Stop warning that a breakend has no END/SVLEN (#497)

[joshfactorial]

A well-formed breakend supplied via input_vcf logged WARN Symbolic SV at 1-based POS 600 has no END/SVLEN — skipping coverage modulation. Skipping is correct: a breakend is a point (VCF 4.2 §5.4) with no copy-number change. But the warning read as a defect in a spec-correct VCF.

Versioning: PATCH-level under versioning.md. A log message changes level; no config key, output, or model format changes.

Fix

build_coverage_multipliers now skips SvType::Bnd before the span lookup and logs it at DEBUG (Breakend at 1-based POS 600: a point event, no coverage modulation). The WARN is unchanged for symbolic SVs that need a span and lack one, such as a <DEL> with no END or SVLEN. The function's doc comment said such SVs were skipped "silently", which was not true; it now describes both cases.

Skipping is safe because coverage_multiplier_for already returned 1.0 for a BND, so the coverage segments are unchanged.

Evidence

• Reproduced first with the binary on the H1N1 fixture: a reciprocal BND pair (H1N1_HA:600 ↔ H1N1_PB2:900, no END or SVLEN) logged the WARN four times on develop, once per breakend per pass. With the fix, the same run logs 0 WARNs and four DEBUG lines.
• New eidolon/tests/bnd_no_span_warning.rs, which runs the binary at --log-level debug and reads the written log:
  • breakend pair: the DEBUG line must be present, which shows the breakend reached the coverage pass, and the WARN must be absent. Red before the fix.
  • must-fire: a <DEL> with no END or SVLEN must still log the WARN.
• Mutation: skipping every symbolic SV (|| true) fails the must-fire test. Confirmed the mutant was applied.
• Full workspace suite (1,097 tests), fmt --check and clippy -D warnings pass locally.

Test note: the tests read the log file because simplelog's TerminalMode::Mixed sends WARN to stdout, not stderr. A stderr assertion would pass even if the warning came back.

Not verified

• Only input_vcf breakends were exercised. De novo BNDs go through the same function, so they get the same skip, but no test runs them.

Closes #497.

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