From 088d63c18a65ebe843993765a2f8a54d928d122a Mon Sep 17 00:00:00 2001 From: edogiuili Date: Fri, 23 Jan 2026 17:05:34 +0100 Subject: [PATCH 1/3] add a new summary file to test the new gt-estimator command available from v2.0.0 of methurator package --- .../downsample_command/methurator_summary.yml | 80 ++++ .../methurator_summary.yml | 427 ++++++++++++++++++ 2 files changed, 507 insertions(+) create mode 100644 data/modules/methurator/v2.0.0/downsample_command/methurator_summary.yml create mode 100644 data/modules/methurator/v2.0.0/gtestimator_command/methurator_summary.yml diff --git a/data/modules/methurator/v2.0.0/downsample_command/methurator_summary.yml b/data/modules/methurator/v2.0.0/downsample_command/methurator_summary.yml new file mode 100644 index 00000000..20697074 --- /dev/null +++ b/data/modules/methurator/v2.0.0/downsample_command/methurator_summary.yml @@ -0,0 +1,80 @@ +methurator_summary: + metadata: + date_generated: '2026-01-22T12:57:56.027724' + methurator_version: 0.1.7 + command: methurator downsample + options: + bam_files: + - tests/data/Ecoli.csorted.bam + outdir: tests/data + fasta: tests/data/genome.fa + genome: null + downsampling_percentages: + - 0.1 + - 0.2 + - 0.4 + - 0.6 + - 0.8 + - 1 + minimum_coverage: [1, 3] + rrbs: true + threads: 6 + keep_temporary_files: false + reads_summary: + - Ecoli: + - [0.1, 2] + - [0.2, 4] + - [0.4, 6] + - [0.6, 6] + - [0.8, 8] + - [1.0, 10] + cpgs_summary: + - Ecoli: + - minimum_coverage: 1 + data: + - [0.1, 11] + - [0.2, 18] + - [0.4, 21] + - [0.6, 21] + - [0.8, 32] + - [1.0, 41] + - minimum_coverage: 3 + data: + - [0.1, 0] + - [0.2, 0] + - [0.4, 0] + - [0.6, 0] + - [0.8, 0] + - [1.0, 0] + saturation_analysis: + - Ecoli: + - minimum_coverage: 1 + fit_success: true + beta0: 32.03862722586334 + beta1: 2.07723659313063 + asymptote: 50 + saturation: 71.9 + data: + - [0.0, 0, 0.0, false] + - [0.1, 7, 13.1, false] + - [0.2, 13, 25.2, false] + - [0.4, 22, 44.4, false] + - [0.6, 29, 57.3, false] + - [0.8, 33, 65.9, false] + - [1.0, 36, 71.9, false] + - [1.2, 38, 76.2, true] + - [1.4, 40, 79.4, true] + - [1.6, 41, 81.9, true] + - [1.8, 42, 83.9, true] + - [2.0, 43, 85.5, true] + - minimum_coverage: 3 + fit_success: false + fit_error: Invalid asymptote value + data: + - [0.0, 0, null, false] + - [0.1, 0, null, false] + - [0.2, 0, null, false] + - [0.4, 0, null, false] + - [0.6, 0, null, false] + - [0.8, 0, null, false] + - [1.0, 0, null, false] diff --git a/data/modules/methurator/v2.0.0/gtestimator_command/methurator_summary.yml b/data/modules/methurator/v2.0.0/gtestimator_command/methurator_summary.yml new file mode 100644 index 00000000..189998a8 --- /dev/null +++ b/data/modules/methurator/v2.0.0/gtestimator_command/methurator_summary.yml @@ -0,0 +1,427 @@ +methurator_summary: + metadata: + date_generated: '2026-01-22T13:02:37.414130' + methurator_version: 2.0.0 + command: methurator gt_estimator + options: + cov_files: + - tests/data/new/covs/Ecoli.csorted_CpG.bedGraph.gz + outdir: tests/data/new + minimum_coverage: 1,3 + t_step: 0.05 + t_max: 10.0 + mu: 0.5 + size: 1.0 + mt: 20 + compute_ci: true + bootstrap_replicates: 30 + conf: 0.95 + verbose: false + gt_summary: + - Ecoli: + - minimum_coverage: 1 + data: + - [0.0, 'False', 0, 0, 0] + - [0.05, 'False', 2, 2, 2] + - [0.1, 'False', 4, 4, 4] + - [0.15, 'False', 6, 6, 6] + - [0.2, 'False', 8, 8, 8] + - [0.25, 'False', 10, 10, 10] + - [0.3, 'False', 12, 12, 12] + - [0.35, 'False', 14, 14, 14] + - [0.4, 'False', 16, 16, 16] + - [0.45, 'False', 18, 18, 18] + - [0.5, 'False', 20, 20, 20] + - [0.55, 'False', 22, 22, 22] + - [0.6, 'False', 24, 24, 24] + - [0.65, 'False', 26, 26, 26] + - [0.7, 'False', 28, 28, 28] + - [0.75, 'False', 30, 30, 30] + - [0.8, 'False', 32, 32, 32] + - [0.85, 'False', 34, 34, 34] + - [0.9, 'False', 36, 36, 36] + - [0.95, 'False', 38, 38, 38] + - [1.0, 'False', 41, 41, 41] + - [1.05, 'True', 43, 43, 43] + - [1.1, 'True', 45, 45, 45] + - [1.15, 'True', 47, 47, 47] + - [1.2, 'True', 49, 49, 49] + - [1.25, 'True', 51, 51, 51] + - [1.3, 'True', 53, 53, 53] + - [1.35, 'True', 55, 55, 55] + - [1.4, 'True', 57, 57, 57] + - [1.45, 'True', 59, 59, 59] + - [1.5, 'True', 61, 61, 61] + - [1.55, 'True', 63, 63, 63] + - [1.6, 'True', 65, 65, 65] + - [1.65, 'True', 67, 67, 67] + - [1.7, 'True', 69, 69, 69] + - [1.75, 'True', 71, 71, 71] + - [1.8, 'True', 73, 73, 73] + - [1.85, 'True', 75, 75, 75] + - [1.9, 'True', 77, 77, 77] + - [1.95, 'True', 79, 79, 