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Add test data for covsnap module #381

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164 changes: 164 additions & 0 deletions data/modules/covsnap/NA12878_panel.covsnap.json
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Original file line number Diff line number Diff line change
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{
"covsnap_version": "0.5.0",
"schema_version": "1.0",
"run": {
"sample_name": "NA12878_panel",
"bam_path": "/data/NA12878_panel.bam",
"reference": null,
"engine_used": "mosdepth",
"engine_version": "0.3.8",
"contig_style": "chr",
"run_date": "2026-06-29",
"bed_path": null,
"exon_only": false,
"thresholds": [
1,
5,
10,
20,
30,
50,
100
],
"classify_params": {
"pass_pct_ge_20": 95.0,
"pass_max_pct_zero": 1.0,
"dropout_pct_zero": 5.0,
"dropout_zero_block_bp": 500,
"uneven_cv": 1.0,
"exon_pct_ge_20": 90.0,
"exon_max_pct_zero": 5.0
}
},
"summary": {
"n_targets": 2,
"n_pass": 2,
"status_counts": {
"PASS": 2
}
},
"targets": [
{
"target_id": "BRCA1",
"contig": "chr17",
"start": 43044294,
"end": 43125483,
"length_bp": 81189,
"mean_depth": 142.3,
"median_depth": 140.0,
"min_depth": 3,
"max_depth": 310,
"stdev_depth": 38.1,
"pct_zero": 0.12,
"pct_thresholds": {
"1": 99.9,
"5": 99.9,
"10": 99.9,
"20": 98.6,
"30": 98.6,
"50": 84.8,
"100": 71.0
},
"coverage_status": "PASS",
"n_lowcov_blocks": 0,
"lowcov_total_bp": 0,
"lowcov_blocks": [],
"histogram": {
"0": 96,
"30": 400,
"140": 12000
},
"exons": [
{
"target_id": "BRCA1_exon1",
"contig": "chr17",
"start": 43125270,
"end": 43125483,
"length_bp": 213,
"mean_depth": 150.0,
"median_depth": 149.0,
"min_depth": 40,
"max_depth": 210,
"stdev_depth": 22.0,
"pct_zero": 0.0,
"pct_thresholds": {
"1": 100.0,
"5": 100.0,
"10": 100.0,
"20": 100.0,
"30": 100.0,
"50": 90.0,
"100": 80.0
},
"coverage_status": "OK",
"n_lowcov_blocks": 0,
"lowcov_total_bp": 0,
"lowcov_blocks": [],
"histogram": {},
"exon_number": 1,
"status": "OK"
},
{
"target_id": "BRCA1_exon2",
"contig": "chr17",
"start": 43124016,
"end": 43124114,
"length_bp": 98,
"mean_depth": 138.0,
"median_depth": 140.0,
"min_depth": 55,
"max_depth": 190,
"stdev_depth": 19.0,
"pct_zero": 0.0,
"pct_thresholds": {
"1": 100.0,
"5": 100.0,
"10": 100.0,
"20": 100.0,
"30": 100.0,
"50": 86.0,
"100": 72.0
},
"coverage_status": "OK",
"n_lowcov_blocks": 0,
"lowcov_total_bp": 0,
"lowcov_blocks": [],
"histogram": {},
"exon_number": 2,
"status": "OK"
}
]
},
{
"target_id": "TP53",
"contig": "chr17",
"start": 7668401,
"end": 7694173,
"length_bp": 25772,
"mean_depth": 160.0,
"median_depth": 158.0,
"min_depth": 20,
"max_depth": 300,
"stdev_depth": 30.0,
"pct_zero": 0.0,
"pct_thresholds": {
"1": 100.0,
"5": 100.0,
"10": 100.0,
"20": 99.5,
"30": 99.5,
"50": 89.75,
"100": 80.0
},
"coverage_status": "PASS",
"n_lowcov_blocks": 0,
"lowcov_total_bp": 0,
"lowcov_blocks": [],
"histogram": {
"50": 2000,
"160": 15000
}
}
],
"genes": []
}
120 changes: 120 additions & 0 deletions data/modules/covsnap/sampleB_lowcov.covsnap.json
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{
"covsnap_version": "0.5.0",
"schema_version": "1.0",
"run": {
"sample_name": "sampleB_lowcov",
"bam_path": "/data/sampleB_lowcov.bam",
"reference": null,
"engine_used": "mosdepth",
"engine_version": "0.3.8",
"contig_style": "chr",
"run_date": "2026-06-29",
"bed_path": null,
"exon_only": false,
