Add T13-T18 Phase 9 verification tests; ASCII cleanup across codebase
Tests added (tests/unit/run_tests.py):
- T13: pure-Python PackPeptide/UnpackPeptide round-trip for all 20 AAs x len 8-12; I/L canonicalization; integer sort == lex sort; known value for ACDEFGHI. 120 checks PASS.
- T14: boundary FASTA (14-AA, len 12-13 no-enzyme); exactly 5 peptides split across short/long paths, each mapping to 1 protein. PASS.
- T15a/b: I/L canonicalization for short (len 8) and long (len 13) paths; equal_IL=1 merges I/L pairs to 1 entry with 2 proteins; equal_IL=0 keeps both separate. PASS.
- T16: two identical 13-AA proteins; 21 unique peptides (len 8-13), every entry maps to 2 proteins (validates cross-path protein list correctness). PASS.
- T17 (–integration): builds human.small.fasta (no-enzyme, len 8-13, equal_IL=1); verifies peptide count in [8.8M, 9.1M] and count == protein-list count. PASS.
- T18 (–integration): two stratified builds of human.small.fasta are byte-identical. PASS.
New FASTA fixtures: t14_boundary, t15_IL_short, t15_IL_long, t16_crosspath.
Also replaces all non-ASCII characters in source and documentation files with ASCII equivalents (em-dash, arrows, checkboxes, special symbols, Cyrillic A, BOM), per CLAUDE.md coding style directive. Third-party file BS_thread_pool.hpp excluded.
Co-Authored-By: Claude Sonnet 4.6 noreply@anthropic.com
版权所有:中国计算机学会技术支持:开源发展技术委员会
京ICP备13000930号-9
京公网安备 11010802047560号
Comet MS/MS
Comet is an open source tandem mass spectrometry (MS/MS) sequence database search tool written primarily in C/C++. The original Comet repository lived on SourceForge since 2012. It was migrated to GitHub on September 2021.
The project website can be found here. This includes release notes and search parameters documentation.
To compile on linux and macOS:
To compile with Microsoft Visual Studio:
We current use build tools v143 with Microsoft Visual Studio 2022.
First install MSFileReader from Thermo Fischer Scientific.
Load “Comet.sln” in Visual Studio.
Set the build to “Release” and “x64”.
Right-mouse-click on the “Comet” project and choose “Build”. This should generate a binary “Comet.exe” in x64/Release.
Comet integrates: