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feat: Add 80 new unit tests for extended coverage across all modules#8

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TianYuan-Liu wants to merge 2 commits intomasterfrom
continuous-claude/iteration-7/2026-01-30-9d4c5d49
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feat: Add 80 new unit tests for extended coverage across all modules#8
TianYuan-Liu wants to merge 2 commits intomasterfrom
continuous-claude/iteration-7/2026-01-30-9d4c5d49

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across TSS, TTS, rules, overlap, GTF parser, BED parser, types, and
config modules. Tests cover:

  • TSS extended tests (8): 1bp regions, boundary conditions, multi-zone
    spanning, negative strand handling, zero-distance edge cases,
    percentage calculation accuracy
  • TTS extended tests (7): 1bp regions, boundary conditions, negative
    strand downstream, large TTS regions, percentage accuracy
  • Rules extended tests (9): empty candidates, no rules, area threshold
    filtering, multiple groups, transcript selection edge cases, merge
    logic with different exon numbers
  • Overlap extended tests (14): binary search indexing, no genes, gene
    distance thresholds, exact/intron/partial overlaps, negative strand
    first exon, report level processing (exon/transcript/gene)
  • GTF parser extended tests (9): file not found, comment-only files,
    mixed features, invalid strand filtering, multi-transcript genes,
    max length calculation, exon numbering for both strands, custom tags
  • BED parser extended tests (11): file not found, empty/whitespace files,
    browser/track headers, BED12 format, chunked reading, header boundaries,
    negative/large coordinates
  • Types extended tests (13): zero/single-base exons, large coordinates,
    transcript/gene size calculations, exon renumbering, region edge cases,
    unicode chromosome names, negative values
  • Config extended tests (12): max lookback calculations with various
    largest values, distance setting edge cases, rule parsing validation,
    default value verification

Total test count increased from 168 to 248 unit tests (303 total with
library tests).

TianYuan-Liu and others added 2 commits January 30, 2026 02:02
Add comprehensive test coverage for edge cases and boundary conditions
across TSS, TTS, rules, overlap, GTF parser, BED parser, types, and
config modules. Tests cover:

- TSS extended tests (8): 1bp regions, boundary conditions, multi-zone
  spanning, negative strand handling, zero-distance edge cases,
  percentage calculation accuracy
- TTS extended tests (7): 1bp regions, boundary conditions, negative
  strand downstream, large TTS regions, percentage accuracy
- Rules extended tests (9): empty candidates, no rules, area threshold
  filtering, multiple groups, transcript selection edge cases, merge
  logic with different exon numbers
- Overlap extended tests (14): binary search indexing, no genes, gene
  distance thresholds, exact/intron/partial overlaps, negative strand
  first exon, report level processing (exon/transcript/gene)
- GTF parser extended tests (9): file not found, comment-only files,
  mixed features, invalid strand filtering, multi-transcript genes,
  max length calculation, exon numbering for both strands, custom tags
- BED parser extended tests (11): file not found, empty/whitespace files,
  browser/track headers, BED12 format, chunked reading, header boundaries,
  negative/large coordinates
- Types extended tests (13): zero/single-base exons, large coordinates,
  transcript/gene size calculations, exon renumbering, region edge cases,
  unicode chromosome names, negative values
- Config extended tests (12): max lookback calculations with various
  largest values, distance setting edge cases, rule parsing validation,
  default value verification

Total test count increased from 168 to 248 unit tests (303 total with
library tests).
Co-Authored-By: Claude (claude-opus-4-5) <noreply@anthropic.com>
@TianYuan-Liu TianYuan-Liu deleted the continuous-claude/iteration-7/2026-01-30-9d4c5d49 branch January 30, 2026 01:04
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