

findOverlaps(x, unlist(transcripts), minoverlap=1L, type="within", ...)

A variant wider than any single exon produces zero hits and is silently excluded from all downstream results.

Fix

locateVariants() — .makeResult()

After mapToTranscripts(), detect variants that overlap the transcript features (type='any') but were not mapped. These are now:

• Included in results with LOCATION='coding'
• LOCSTART/LOCEND set to NA (transcript coordinates cannot be computed)
• A warning is emitted identifying the rescued variants

predictCoding() — .localCoordinates()

Emit a warning when variants overlap CDS regions but cannot be mapped to transcript coordinates, directing users to locateVariants() for identification.

Design Decision

This is the minimal fix that prevents silent data loss — the most dangerous failure mode (users making decisions on incomplete output without knowing it).

Full amino acid consequence prediction for multi-exon spanning variants would require changes to GenomicFeatures::mapToTranscripts() itself (changing the overlap type or adding a parameter), which is outside the scope of this package. The warning directs users to identify affected variants so they can be handled appropriately (e.g., via VEP/SnpEff for full structural consequence annotation).

Testing

Added inst/unitTests/test_large_indels.R with 4 test cases:

1. Large INDEL spanning 3 exons is no longer dropped from locateVariants()
2. Small INDELs within a single exon continue to work normally
3. predictCoding() emits a warning for multi-exon spanning variants
4. Mixed queries (small + large) both appear in results

Reproducer (from issue)

A 2542bp Sniffles2 deletion is read successfully by readVcf() but disappears from locateVariants() and predictCoding() results. After this fix, it appears with LOCATION='coding' and a warning.

Fixes #81