Update SVDB to v2.12.0

[aksenia]

Version changes (2.8.4 to 2.12.0)

Current pin: 2.8.4(merge + query modules). Key changes:

• v2.10.0: added --ins_svlen_ratio (SVLEN ratio filter), --ins_seq_similarity (Levenshtein distance), and --data_profile with three presets: sample (dist=25, ratio=0.90, sim=0.85), cohort (dist=50, ratio=0.80, sim=0.75), position_only (dist=50, ratio=0.90, no seq filter). This is an entirely new INS matching model absent in 2.8.x.
• v2.12.0: --ins_distance raw default changed 50 bp to 25 bp.

The query module uses the same INS parameter space as merge: --ins_distance, --ins_svlen_ratio, --ins_seq_similarity, --data_profile. The new ext.args block in conf/modules/annotate_svs.config for SVDB_QUERY must be written as part of this upgrade with values calibrated against loqusDB, not left to default.

The deterministic sort fix (nallo PR #1196) updated the module wrapper; this upgrade targets the binary pin in environment.yml.

[aksenia]

Separate but related in scope problem:

Insertions appear with ~2% AF via SVDB in the pipeline but ~50% AF in Scout via loqusDB - same variants, different frequencies.

This is caused by differences in the tools models as well as parameters they are run with. loqusDB uses an adaptive two-breakpoint interval: min(round(svlen/2, -2), 2000) bp, synthesizing END = POS+SVLEN, with no ratio filter. SVDB 2.8.x had no INS-specific model at all; v2.10+ introduced dedicated INS gates which can be tuned to match loqusDB's magnitude somewhat. But since the models are intrinsically different we will not get identical results from these two tools.

[Stautis]

Wanted to note for reference here what seems to be a parsing error I ran into in process SVDB_QUERY. I'll note it here since v2.12.0 raises no such error, but as @aksenia mentions the upgrade involves additional parameters.

Traceback (most recent call last):
  File "/opt/conda/bin/svdb", line 11, in <module>
    sys.exit(main())
             ~~~~^^
  File "/opt/conda/lib/python3.13/site-packages/svdb/__main__.py", line 99, in main
    make_query_calls(args, queries, "db")
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^
  File "/opt/conda/lib/python3.13/site-packages/svdb/__main__.py", line 33, in make_query_calls
    query_module.main(args, output_file)
    ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^
  File "svdb/query_module.py", line 157, in svdb.query_module.main
ValueError: invalid literal for int() with base 10: np.str_('0.0769')