"thresholds": [
1,
5,
10,
20,
30,
50,
100
],
"classify_params": {
"pass_pct_ge_20": 95.0,
"pass_max_pct_zero": 1.0,
"dropout_pct_zero": 5.0,
"dropout_zero_block_bp": 500,
"uneven_cv": 1.0,
"exon_pct_ge_20": 90.0,
"exon_max_pct_zero": 5.0
}
},
"summary": {
"n_targets": 2,
"n_pass": 0,
"status_counts": {
"LOW_COVERAGE": 1,
"DROP_OUT": 1
}
},
"targets": [
{
"target_id": "BRCA1",
"contig": "chr17",
"start": 43044294,
"end": 43125483,
"length_bp": 81189,
"mean_depth": 55.0,
"median_depth": 52.0,
"min_depth": 0,
"max_depth": 140,
"stdev_depth": 16.0,
"pct_zero": 4.2,
"pct_thresholds": {
"1": 96.0,
"5": 96.0,
"10": 96.0,
"20": 70.0,
"30": 70.0,
"50": 37.5,
"100": 5.0
},
"coverage_status": "LOW_COVERAGE",
"n_lowcov_blocks": 1,
"lowcov_total_bp": 600,
"lowcov_blocks": [
{
"contig": "chr17",
"start": 43100000,
"end": 43100600,
"length": 600,
"mean_depth": 2.1
}
],
"histogram": {
"0": 3400,
"50": 40000
}
},
{
"target_id": "ETFDH",
"contig": "chr4",
"start": 158680400,
"end": 158716400,
"length_bp": 36000,
"mean_depth": 0.8,
"median_depth": 0.0,
"min_depth": 0,
"max_depth": 12,
"stdev_depth": 1.5,
"pct_zero": 82.0,
"pct_thresholds": {
"1": 18.0,
"5": 18.0,
"10": 18.0,
"20": 3.0,
"30": 3.0,
"50": 1.5,
"100": 0.0
},
"coverage_status": "DROP_OUT",
"n_lowcov_blocks": 1,
"lowcov_total_bp": 29600,
"lowcov_blocks": [
{
"contig": "chr4",
"start": 158680400,
"end": 158710000,
"length": 29600,
"mean_depth": 0.2
}
],
"histogram": {
"0": 29600,
"5": 6400
}
}
],
"genes": []
}
105 changes: 105 additions & 0 deletions data/modules/covsnap/sampleC_uneven.covsnap.json
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Original file line number Diff line number Diff line change
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{
"covsnap_version": "0.5.0",
"schema_version": "1.0",
"run": {
"sample_name": "sampleC_uneven",
"bam_path": "/data/sampleC_uneven.bam",
"reference": null,
"engine_used": "mosdepth",
"engine_version": "0.3.8",
"contig_style": "chr",
"run_date": "2026-06-29",
"bed_path": null,
"exon_only": false,
"thresholds": [
1,
5,
10,
20,
30,
50,
100
],
"classify_params": {
"pass_pct_ge_20": 95.0,
"pass_max_pct_zero": 1.0,
"dropout_pct_zero": 5.0,
"dropout_zero_block_bp": 500,
"uneven_cv": 1.0,
"exon_pct_ge_20": 90.0,
"exon_max_pct_zero": 5.0
}
},
"summary": {
"n_targets": 2,
"n_pass": 1,
"status_counts": {
"UNEVEN": 1,
"PASS": 1
}
},
"targets": [
{
"target_id": "EGFR",
"contig": "chr7",
"start": 55019016,
"end": 55211627,
"length_bp": 192611,
"mean_depth": 210.0,
"median_depth": 180.0,
"min_depth": 0,
"max_depth": 1400,
"stdev_depth": 260.0,
"pct_zero": 0.3,
"pct_thresholds": {
"1": 99.0,
"5": 99.0,
"10": 99.0,
"20": 96.0,
"30": 96.0,
"50": 78.0,
"100": 60.0
},
"coverage_status": "UNEVEN",
"n_lowcov_blocks": 0,
"lowcov_total_bp": 0,
"lowcov_blocks": [],
"histogram": {
"0": 600,
"180": 80000,
"1400": 200
}
},
{
"target_id": "KRAS",
"contig": "chr12",
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"end": 25250462,
"length_bp": 45674,
"mean_depth": 120.0,
"median_depth": 119.0,
"min_depth": 30,
"max_depth": 240,
"stdev_depth": 28.0,
"pct_zero": 0.0,
"pct_thresholds": {
"1": 100.0,
"5": 100.0,
"10": 100.0,
"20": 99.0,
"30": 99.0,
"50": 84.5,
"100": 70.0
},
"coverage_status": "PASS",
"n_lowcov_blocks": 0,
"lowcov_total_bp": 0,
"lowcov_blocks": [],
"histogram": {
"30": 1000,
"120": 40000
}
}
],
"genes": []
}