fix: expand() preserves non-standard rowRanges columns (#85)

[jmg421]

Summary

expand() on a CollapsedVCF with multi-allelic sites was dropping all user-added mcols from rowRanges. For example, a column like SNP_name added via mcols(rowRanges(vcf))$SNP_name <- ... would disappear after expand().

Root Cause

In methods-expand.R, the multi-allelic expansion path had:

rdexp <- rd[idx, ]
mcols(rdexp) <- NULL

This wiped ALL metadata columns. The rd[idx, ] subsetting already correctly repeats rows for multi-allelic sites — the mcols <- NULL was unnecessary and destructive.

Note: the fast path (all(elt == 1L), no multi-allelic sites) already preserved user columns correctly by passing rd directly to VCF().

Fix

Remove the mcols(rdexp) <- NULL line. Simply use rd[idx, ] which preserves all columns. The VCF() constructor stores these in the rowRanges slot separately from the fixed fields (REF/ALT/QUAL/FILTER are in the fixed slot).

Testing

Added test_expand_preserves_nonstandard_mcols to existing test file using the exact reproducer from the issue.

Reproducer (from issue)

vcf <- VCF(rowRanges = GRanges("chr1", IRanges(1:4*3, width=c(1, 2, 1, 1))))
alt(vcf) <- DNAStringSetList("A", c("TT"), c("G", "A"), c("TT", "C"))
ref(vcf) <- DNAStringSet(c("G", "AA", "T", "G"))
mcols(rowRanges(vcf))$SNP_name <- paste0("SNP_", 1:4)

vcfLong <- expand(vcf)
# Before fix: SNP_name is gone
# After fix: SNP_name is preserved and correctly expanded
mcols(rowRanges(vcfLong, fixed=FALSE))$SNP_name
# [1] "SNP_1" "SNP_2" "SNP_3" "SNP_3" "SNP_4" "SNP_4"

Fixes #85