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v0.0.11: stats and compare subcommands - #10
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- stats: single streaming pass summarizing alignment amount, within-chain gaps, query strands, and chain fragmentation (aligned-bp N50/L50, per-target top-1/top-3 concentration, chains-to-50/90/95%, median/max fragmentation). --by-sequence adds per-target tables and top scored chains; reads stdin when --chain is omitted. - compare: canonical base-pair mapping agreement invariant to chain IDs, order, and harmless splitting, reported separately from unique coverage, multi-mapped bp, continuity, and gaps. Name interning plus a fixed 8 GiB memory budget checked before canonicalization; --by-sequence adds per-target agreement and top chains. - Bump to 0.0.11, add tool docs (assets/tools/stats.md, compare.md), README statistics section, and changelog entries.
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Summary
Adds two new subcommands.
chaintools statsSingle streaming pass summarizing alignment amount, within-chain gaps, query strands, and chain fragmentation:
--by-sequenceadds per-target tables and top scored chains (--top N, default 3)--chainis omitted; full chain validation with byte-offset errorschaintools compareCompares two chain files by the exact base-pair relations they encode, not by chain identity:
(target, query, strand, diagonal)mapping segments — invariant to chain IDs, order, and harmless splitting; overlapping/adjacent intervals merged, duplicates removed--by-sequenceadds per-target agreement (A-only/B-only/shared bp, Dice) and top chainsTests / validation
cargo test --all-features), clippy-D warningsandfmt --checkcleanqStart < qEnd)Docs
assets/tools/stats.md,assets/tools/compare.mdwith real captured output[Unreleased]entries