fix: correct BED coordinate system calculation

[nh13]

Summary

BED format uses 0-based, half-open intervals [start, end).
Changed length calculation from end - start + 1 to end - start.

Closes #102

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Summary by CodeRabbit

• Bug Fixes
  • Fixed BED file interval coordinate handling to comply with standard genomic conventions. This improves the accuracy of region length calculations, validation checks, and position processing across all genomic operations. The changes ensure consistent and precise handling of genomic intervals from BED file inputs throughout the application.

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📝 Walkthrough

Walkthrough

Corrects BED interval length calculations across two files from inclusive end (end - start + 1) to half-open convention (end - start), aligning with BED 0-based coordinate system semantics in interval length and related position computations.

Changes

Cohort / File(s)	Summary
BED interval calculation in simulator src/dwgsim.c	Updated three occurrences of interval length computation from end - start + 1 to end - start: tot_len recalculation for regions_bed, accumulation of m for matching contig regions, and j calculation for pos-conditioned logic.
BED interval validation src/regions_bed.c	Changed len calculation from end - start + 1 to end - start in validation logic; updated corresponding conditional check and warning message text to reflect half-open interval semantics.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Poem

🐰 Half-open intervals, now we've got it right,
BED coordinates gleaming in the morning light,
Start to end with proper math so true,
Fixing off-by-one bugs—hopping straight on through! 🥕

Pre-merge checks and finishing touches

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	You can run @coderabbitai generate docstrings to improve docstring coverage.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title directly and clearly summarizes the main change: correcting BED coordinate system calculation from inclusive to half-open intervals.
Linked Issues check	✅ Passed	Changes correctly implement issue #102 requirements by replacing all occurrences of end - start + 1 with end - start in BED length calculations across both files.
Out of Scope Changes check	✅ Passed	All changes are directly scoped to correcting BED interval calculations as required by issue #102; no unrelated modifications detected.

✨ Finishing touches

• 📝 Generate docstrings

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Post copyable unit tests in a comment
• Commit unit tests in branch fix/bed-coordinate-system

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[nh13]

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Actionable comments posted: 0

Caution

Some comments are outside the diff and can’t be posted inline due to platform limitations.

⚠️ Outside diff range comments (1)

src/dwgsim.c (1)

693-704: Remove the -1 adjustment from line 697 after BED length correction.

The position mapping formula on line 697 has an off-by-one error. With the corrected length calculation on line 695 (j = end - start), the -1 adjustment produces positions outside the valid BED region [start, end). Change line 697 from:

pos = regions_bed->start[i] + pos - 1; // zero-based

to:

pos = regions_bed->start[i] + pos;

🧹 Nitpick comments (1)

src/regions_bed.c (1)

81-83: Validation check appears to be dead code.

The condition if(end - start != len) should never be true since len = end - start is assigned on line 55, and underflow is prevented by the end < start check on lines 72-75. While the update to match the new BED calculation is correct, this validation block appears to be dead code that could optionally be removed in a future cleanup.

Optional: Remove unreachable validation

-    if(end - start != len) {
-        fprintf(stderr, "Warning: len != end - start [%s,%u,%u,%u]\n", name, start, end, len);
-    }
-    

📜 Review details

Configuration used: defaults

Review profile: CHILL

Plan: Pro

📥 Commits

Reviewing files that changed from the base of the PR and between ae9cd92 and e20b270.

📒 Files selected for processing (2)

• src/dwgsim.c
• src/regions_bed.c

🔇 Additional comments (3)

src/dwgsim.c (2)

496-503: Correct BED interval length calculation.

The change from end - start + 1 to end - start correctly implements BED's 0-based, half-open [start, end) convention. The inline comment clearly documents the semantics.

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536-543: Correct BED interval length calculation for contig regions.

The change correctly applies BED half-open semantics when accumulating region lengths for a specific contig, consistent with the fix at line 501.

src/regions_bed.c (1)

54-56: Correct BED interval length calculation.

The change from end - start + 1 to end - start correctly implements BED's 0-based, half-open [start, end) convention. The added comment clearly documents this semantic.