79] + - [2.0, 'True', 81, 81, 81] + - [2.05, 'True', 84, 84, 84] + - [2.1, 'True', 86, 86, 86] + - [2.15, 'True', 88, 88, 88] + - [2.2, 'True', 90, 90, 90] + - [2.25, 'True', 92, 92, 92] + - [2.3, 'True', 94, 94, 94] + - [2.35, 'True', 96, 96, 96] + - [2.4, 'True', 98, 98, 98] + - [2.45, 'True', 100, 100, 100] + - [2.5, 'True', 102, 102, 102] + - [2.55, 'True', 104, 104, 104] + - [2.6, 'True', 106, 106, 106] + - [2.65, 'True', 108, 108, 108] + - [2.7, 'True', 110, 110, 110] + - [2.75, 'True', 112, 112, 112] + - [2.8, 'True', 114, 114, 114] + - [2.85, 'True', 116, 116, 116] + - [2.9, 'True', 118, 118, 118] + - [2.95, 'True', 120, 120, 120] + - [3.0, 'True', 122, 122, 122] + - [3.05, 'True', 125, 125, 125] + - [3.1, 'True', 127, 127, 127] + - [3.15, 'True', 129, 129, 129] + - [3.2, 'True', 131, 131, 131] + - [3.25, 'True', 133, 133, 133] + - [3.3, 'True', 135, 135, 135] + - [3.35, 'True', 137, 137, 137] + - [3.4, 'True', 139, 139, 139] + - [3.45, 'True', 141, 141, 141] + - [3.5, 'True', 143, 143, 143] + - [3.55, 'True', 145, 145, 145] + - [3.6, 'True', 147, 147, 147] + - [3.65, 'True', 149, 149, 149] + - [3.7, 'True', 151, 151, 151] + - [3.75, 'True', 153, 153, 153] + - [3.8, 'True', 155, 155, 155] + - [3.85, 'True', 157, 157, 157] + - [3.9, 'True', 159, 159, 159] + - [3.95, 'True', 161, 161, 161] + - [4.0, 'True', 163, 163, 163] + - [4.05, 'True', 166, 166, 166] + - [4.1, 'True', 168, 168, 168] + - [4.15, 'True', 170, 170, 170] + - [4.2, 'True', 172, 172, 172] + - [4.25, 'True', 174, 174, 174] + - [4.3, 'True', 176, 176, 176] + - [4.35, 'True', 178, 178, 178] + - [4.4, 'True', 180, 180, 180] + - [4.45, 'True', 182, 182, 182] + - [4.5, 'True', 184, 184, 184] + - [4.55, 'True', 186, 186, 186] + - [4.6, 'True', 188, 188, 188] + - [4.65, 'True', 190, 190, 190] + - [4.7, 'True', 192, 192, 192] + - [4.75, 'True', 194, 194, 194] + - [4.8, 'True', 196, 196, 196] + - [4.85, 'True', 198, 198, 198] + - [4.9, 'True', 200, 200, 200] + - [4.95, 'True', 202, 202, 202] + - [5.0, 'True', 204, 204, 204] + - [5.05, 'True', 207, 207, 207] + - [5.1, 'True', 209, 209, 209] + - [5.15, 'True', 211, 211, 211] + - [5.2, 'True', 213, 213, 213] + - [5.25, 'True', 215, 215, 215] + - [5.3, 'True', 217, 217, 217] + - [5.35, 'True', 219, 219, 219] + - [5.4, 'True', 221, 221, 221] + - [5.45, 'True', 223, 223, 223] + - [5.5, 'True', 225, 225, 225] + - [5.55, 'True', 227, 227, 227] + - [5.6, 'True', 229, 229, 229] + - [5.65, 'True', 231, 231, 231] + - [5.7, 'True', 233, 233, 233] + - [5.75, 'True', 235, 235, 235] + - [5.8, 'True', 237, 237, 237] + - [5.85, 'True', 239, 239, 239] + - [5.9, 'True', 241, 241, 241] + - [5.95, 'True', 243, 243, 243] + - [6.0, 'True', 245, 245, 245] + - [6.05, 'True', 248, 248, 248] + - [6.1, 'True', 250, 250, 250] + - [6.15, 'True', 252, 252, 252] + - [6.2, 'True', 254, 254, 254] + - [6.25, 'True', 256, 256, 256] + - [6.3, 'True', 258, 258, 258] + - [6.35, 'True', 260, 260, 260] + - [6.4, 'True', 262, 262, 262] + - [6.45, 'True', 264, 264, 264] + - [6.5, 'True', 266, 266, 266] + - [6.55, 'True', 268, 268, 268] + - [6.6, 'True', 270, 270, 270] + - [6.65, 'True', 272, 272, 272] + - [6.7, 'True', 274, 274, 274] + - [6.75, 'True', 276, 276, 276] + - [6.8, 'True', 278, 278, 278] + - [6.85, 'True', 280, 280, 280] + - [6.9, 'True', 282, 282, 282] + - [6.95, 'True', 284, 284, 284] + - [7.0, 'True', 286, 286, 286] + - [7.05, 'True', 289, 289, 289] + - [7.1, 'True', 291, 291, 291] + - [7.15, 'True', 293, 293, 293] + - [7.2, 'True', 295, 295, 295] + - [7.25, 'True', 297, 297, 297] + - [7.3, 'True', 299, 299, 299] + - [7.35, 'True', 301, 301, 301] + - [7.4, 'True', 303, 303, 303] + - [7.45, 'True', 305, 305, 305] + - [7.5, 'True', 307, 307, 307] + - [7.55, 'True', 309, 309, 309] + - [7.6, 'True', 311, 311, 311] + - [7.65, 'True', 313, 313, 313] + - [7.7, 'True', 315, 315, 315] + - [7.75, 'True', 317, 317, 317] + - [7.8, 'True', 319, 319, 319] + - [7.85, 'True', 321, 321, 321] + - [7.9, 'True', 323, 323, 323] + - [7.95, 'True', 325, 325, 325] + - [8.0, 'True', 327, 327, 327] + - [8.05, 'True', 330, 330, 330] + - [8.1, 'True', 332, 332, 332] + - [8.15, 'True', 334, 334, 334] + - [8.2, 'True', 336, 336, 336] + - [8.25, 'True', 338, 338, 338] + - [8.3, 'True', 340, 340, 340] + - [8.35, 'True', 342, 342, 342] + - [8.4, 'True', 344, 344, 344] + - [8.45, 'True', 346, 346, 346] + - [8.5, 'True', 348, 348, 348] + - [8.55, 'True', 350, 350, 350] + - [8.6, 'True', 352, 352, 352] + - [8.65, 'True', 354, 354, 354] + - [8.7, 'True', 356, 356, 356] + - [8.75, 'True', 358, 358, 358] + - [8.8, 'True', 360, 360, 360] + - [8.85, 'True', 362, 362, 362] + - [8.9, 'True', 364, 364, 364] + - [8.95, 'True', 366, 366, 366] + - [9.0, 'True', 368, 368, 368] + - [9.05, 'True', 370, 370, 370] + - [9.1, 'True', 373, 373, 373] + - [9.15, 'True', 375, 375, 375] + - [9.2, 'True', 377, 377, 377] + - [9.25, 'True', 379, 379, 379] + - [9.3, 'True', 381, 381, 381] + - [9.35, 'True', 383, 383, 383] + - [9.4, 'True', 385, 385, 385] + - [9.45, 'True', 387, 387, 387] + - [9.5, 'True', 389, 389, 389] + - [9.55, 'True', 391, 391, 391] + - [9.6, 'True', 393, 393, 393] + - [9.65, 'True', 395, 395, 395] + - [9.7, 'True', 397, 397, 397] + - [9.75, 'True', 399, 399, 399] + - [9.8, 'True', 401, 401, 401] + - [9.85, 'True', 403, 403, 403] + - [9.9, 'True', 405, 405, 405] + - [9.95, 'True', 407, 407, 407] + - [10.0, 'True', 409, 409, 409] + - minimum_coverage: 3 + data: + - [0.0, 'False', 0, 0, 0] + - [0.05, 'False', 0, 0, 0] + - [0.1, 'False', 0, 0, 0] + - [0.15, 'False', 0, 0, 0] + - [0.2, 'False', 0, 0, 0] + - [0.25, 'False', 0, 0, 0] + - [0.3, 'False', 0, 0, 0] + - [0.35, 'False', 0, 0, 0] + - [0.4, 'False', 0, 0, 0] + - [0.45, 'False', 0, 0, 0] + - [0.5, 'False', 0, 0, 0] + - [0.55, 'False', 0, 0, 0] + - [0.6, 'False', 0, 0, 0] + - [0.65, 'False', 0, 0, 0] + - [0.7, 'False', 0, 0, 0] + - [0.75, 'False', 0, 0, 0] + - [0.8, 'False', 0, 0, 0] + - [0.85, 'False', 0, 0, 0] + - [0.9, 'False', 0, 0, 0] + - [0.95, 'False', 0, 0, 0] + - [1.0, 'False', 0, 0, 0] + - [1.05, 'True', 0, 0, 0] + - [1.1, 'True', 0, 0, 0] + - [1.15, 'True', 0, 0, 0] + - [1.2, 'True', 0, 0, 0] + - [1.25, 'True', 0, 0, 0] + - [1.3, 'True', 0, 0, 0] + - [1.35, 'True', 0, 0, 0] + - [1.4, 'True', 0, 0, 0] + - [1.45, 'True', 0, 0, 0] + - [1.5, 'True', 0, 0, 0] + - [1.55, 'True', 0, 0, 0] + - [1.6, 'True', 0, 0, 0] + - [1.65, 'True', 0, 0, 0] + - [1.7, 'True', 0, 0, 0] + - [1.75, 'True', 0, 0, 0] + - [1.8, 'True', 0, 0, 0] + - [1.85, 'True', 0, 0, 0] + - [1.9, 'True', 0, 0, 0] + - [1.95, 'True', 0, 0, 0] + - [2.0, 'True', 0, 0, 0] + - [2.05, 'True', 0, 0, 0] + - [2.1, 'True', 0, 0, 0] + - [2.15, 'True', 0, 0, 0] + - [2.2, 'True', 0, 0, 0] + - [2.25, 'True', 0, 0, 0] + - [2.3, 'True', 0, 0, 0] + - [2.35, 'True', 0, 0, 0] + - [2.4, 'True', 0, 0, 0] + - [2.45, 'True', 0, 0, 0] + - [2.5, 'True', 0, 0, 0] + - [2.55, 'True', 0, 0, 0] + - [2.6, 'True', 0, 0, 0] + - [2.65, 'True', 0, 0, 0] + - [2.7, 'True', 0, 0, 0] + - [2.75, 'True', 0, 0, 0] + - [2.8, 'True', 0, 0, 0] + - [2.85, 'True', 0, 0, 0] + - [2.9, 'True', 0, 0, 0] + - [2.95, 'True', 0, 0, 0] + - [3.0, 'True', 0, 0, 0] + - [3.05, 'True', 0, 0, 0] + - [3.1, 'True', 0, 0, 0] + - [3.15, 'True', 0, 0, 0] + - [3.2, 'True', 0, 0, 0] + - [3.25, 'True', 0, 0, 0] + - [3.3, 'True', 0, 0, 0] + - [3.35, 'True', 0, 0, 0] + - [3.4, 'True', 0, 0, 0] + - [3.45, 'True', 0, 0, 0] + - [3.5, 'True', 0, 0, 0] + - [3.55, 'True', 0, 0, 0] + - [3.6, 'True', 0, 0, 0] + - [3.65, 'True', 0, 0, 0] + - [3.7, 'True', 0, 0, 0] + - [3.75, 'True', 0, 0, 0] + - [3.8, 'True', 0, 0, 0] + - [3.85, 'True', 0, 0, 0] + - [3.9, 'True', 0, 0, 0] + - [3.95, 'True', 0, 0, 0] + - [4.0, 'True', 0, 0, 0] + - [4.05, 'True', 0, 0, 0] + - [4.1, 'True', 0, 0, 0] + - [4.15, 'True', 0, 0, 0] + - [4.2, 'True', 0, 0, 0] + - [4.25, 'True', 0, 0, 0] + - [4.3, 'True', 0, 0, 0] + - [4.35, 'True', 0, 0, 0] + - [4.4, 'True', 0, 0, 0] + - [4.45, 'True', 0, 0, 0] + - [4.5, 'True', 0, 0, 0] + - [4.55, 'True', 0, 0, 0] + - [4.6, 'True', 0, 0, 0] + - [4.65, 'True', 0, 0, 0] + - [4.7, 'True', 0, 0, 0] + - [4.75, 'True', 0, 0, 0] + - [4.8, 'True', 0, 0, 0] + - [4.85, 'True', 0, 0, 0] + - [4.9, 'True', 0, 0, 0] + - [4.95, 'True', 0, 0, 0] + - [5.0, 'True', 0, 0, 0] + - [5.05, 'True', 0, 0, 0] + - [5.1, 'True', 0, 0, 0] + - [5.15, 'True', 0, 0, 0] + - [5.2, 'True', 0, 0, 0] + - [5.25, 'True', 0, 0, 0] + - [5.3, 'True', 0, 0, 0] + - [5.35, 'True', 0, 0, 0] + - [5.4, 'True', 0, 0, 0] + - [5.45, 'True', 0, 0, 0] + - [5.5, 'True', 0, 0, 0] + - [5.55, 'True', 0, 0, 0] + - [5.6, 'True', 0, 0, 0] + - [5.65, 'True', 0, 0, 0] + - [5.7, 'True', 0, 0, 0] + - [5.75, 'True', 0, 0, 0] + - [5.8, 'True', 0, 0, 0] + - [5.85, 'True', 0, 0, 0] + - [5.9, 'True', 0, 0, 0] + - [5.95, 'True', 0, 0, 0] + - [6.0, 'True', 0, 0, 0] + - [6.05, 'True', 0, 0, 0] + - [6.1, 'True', 0, 0, 0] + - [6.15, 'True', 0, 0, 0] + - [6.2, 'True', 0, 0, 0] + - [6.25, 'True', 0, 0, 0] + - [6.3, 'True', 0, 0, 0] + - [6.35, 'True', 0, 0, 0] + - [6.4, 'True', 0, 0, 0] + - [6.45, 'True', 0, 0, 0] + - [6.5, 'True', 0, 0, 0] + - [6.55, 'True', 0, 0, 0] + - [6.6, 'True', 0, 0, 0] + - [6.65, 'True', 0, 0, 0] + - [6.7, 'True', 0, 0, 0] + - [6.75, 'True', 0, 0, 0] + - [6.8, 'True', 0, 0, 0] + - [6.85, 'True', 0, 0, 0] + - [6.9, 'True', 0, 0, 0] + - [6.95, 'True', 0, 0, 0] + - [7.0, 'True', 0, 0, 0] + - [7.05, 'True', 0, 0, 0] + - [7.1, 'True', 0, 0, 0] + - [7.15, 'True', 0, 0, 0] + - [7.2, 'True', 0, 0, 0] + - [7.25, 'True', 0, 0, 0] + - [7.3, 'True', 0, 0, 0] + - [7.35, 'True', 0, 0, 0] + - [7.4, 'True', 0, 0, 0] + - [7.45, 'True', 0, 0, 0] + - [7.5, 'True', 0, 0, 0] + - [7.55, 'True', 0, 0, 0] + - [7.6, 'True', 0, 0, 0] + - [7.65, 'True', 0, 0, 0] + - [7.7, 'True', 0, 0, 0] + - [7.75, 'True', 0, 0, 0] + - [7.8, 'True', 0, 0, 0] + - [7.85, 'True', 0, 0, 0] + - [7.9, 'True', 0, 0, 0] + - [7.95, 'True', 0, 0, 0] + - [8.0, 'True', 0, 0, 0] + - [8.05, 'True', 0, 0, 0] + - [8.1, 'True', 0, 0, 0] + - [8.15, 'True', 0, 0, 0] + - [8.2, 'True', 0, 0, 0] + - [8.25, 'True', 0, 0, 0] + - [8.3, 'True', 0, 0, 0] + - [8.35, 'True', 0, 0, 0] + - [8.4, 'True', 0, 0, 0] + - [8.45, 'True', 0, 0, 0] + - [8.5, 'True', 0, 0, 0] + - [8.55, 'True', 0, 0, 0] + - [8.6, 'True', 0, 0, 0] + - [8.65, 'True', 0, 0, 0] + - [8.7, 'True', 0, 0, 0] + - [8.75, 'True', 0, 0, 0] + - [8.8, 'True', 0, 0, 0] + - [8.85, 'True', 0, 0, 0] + - [8.9, 'True', 0, 0, 0] + - [8.95, 'True', 0, 0, 0] + - [9.0, 'True', 0, 0, 0] + - [9.05, 'True', 0, 0, 0] + - [9.1, 'True', 0, 0, 0] + - [9.15, 'True', 0, 0, 0] + - [9.2, 'True', 0, 0, 0] + - [9.25, 'True', 0, 0, 0] + - [9.3, 'True', 0, 0, 0] + - [9.35, 'True', 0, 0, 0] + - [9.4, 'True', 0, 0, 0] + - [9.45, 'True', 0, 0, 0] + - [9.5, 'True', 0, 0, 0] + - [9.55, 'True', 0, 0, 0] + - [9.6, 'True', 0, 0, 0] + - [9.65, 'True', 0, 0, 0] + - [9.7, 'True', 0, 0, 0] + - [9.75, 'True', 0, 0, 0] + - [9.8, 'True', 0, 0, 0] + - [9.85, 'True', 0, 0, 0] + - [9.9, 'True', 0, 0, 0] + - [9.95, 'True', 0, 0, 0] + - [10.0, 'True', 0, 0, 0] From 4c695c14f5364aa883b5fb9ef9dedd2346601721 Mon Sep 17 00:00:00 2001 From: edogiuili Date: Tue, 27 Jan 2026 18:02:11 +0100 Subject: [PATCH 2/3] add test data for v2.1.0 --- .../methurator_summary.yml | 427 ----------------- .../downsample_command/methurator_summary.yml | 0 .../methurator_summary.yml | 429 ++++++++++++++++++ 3 files changed, 429 insertions(+), 427 deletions(-) delete mode 100644 data/modules/methurator/v2.0.0/gtestimator_command/methurator_summary.yml rename data/modules/methurator/{v2.0.0 => v2.1.0}/downsample_command/methurator_summary.yml (100%) create mode 100644 data/modules/methurator/v2.1.0/gtestimator_command/methurator_summary.yml diff --git a/data/modules/methurator/v2.0.0/gtestimator_command/methurator_summary.yml b/data/modules/methurator/v2.0.0/gtestimator_command/methurator_summary.yml deleted file mode 100644 index 189998a8..00000000 --- a/data/modules/methurator/v2.0.0/gtestimator_command/methurator_summary.yml +++ /dev/null @@ -1,427 +0,0 @@ -methurator_summary: - metadata: - date_generated: '2026-01-22T13:02:37.414130' - methurator_version: 2.0.0 - command: methurator gt_estimator - options: - cov_files: - - tests/data/new/covs/Ecoli.csorted_CpG.bedGraph.gz - outdir: tests/data/new - minimum_coverage: 1,3 - t_step: 0.05 - t_max: 10.0 - mu: 0.5 - size: 1.0 - mt: 20 - compute_ci: true - bootstrap_replicates: 30 - conf: 0.95 - verbose: false - gt_summary: - - Ecoli: - - minimum_coverage: 1 - data: - - [0.0, 'False', 0, 0, 0] - - [0.05, 'False', 2, 2, 2] - - [0.1, 'False', 4, 4, 4] - - [0.15, 'False', 6, 6, 6] - - [0.2, 'False', 8, 8, 8] - - [0.25, 'False', 10, 10, 10] - - [0.3, 'False', 12, 12, 12] - - [0.35, 'False', 14, 14, 14] - - [0.4, 'False', 16, 16, 16] - - [0.45, 'False', 18, 18, 18] - - [0.5, 'False', 20, 20, 20] - - [0.55, 'False', 22, 22, 22] - - [0.6, 'False', 24, 24, 24] - - [0.65, 'False', 26, 26, 26] - - [0.7, 'False', 28, 28, 28] - - [0.75, 'False', 30, 30, 30] - - [0.8, 'False', 32, 32, 32] - - [0.85, 'False', 34, 34, 34] - - [0.9, 'False', 36, 36, 36] - - [0.95, 'False', 38, 38, 38] - - [1.0, 'False', 41, 41, 41] - - [1.05, 'True', 43, 43, 43] - - [1.1, 'True', 45, 45, 45] - - [1.15, 'True', 47, 47, 47] - - [1.2, 'True', 49, 49, 49] - - [1.25, 'True', 51, 51, 51] - - [1.3, 'True', 53, 53, 53] - - [1.35, 'True', 55, 55, 55] - - [1.4, 'True', 57, 57, 57] - - [1.45, 'True', 59, 59, 59] - - [1.5, 'True', 61, 61, 61] - - [1.55, 'True', 63, 63, 63] - - [1.6, 'True', 65, 65, 65] - - [1.65, 'True', 67, 67, 67] - - [1.7, 'True', 69, 69, 69] - - [1.75, 'True', 71, 71, 71] - - [1.8, 'True', 73, 73, 73] - - [1.85, 'True', 75, 75, 75] - - [1.9, 'True', 77, 77, 77] - - [1.95, 'True', 79, 79, 79] - - [2.0, 'True', 81, 81, 81] - - [2.05, 'True', 84, 84, 84] - - [2.1, 'True', 86, 86, 86] - - [2.15, 'True', 88, 88, 88] - - [2.2, 'True', 90, 90, 90] - - [2.25, 'True', 92, 92, 92] - - [2.3, 'True', 94, 94, 94] - - [2.35, 'True', 96, 96, 96] - - [2.4, 'True', 98, 98, 98] - - [2.45, 'True', 100, 100, 100] - - [2.5, 'True', 102, 102, 102] - - [2.55, 'True', 104, 104, 104] - - [2.6, 'True', 106, 106, 106] - - [2.65, 'True', 108, 108, 108] - - [2.7, 'True', 110, 110, 110] - - [2.75, 'True', 112, 112, 112] - - [2.8, 'True', 114, 114, 114] - - [2.85, 'True', 116, 116, 116] - - [2.9, 'True', 118, 118, 118] - - [2.95, 'True', 120, 120, 120] - - [3.0, 'True', 122, 122, 122] - - [3.05, 'True', 125, 125, 125] - - [3.1, 'True', 127, 127, 127] - - [3.15, 'True', 129, 129, 129] - - [3.2, 'True', 131, 131, 131] - - [3.25, 'True', 133, 133, 133] - - [3.3, 'True', 135, 135, 135] - - [3.35, 'True', 137, 137, 137] - - [3.4, 'True', 139, 139, 139] - - [3.45, 'True', 141, 141, 141] - - [3.5, 'True', 143, 143, 143] - - [3.55, 'True', 145, 145, 145] - - [3.6, 'True', 147, 147, 147] - - [3.65, 'True', 149, 149, 149] - - [3.7, 'True', 151, 151, 151] - - [3.75, 'True', 153, 153, 153] - - [3.8, 'True', 155, 155, 155] - - [3.85, 'True', 157, 157, 157] - - [3.9, 'True', 159, 159, 159] - - [3.95, 'True', 161, 161, 161] - - [4.0, 'True', 163, 163, 163] - - [4.05, 'True', 166, 166, 166] - - [4.1, 'True', 168, 168, 168] - - [4.15, 'True', 170, 170, 170] - - [4.2, 'True', 172, 172, 172] - - [4.25, 'True', 174, 174, 174] - - [4.3, 'True', 176, 176, 176] - - [4.35, 'True', 178, 178, 178] - - [4.4, 'True', 180, 180, 180] - - [4.45, 'True', 182, 182, 182] - - [4.5, 'True', 184, 184, 184] - - [4.55, 'True', 186, 186, 186] - - [4.6, 'True', 188, 188, 188] - - [4.65, 'True', 190, 190, 190] - - [4.7, 'True', 192, 192, 192] - - [4.75, 'True', 194, 194, 194] - - [4.8, 'True', 196, 196, 196] - - [4.85, 'True', 198, 198, 198] - - [4.9, 'True', 200, 200, 200] - - [4.95, 'True', 202, 202, 202] - - [5.0, 'True', 204, 204, 204] - - [5.05, 'True', 207, 207, 207] - - [5.1, 'True', 209, 209, 209] - - [5.15, 'True', 211, 211, 211] - - [5.2, 'True', 213, 213, 213] - - [5.25, 'True', 215, 215, 215] - - [5.3, 'True', 217, 217, 217] - - [5.35, 'True', 219, 219, 219] - - [5.4, 'True', 221, 221, 221] - - [5.45, 'True', 223, 223, 223] - - [5.5, 'True', 225, 225, 225] - - [5.55, 'True', 227, 227, 227] - - [5.6, 'True', 229, 229, 229] - - [5.65, 'True', 231, 231, 231] - - [5.7, 'True', 233, 233, 233] - - [5.75, 'True', 235, 235, 235] - - [5.8, 'True', 237, 237, 237] - - [5.85, 'True', 239, 239, 239] - - [5.9, 'True', 241, 241, 241] - - [5.95, 'True', 243, 243, 243] - - [6.0, 'True', 245, 245, 245] - - [6.05, 'True', 248, 248, 248] - - [6.1, 'True', 250, 250, 250] - - [6.15, 'True', 252, 252, 252] - - [6.2, 'True', 254, 254, 254] - - [6.25, 'True', 256, 256, 256] - - [6.3, 'True', 258, 258, 258] - - [6.35, 'True', 260, 260, 260] - - [6.4, 'True', 262, 262, 262] - - [6.45, 'True', 264, 264, 264] - - [6.5, 'True', 266, 266, 266] - - [6.55, 'True', 268, 268, 268] - - [6.6, 'True', 270, 270, 270] - - [6.65, 'True', 272, 272, 272] - - [6.7, 'True', 274, 274, 274] - - [6.75, 'True', 276, 276, 276] - - [6.8, 'True', 278, 278, 278] - - [6.85, 'True', 280, 280, 280] - - [6.9, 'True', 282, 282, 282] - - [6.95, 'True', 284, 284, 284] - - [7.0, 'True', 286, 286, 286] - - [7.05, 'True', 289, 289, 289] - - [7.1, 'True', 291, 291, 291] - - [7.15, 'True', 293, 293, 293] - - [7.2, 'True', 295, 295, 295] - - [7.25, 'True', 297, 297, 297] - - [7.3, 'True', 299, 299, 299] - - [7.35, 'True', 301, 301, 301] - - [7.4, 'True', 303, 303, 303] - - [7.45, 'True', 305, 305, 305] - - [7.5, 'True', 307, 307, 307] - - [7.55, 'True', 309, 309, 309] - - [7.6, 'True', 311, 311, 311] - - [7.65, 'True', 313, 313, 313] - - [7.7, 'True', 315, 315, 315] - - [7.75, 'True', 317, 317, 317] - - [7.8, 'True', 319, 319, 319] - - [7.85, 'True', 321, 321, 321] - - [7.9, 'True', 323, 323, 323] - - [7.95, 'True', 325, 325, 325] - - [8.0, 'True', 327, 327, 327] - - [8.05, 'True', 330, 330, 330] - - [8.1, 'True', 332, 332, 332] - - [8.15, 'True', 334, 334, 334] - - [8.2, 'True', 336, 336, 336] - - [8.25, 'True', 338, 338, 338] - - [8.3, 'True', 340, 340, 340] - - [8.35, 'True', 342, 342, 342] - - [8.4, 'True', 344, 344, 344] - - [8.45, 'True', 346, 346, 346] - - [8.5, 'True', 348, 348, 348] - - [8.55, 'True', 350, 350, 350] - - [8.6, 'True', 352, 352, 352] - - [8.65, 'True', 354, 354, 354] - - [8.7, 'True', 356, 356, 356] - - [8.75, 'True', 358, 358, 358] - - [8.8, 'True', 360, 360, 360] - - [8.85, 'True', 362, 362, 362] - - [8.9, 'True', 364, 364, 364] - - [8.95, 'True', 366, 366, 366] - - [9.0, 'True', 368, 368, 368] - - [9.05, 'True', 370, 370, 370] - - [9.1, 'True', 373, 373, 373] - - [9.15, 'True', 375, 375, 375] - - [9.2, 'True', 377, 377, 377] - - [9.25, 'True', 379, 379, 379] - - [9.3, 'True', 381, 381, 381] - - [9.35, 'True', 383, 383, 383] - - [9.4, 'True', 385, 385, 385] - - [9.45, 'True', 387, 387, 387] - - [9.5, 'True', 389, 389, 389] - - [9.55, 'True', 391, 391, 391] - - [9.6, 'True', 393, 393, 393] - - [9.65, 'True', 395, 395, 395] - - [9.7, 'True', 397, 397, 397] - - [9.75, 'True', 399, 399, 399] - - [9.8, 'True', 401, 401, 401] - - [9.85, 'True', 403, 403, 403] - - [9.9, 'True', 405, 405, 405] - - [9.95, 'True', 407, 407, 407] - - [10.0, 'True', 409, 409, 409] - - minimum_coverage: 3 - data: - - [0.0, 'False', 0, 0, 0] - - [0.05, 'False', 0, 0, 0] - - [0.1, 'False', 0, 0, 0] - - [0.15, 'False', 0, 0, 0] - - [0.2, 'False', 0, 0, 0] - - [0.25, 'False', 0, 0, 0] - - [0.3, 'False', 0, 0, 0] - - [0.35, 'False', 0, 0, 0] - - [0.4, 'False', 0, 0, 0] - - [0.45, 'False', 0, 0, 0] - - [0.5, 'False', 0, 0, 0] - - [0.55, 'False', 0, 0, 0] - - [0.6, 'False', 0, 0, 0] - - [0.65, 'False', 0, 0, 0] - - [0.7, 'False', 0, 0, 0] - - [0.75, 'False', 0, 0, 0] - - [0.8, 'False', 0, 0, 0] - - [0.85, 'False', 0, 0, 0] - - [0.9, 'False', 0, 0, 0] - - [0.95, 'False', 0, 0, 0] - - [1.0, 'False', 0, 0, 0] - - [1.05, 'True', 0, 0, 0] - - [1.1, 'True', 0, 0, 0] - - [1.15, 'True', 0, 0, 0] - - [1.2, 'True', 0, 0, 0] - - [1.25, 'True', 0, 0, 0] - - [1.3, 'True', 0, 0, 0] - - [1.35, 'True', 0, 0, 0] - - [1.4, 'True', 0, 0, 0] - - [1.45, 'True', 0, 0, 0] - - [1.5, 'True', 0, 0, 0] - - [1.55, 'True', 0, 0, 0] - - [1.6, 'True', 0, 0, 0] - - [1.65, 'True', 0, 0, 0] - - [1.7, 'True', 0, 0, 0] - - [1.75, 'True', 0, 0, 0] - - [1.8, 'True', 0, 0, 0] - - [1.85, 'True', 0, 0, 0] - - [1.9, 'True', 0, 0, 0] - - [1.95, 'True', 0, 0, 0] - - [2.0, 'True', 0, 0, 0] - - [2.05, 'True', 0, 0, 0] - - [2.1, 'True', 0, 0, 0] - - [2.15, 'True', 0, 0, 0] - - [2.2, 'True', 0, 0, 0] - - [2.25, 'True', 0, 0, 0] - - [2.3, 'True', 0, 0, 0] - - [2.35, 'True', 0, 0, 0] - - [2.4, 'True', 0, 0, 0] - - [2.45, 'True', 0, 0, 0] - - [2.5, 'True', 0, 0, 0] - - [2.55, 'True', 0, 0, 0] - - [2.6, 'True', 0, 0, 0] - - [2.65, 'True', 0, 0, 0] - - [2.7, 'True', 0, 0, 0] - - [2.75, 'True', 0, 0, 0] - - [2.8, 'True', 0, 0, 0] - - [2.85, 'True', 0, 0, 0] - - [2.9, 'True', 0, 0, 0] - - [2.95, 'True', 0, 0, 0] - - [3.0, 'True', 0, 0, 0] - - [3.05, 'True', 0, 0, 0] - - [3.1, 'True', 0, 0, 0] - - [3.15, 'True', 0, 0, 0] - - [3.2, 'True', 0, 0, 0] - - [3.25, 'True', 0, 0, 0] - - [3.3, 'True', 0, 0, 0] - - [3.35, 'True', 0, 0, 0] - - [3.4, 'True', 0, 0, 0] - - [3.45, 'True', 0, 0, 0] - - [3.5, 'True', 0, 0, 0] - - [3.55, 'True', 0, 0, 0] - - [3.6, 'True', 0, 0, 0] - - [3.65, 'True', 0, 0, 0] - - [3.7, 'True', 0, 0, 0] - - [3.75, 'True', 0, 0, 0] - - [3.8, 'True', 0, 0, 0] - - [3.85, 'True', 0, 0, 0] - - [3.9, 'True', 0, 0, 0] - - [3.95, 'True', 0, 0, 0] - - [4.0, 'True', 0, 0, 0] - - [4.05, 'True', 0, 0, 0] - - [4.1, 'True', 0, 0, 0] - - [4.15, 'True', 0, 0, 0] - - [4.2, 'True', 0, 0, 0] - - [4.25, 'True', 0, 0, 0] - - [4.3, 'True', 0, 0, 0] - - [4.35, 'True', 0, 0, 0] - - [4.4, 'True', 0, 0, 0] - - [4.45, 'True', 0, 0, 0] - - [4.5, 'True', 0, 0, 0] - - [4.55, 'True', 0, 0, 0] - - [4.6, 'True', 0, 0, 0] - - [4.65, 'True', 0, 0, 0] - - [4.7, 'True', 0, 0, 0] - - [4.75, 'True', 0, 0, 0] - - [4.8, 'True', 0, 0, 0] - - [4.85, 'True', 0, 0, 0] - - [4.9, 'True', 0, 0, 0] - - [4.95, 'True', 0, 0, 0] - - [5.0, 'True', 0, 0, 0] - - [5.05, 'True', 0, 0, 0] - - [5.1, 'True', 0, 0, 0] - - [5.15, 'True', 0, 0, 0] - - [5.2, 'True', 0, 0, 0] - - [5.25, 'True', 0, 0, 0] - - [5.3, 'True', 0, 0, 0] - - [5.35, 'True', 0, 0, 0] - - [5.4, 'True', 0, 0, 0] - - [5.45, 'True', 0, 0, 0] - - [5.5, 'True', 0, 0, 0] - - [5.55, 'True', 0, 0, 0] - - [5.6, 'True', 0, 0, 0] - - [5.65, 'True', 0, 0, 0] - - [5.7, 'True', 0, 0, 0] - - [5.75, 'True', 0, 0, 0] - - [5.8, 'True', 0, 0, 0] - - [5.85, 'True', 0, 0, 0] - - [5.9, 'True', 0, 0, 0] - - [5.95, 'True', 0, 0, 0] - - [6.0, 'True', 0, 0, 0] - - [6.05, 'True', 0, 0, 0] - - [6.1, 'True', 0, 0, 0] - - [6.15, 'True', 0, 0, 0] - - [6.2, 'True', 0, 0, 0] - - [6.25, 'True', 0, 0, 0] - - [6.3, 'True', 0, 0, 0] - - [6.35, 'True', 0, 0, 0] - - [6.4, 'True', 0, 0, 0] - - [6.45, 'True', 0, 0, 0] - - [6.5, 'True', 0, 0, 0] - - [6.55, 'True', 0, 0, 0] - - [6.6, 'True', 0, 0, 0] - - [6.65, 'True', 0, 0, 0] - - [6.7, 'True', 0, 0, 0] - - [6.75, 'True', 0, 0, 0] - - [6.8, 'True', 0, 0, 0] - - [6.85, 'True', 0, 0, 0] - - [6.9, 'True', 0, 0, 0] - - [6.95, 'True', 0, 0, 0] - - [7.0, 'True', 0, 0, 0] - - [7.05, 'True', 0, 0, 0] - - [7.1, 'True', 0, 0, 0] - - [7.15, 'True', 0, 0, 0] - - [7.2, 'True', 0, 0, 0] - - [7.25, 'True', 0, 0, 0] - - [7.3, 'True', 0, 0, 0] - - [7.35, 'True', 0, 0, 0] - - [7.4, 'True', 0, 0, 0] - - [7.45, 'True', 0, 0, 0] - - [7.5, 'True', 0, 0, 0] - - [7.55, 'True', 0, 0, 0] - - [7.6, 'True', 0, 0, 0] - - [7.65, 'True', 0, 0, 0] - - [7.7, 'True', 0, 0, 0] - - [7.75, 'True', 0, 0, 0] - - [7.8, 'True', 0, 0, 0] - - [7.85, 'True', 0, 0, 0] - - [7.9, 'True', 0, 0, 0] - - [7.95, 'True', 0, 0, 0] - - [8.0, 'True', 0, 0, 0] - - [8.05, 'True', 0, 0, 0] - - [8.1, 'True', 0, 0, 0] - - [8.15, 'True', 0, 0, 0] - - [8.2, 'True', 0, 0, 0] - - [8.25, 'True', 0, 0, 0] - - [8.3, 'True', 0, 0, 0] - - [8.35, 'True', 0, 0, 0] - - [8.4, 'True', 0, 0, 0] - - [8.45, 'True', 0, 0, 0] - - [8.5, 'True', 0, 0, 0] - - [8.55, 'True', 0, 0, 0] - - [8.6, 'True', 0, 0, 0] - - [8.65, 'True', 0, 0, 0] - - [8.7, 'True', 0, 0, 0] - - [8.75, 'True', 0, 0, 0] - - [8.8, 'True', 0, 0, 0] - - [8.85, 'True', 0, 0, 0] - - [8.9, 'True', 0, 0, 0] - - [8.95, 'True', 0, 0, 0] - - [9.0, 'True', 0, 0, 0] - - [9.05, 'True', 0, 0, 0] - - [9.1, 'True', 0, 0, 0] - - [9.15, 'True', 0, 0, 0] - - [9.2, 'True', 0, 0, 0] - - [9.25, 'True', 0, 0, 0] - - [9.3, 'True', 0, 0, 0] - - [9.35, 'True', 0, 0, 0] - - [9.4, 'True', 0, 0, 0] - - [9.45, 'True', 0, 0, 0] - - [9.5, 'True', 0, 0, 0] - - [9.55, 'True', 0, 0, 0] - - [9.6, 'True', 0, 0, 0] - - [9.65, 'True', 0, 0, 0] - - [9.7, 'True', 0, 0, 0] - - [9.75, 'True', 0, 0, 0] - - [9.8, 'True', 0, 0, 0] - - [9.85, 'True', 0, 0, 0] - - [9.9, 'True', 0, 0, 0] - - [9.95, 'True', 0, 0, 0] - - [10.0, 'True', 0, 0, 0] diff --git a/data/modules/methurator/v2.0.0/downsample_command/methurator_summary.yml b/data/modules/methurator/v2.1.0/downsample_command/methurator_summary.yml similarity index 100% rename from data/modules/methurator/v2.0.0/downsample_command/methurator_summary.yml rename to data/modules/methurator/v2.1.0/downsample_command/methurator_summary.yml diff --git a/data/modules/methurator/v2.1.0/gtestimator_command/methurator_summary.yml b/data/modules/methurator/v2.1.0/gtestimator_command/methurator_summary.yml new file mode 100644 index 00000000..7e4d1d60 --- /dev/null +++ b/data/modules/methurator/v2.1.0/gtestimator_command/methurator_summary.yml @@ -0,0 +1,429 @@ +methurator_summary: + metadata: + date_generated: '2026-01-27T17:04:56.600219' + methurator_version: 2.1.0 + command: methurator gt_estimator + options: + cov_files: + - output/covs/Ecoli.csorted_CpG.bedGraph.gz + outdir: output + minimum_coverage: 1,3 + t_step: 0.05 + t_max: 10.0 + mu: 0.5 + size: 1.0 + mt: 20 + compute_ci: false + bootstrap_replicates: 30 + conf: 0.95 + verbose: false + gt_summary: + - Ecoli.csorted_CpG.bedGraph: + - minimum_coverage: 1 + asymptote(1000t): 39894 + data: + - [0.0, 0.0, 0, .nan, .nan] + - [0.05, 0.0001, 2, .nan, .nan] + - [0.1, 0.0001, 4, .nan, .nan] + - [0.15, 0.0002, 6, .nan, .nan] + - [0.2, 0.0002, 8, .nan, .nan] + - [0.25, 0.0003, 10, .nan, .nan] + - [0.3, 0.0003, 12, .nan, .nan] + - [0.35, 0.0004, 14, .nan, .nan] + - [0.4, 0.0004, 16, .nan, .nan] + - [0.45, 0.0005, 18, .nan, .nan] + - [0.5, 0.0005, 20, .nan, .nan] + - [0.55, 0.0006, 22, .nan, .nan] + - [0.6, 0.0006, 24, .nan, .nan] + - [0.65, 0.0007, 26, .nan, .nan] + - [0.7, 0.0007, 28, .nan, .nan] + - [0.75, 0.0008, 30, .nan, .nan] + - [0.8, 0.0008, 32, .nan, .nan] + - [0.85, 0.0009, 34, .nan, .nan] + - [0.9, 0.0009, 36, .nan, .nan] + - [0.95, 0.001, 38, .nan, .nan] + - [1.0, 0.001, 41, .nan, .nan] + - [1.05, 0.0011, 43, .nan, .nan] + - [1.1, 0.0011, 45, .nan, .nan] + - [1.15, 0.0012, 47, .nan, .nan] + - [1.2, 0.0012, 49, .nan, .nan] + - [1.25, 0.0013, 51, .nan, .nan] + - [1.3, 0.0013, 53, .nan, .nan] + - [1.35, 0.0014, 55, .nan, .nan] + - [1.4, 