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lines changed Original file line number Diff line number Diff line change @@ -29,14 +29,41 @@ Pkg.add("RepertoireMetrics")
2929``` julia
3030using RepertoireMetrics
3131
32- # Read and analyze a repertoire
33- rep = read_repertoire(" data.tsv" , VJCdr3Definition())
32+ # Read a repertoire file (supports .tsv and .tsv.gz)
33+ rep = read_repertoire(" sample-001.tsv.gz" , VJCdr3Definition();
34+ length_column= :cdr3)
35+ ```
3436
35- # Compute all metrics (default)
36- metrics = compute_metrics(rep)
37+ ```
38+ Repertoire{Int64}:
39+ Donor: sample-001
40+ Lineages: 15420
41+ Total count: 198350
42+ Top 5 lineages:
43+ IGHV3-23*01|IGHJ4*02|GCGAGAGATCTTGACTACTGGGGCCAGGGAACC: 856 (0.43%)
44+ IGHV4-39*01|IGHJ5*02|TGTGCGAGAGTCGATTACTATGATAGTAGTGGT: 724 (0.37%)
45+ IGHV1-69*01|IGHJ3*02|GCGAGAGATAGTGGCTACGATTTTGACTACTGG: 512 (0.26%)
46+ IGHV5-51*01|IGHJ4*02|TGTGCGAGACATATTGTGGTGGTAACTGCCCC: 398 (0.2%)
47+ IGHV3-48*01|IGHJ6*02|GCGAGAGGGGATAGCAGCAGCTGGTACTTTGAC: 287 (0.14%)
48+ ... and 15415 more
49+ ```
50+
51+ ``` julia
52+ # Compute selected metrics using the composable + operator
53+ metrics = compute_metrics(rep, Depth() + SimpsonDiversity() + Clonality() + GiniCoefficient())
54+ ```
55+
56+ ```
57+ Metrics (4 computed):
58+ depth: 198350.0
59+ simpson_diversity: 0.9997
60+ clonality: 0.0612
61+ gini_coefficient: 0.548
62+ ```
3763
38- # Or select specific metrics
39- metrics = compute_metrics(rep, ShannonEntropy() + Clonality() + D50())
64+ ``` julia
65+ # Or compute all available metrics (default)
66+ metrics = compute_metrics(rep)
4067```
4168
4269## Documentation
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