Invokes GLIMPSE2_split_reference once. output_region must be contained
within input_region; both regions must name the same contig. Before the
child process starts, RGlimpse2 scans the requested reference region and
rejects records whose allele count is not exactly two. Reference preparation
must split or otherwise resolve multiallelic records before this call.
Usage
rglimpse2_split_reference(
reference_bcf,
input_region,
output_region,
output_prefix,
executable,
genetic_map,
seed,
threads = 1L,
sparse_maf = 0.001,
keep_monomorphic_ref_sites = FALSE,
log = character()
)Arguments
- reference_bcf
Absolute phased reference VCF/BCF path.
- input_region
Buffered region in
contig:start-endform.- output_region
Unbuffered region in
contig:start-endform.- output_prefix
Absolute output prefix. GLIMPSE2 appends the normalized input region and
.bin.- executable
Absolute
GLIMPSE2_split_referencepath.- genetic_map
Absolute genetic-map path, such as one returned by
rglimpse2_genetic_map().- seed
Non-negative random seed.
- threads
Positive worker count.
- sparse_maf
Rare-variant threshold in
[0, 0.5).- keep_monomorphic_ref_sites
Whether to retain monomorphic reference records.
- log
Empty or one absolute log output path.