fix: readVcfStack(param=ScanVcfParam()) reads all files when which= is empty (#50)

[jmg421]

Problem

When param is provided but which= is not specified (e.g. param=ScanVcfParam()), readVcfStack() silently returned a 0-row VCF.

Root cause: in the else { # use param } branch, gr <- GRanges(vcfWhich(param)) produces an empty GRanges, and i = intersect(names(files(x)), as.character(seqnames(gr))) then evaluates to character(0) — so x = x[i] produces an empty stack and nothing is read.

This is inconsistent with both:

• readVcfStack(rstack) (no param) which reads everything
• readVcf(vf, genome, param=ScanVcfParam()) which correctly reads all variants

Fix

In R/VcfStack-class.R, when param is provided but gr is empty, fall back to i = names(files(x)) so all files are read — matching the documented behaviour of ScanVcfParam() where an unspecified which= means "return all ranges".

Test

Added two checks to inst/unitTests/test_VcfStack-class.R:

• readVcfStack(Rstack, param=ScanVcfParam()) returns same dims as readVcfStack(Rstack)
• readVcfStack(stack, param=ScanVcfParam()) returns same dims as readVcfStack(stack)

Fixes #50