qcezads123456/rare-seq-finder

How qcezads123456/rare-seq-finder works

Rare Sequence Finder is a C++ command-line detector: users supply reference and target FASTA files plus optional thresholds; the program parses arguments, reads both inputs, indexes reference k-mers, finds rare target k-mers, and writes candidate-region reports and metadata. A separate, optional simulation-and-analysis workflow validates detections against mutation ground truth. The detector’s call relationships are supported by excerpts; validation links reflect README descriptions, since its runtime implementation was not sampled.

Main entry points: main.cpp Program entry · result_processor.cpp Result processor · Kmer_encoder.cpp Reference k-mers · result TXT, TSV, JSON

Components 13

Detection inputs

CLI parsing src/cli.cpp
FASTA reader src/Fasta_reader.cpp

K-mer detection

Program entry src/main.cpp
Result processor src/result_processor.cpp
Reference k-mers src/Kmer_encoder.cpp
Rare k-mers src/Kmer_encoder.cpp
K-mer utilities src/decoder.cpp

Detection reports

TXT, TSV, JSON result

Optional validation

Simulated sequences data/MS_output
Ground truth data
Validation summaries analysis/summary_create.py

Other components

User
Mutation Simulator

Connections 13

User → Program entry: runs README.md
Program entry → CLI parsing: parses arguments src/main.cpp
Program entry → FASTA reader: reads FASTA src/main.cpp
Program entry → Result processor: processes sequences src/main.cpp
Result processor → Reference k-mers: builds index src/result_processor.cpp
Result processor → Rare k-mers: finds candidates src/result_processor.cpp
Reference k-mers → K-mer utilities: counts references src/Kmer_encoder.cpp
Rare k-mers → K-mer utilities: counts references src/Kmer_encoder.cpp
Result processor → TXT, TSV, JSON: writes reports src/result_processor.cpp
Mutation Simulator → Simulated sequences: generates sequences README.md
Mutation Simulator → Ground truth: generates ground truth README.md
TXT, TSV, JSON → Validation summaries: evaluated against README.md
Ground truth → Validation summaries: compared with README.md

Drawn by GitDiagram on November 13, 2026 from the repository's file tree, README and source files. Read as Markdown ·