Skip to content

[P0][Correctness] unique marker が複数contigへ分散した場合に少数側を黙って捨てない - #55

Merged
light-suzuki merged 1 commit into
mainfrom
issue/50-marker-split-warning
Aug 9, 2026
Merged

[P0][Correctness] unique marker が複数contigへ分散した場合に少数側を黙って捨てない#55
light-suzuki merged 1 commit into
mainfrom
issue/50-marker-split-warning

Conversation

@light-suzuki

Copy link
Copy Markdown
Owner

Fixes #50

実施内容

  • \marker_interval()\ が unique marker hit の contig 分布を検査し、2つ以上のcontigに分散した場合:
    • 必ず warning を返す(major 側の本数/合計と、minority marker の名前と contig を明示)
    • split 詳細(major_contig / major_count / total / minority一覧)を3つ目の戻り値として返し、summary の \marker_split\ に保存(minority marker は従来通り \marker_hits\ / marker_hits.tsv にも残る)
  • \score_confidence()\ に \marker_split\ フラグを追加し、split marker evidence は High 判定の材料にしない(Medium 止まり)。split 時は専用 warning を追加
  • \chr1, chr1\ の従来ケースは interval を返す動作を不変に

テスト

  • 同contig 2本 → 従来通り interval・warningなし
  • chr1×2 + chr2×1 → interval + warning + split詳細(minority marker 名/contig 確認可能)
  • split 時は High にならない(同証拠でも split なしなら High のまま)
  • 全44テスト成功、
    uff check\ パス

Copilot AI lite review requested due to automatic review settings August 9, 2026 01:02

Copilot AI left a comment

Copy link
Copy Markdown

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Copilot was unable to review this pull request because the user who requested the review has reached their quota limit.

@chatgpt-codex-connector chatgpt-codex-connector Bot left a comment

Copy link
Copy Markdown

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

💡 Codex Review

Here are some automated review suggestions for this pull request.

Reviewed commit: 8050cbc19c

ℹ️ About Codex in GitHub

Your team has set up Codex to review pull requests in this repo. Reviews are triggered when you

  • Open a pull request for review
  • Mark a draft as ready
  • Comment "@codex review".

If Codex has suggestions, it will comment; otherwise it will react with 👍.

Codex can also answer questions or update the PR. Try commenting "@codex address that feedback".

Comment on lines +90 to +92
def _marker_split_message(split: dict) -> str:
names = ", ".join(f"{x['marker']}->{x['contig']}" for x in split["minority"][:5])
return f"Unique marker hits are split across target contigs: {split['major_count']}/{split['total']} on {split['major_contig']}; minority: {names}."

Copy link
Copy Markdown

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

P2 Badge Localize the new marker-split warnings

When the Japanese locale is active, both this dynamic split warning and the new fixed warning from score_confidence fall through localizeMessage and are displayed verbatim in English because this change adds neither translation patterns nor locale strings. Add Japanese handling for both messages so users can understand why confidence was reduced.

AGENTS.md reference: AGENTS.md:L110-L110

Useful? React with 👍 / 👎.

# Conflicts:
#	backend/qtlift/analysis.py
#	backend/qtlift/pipeline.py
@light-suzuki
light-suzuki force-pushed the issue/50-marker-split-warning branch from 8050cbc to 112898f Compare August 9, 2026 02:20
@light-suzuki
light-suzuki merged commit d3978fc into main Aug 9, 2026
8 checks passed
@light-suzuki
light-suzuki deleted the issue/50-marker-split-warning branch August 9, 2026 02:20
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

[P0][Correctness] unique marker が複数contigへ分散した場合に少数側を黙って捨てない

2 participants