Follow-up from #333.
#333 made _write_from_svar2 honour gvl.write's max_mem by consuming genoray's chunked _find_ranges_chunked stream. The SVAR1 path, _write_from_svar, still ignores max_mem entirely.
Lower priority than the SVAR2 case was, for two reasons:
But the gvl.write docstring now singles out .svar2 as the source that honours max_mem, which documents the SVAR1 gap without tracking it. This issue tracks it.
Related: the SVAR1 max_ends tie-break at same-POS SNP+DEL differs from SVAR2's (SVAR2 is the correct one).
Follow-up from #333.
#333 made
_write_from_svar2honourgvl.write'smax_memby consuming genoray's chunked_find_ranges_chunkedstream. The SVAR1 path,_write_from_svar, still ignoresmax_mementirely.Lower priority than the SVAR2 case was, for two reasons:
_find_starts_ends_with_length(..., out=), writing into a caller-provided array,gvl.writeignoresmax_memand OOMs on whole-contig range materialization at 414k samples #333 fatal.But the
gvl.writedocstring now singles out.svar2as the source that honoursmax_mem, which documents the SVAR1 gap without tracking it. This issue tracks it.Related: the SVAR1 max_ends tie-break at same-POS SNP+DEL differs from SVAR2's (SVAR2 is the correct one).