0.0014, 57, .nan, .nan] + - [1.45, 0.0015, 59, .nan, .nan] + - [1.5, 0.0015, 61, .nan, .nan] + - [1.55, 0.0016, 63, .nan, .nan] + - [1.6, 0.0016, 65, .nan, .nan] + - [1.65, 0.0017, 67, .nan, .nan] + - [1.7, 0.0017, 69, .nan, .nan] + - [1.75, 0.0018, 71, .nan, .nan] + - [1.8, 0.0018, 73, .nan, .nan] + - [1.85, 0.0019, 75, .nan, .nan] + - [1.9, 0.0019, 77, .nan, .nan] + - [1.95, 0.002, 79, .nan, .nan] + - [2.0, 0.002, 81, .nan, .nan] + - [2.05, 0.0021, 84, .nan, .nan] + - [2.1, 0.0022, 86, .nan, .nan] + - [2.15, 0.0022, 88, .nan, .nan] + - [2.2, 0.0023, 90, .nan, .nan] + - [2.25, 0.0023, 92, .nan, .nan] + - [2.3, 0.0024, 94, .nan, .nan] + - [2.35, 0.0024, 96, .nan, .nan] + - [2.4, 0.0025, 98, .nan, .nan] + - [2.45, 0.0025, 100, .nan, .nan] + - [2.5, 0.0026, 102, .nan, .nan] + - [2.55, 0.0026, 104, .nan, .nan] + - [2.6, 0.0027, 106, .nan, .nan] + - [2.65, 0.0027, 108, .nan, .nan] + - [2.7, 0.0028, 110, .nan, .nan] + - [2.75, 0.0028, 112, .nan, .nan] + - [2.8, 0.0029, 114, .nan, .nan] + - [2.85, 0.0029, 116, .nan, .nan] + - [2.9, 0.003, 118, .nan, .nan] + - [2.95, 0.003, 120, .nan, .nan] + - [3.0, 0.0031, 122, .nan, .nan] + - [3.05, 0.0031, 125, .nan, .nan] + - [3.1, 0.0032, 127, .nan, .nan] + - [3.15, 0.0032, 129, .nan, .nan] + - [3.2, 0.0033, 131, .nan, .nan] + - [3.25, 0.0033, 133, .nan, .nan] + - [3.3, 0.0034, 135, .nan, .nan] + - [3.35, 0.0034, 137, .nan, .nan] + - [3.4, 0.0035, 139, .nan, .nan] + - [3.45, 0.0035, 141, .nan, .nan] + - [3.5, 0.0036, 143, .nan, .nan] + - [3.55, 0.0036, 145, .nan, .nan] + - [3.6, 0.0037, 147, .nan, .nan] + - [3.65, 0.0037, 149, .nan, .nan] + - [3.7, 0.0038, 151, .nan, .nan] + - [3.75, 0.0038, 153, .nan, .nan] + - [3.8, 0.0039, 155, .nan, .nan] + - [3.85, 0.0039, 157, .nan, .nan] + - [3.9, 0.004, 159, .nan, .nan] + - [3.95, 0.004, 161, .nan, .nan] + - [4.0, 0.0041, 163, .nan, .nan] + - [4.05, 0.0042, 166, .nan, .nan] + - [4.1, 0.0042, 168, .nan, .nan] + - [4.15, 0.0043, 170, .nan, .nan] + - [4.2, 0.0043, 172, .nan, .nan] + - [4.25, 0.0044, 174, .nan, .nan] + - [4.3, 0.0044, 176, .nan, .nan] + - [4.35, 0.0045, 178, .nan, .nan] + - [4.4, 0.0045, 180, .nan, .nan] + - [4.45, 0.0046, 182, .nan, .nan] + - [4.5, 0.0046, 184, .nan, .nan] + - [4.55, 0.0047, 186, .nan, .nan] + - [4.6, 0.0047, 188, .nan, .nan] + - [4.65, 0.0048, 190, .nan, .nan] + - [4.7, 0.0048, 192, .nan, .nan] + - [4.75, 0.0049, 194, .nan, .nan] + - [4.8, 0.0049, 196, .nan, .nan] + - [4.85, 0.005, 198, .nan, .nan] + - [4.9, 0.005, 200, .nan, .nan] + - [4.95, 0.0051, 202, .nan, .nan] + - [5.0, 0.0051, 204, .nan, .nan] + - [5.05, 0.0052, 207, .nan, .nan] + - [5.1, 0.0052, 209, .nan, .nan] + - [5.15, 0.0053, 211, .nan, .nan] + - [5.2, 0.0053, 213, .nan, .nan] + - [5.25, 0.0054, 215, .nan, .nan] + - [5.3, 0.0054, 217, .nan, .nan] + - [5.35, 0.0055, 219, .nan, .nan] + - [5.4, 0.0055, 221, .nan, .nan] + - [5.45, 0.0056, 223, .nan, .nan] + - [5.5, 0.0056, 225, .nan, .nan] + - [5.55, 0.0057, 227, .nan, .nan] + - [5.6, 0.0057, 229, .nan, .nan] + - [5.65, 0.0058, 231, .nan, .nan] + - [5.7, 0.0058, 233, .nan, .nan] + - [5.75, 0.0059, 235, .nan, .nan] + - [5.8, 0.0059, 237, .nan, .nan] + - [5.85, 0.006, 239, .nan, .nan] + - [5.9, 0.006, 241, .nan, .nan] + - [5.95, 0.0061, 243, .nan, .nan] + - [6.0, 0.0061, 245, .nan, .nan] + - [6.05, 0.0062, 248, .nan, .nan] + - [6.1, 0.0063, 250, .nan, .nan] + - [6.15, 0.0063, 252, .nan, .nan] + - [6.2, 0.0064, 254, .nan, .nan] + - [6.25, 0.0064, 256, .nan, .nan] + - [6.3, 0.0065, 258, .nan, .nan] + - [6.35, 0.0065, 260, .nan, .nan] + - [6.4, 0.0066, 262, .nan, .nan] + - [6.45, 0.0066, 264, .nan, .nan] + - [6.5, 0.0067, 266, .nan, .nan] + - [6.55, 0.0067, 268, .nan, .nan] + - [6.6, 0.0068, 270, .nan, .nan] + - [6.65, 0.0068, 272, .nan, .nan] + - [6.7, 0.0069, 274, .nan, .nan] + - [6.75, 0.0069, 276, .nan, .nan] + - [6.8, 0.007, 278, .nan, .nan] + - [6.85, 0.007, 280, .nan, .nan] + - [6.9, 0.0071, 282, .nan, .nan] + - [6.95, 0.0071, 284, .nan, .nan] + - [7.0, 0.0072, 286, .nan, .nan] + - [7.05, 0.0072, 289, .nan, .nan] + - [7.1, 0.0073, 291, .nan, .nan] + - [7.15, 0.0073, 293, .nan, .nan] + - [7.2, 0.0074, 295, .nan, .nan] + - [7.25, 0.0074, 297, .nan, .nan] + - [7.3, 0.0075, 299, .nan, .nan] + - [7.35, 0.0075, 301, .nan, .nan] + - [7.4, 0.0076, 303, .nan, .nan] + - [7.45, 0.0076, 305, .nan, .nan] + - [7.5, 0.0077, 307, .nan, .nan] + - [7.55, 0.0077, 309, .nan, .nan] + - [7.6, 0.0078, 311, .nan, .nan] + - [7.65, 0.0078, 313, .nan, .nan] + - [7.7, 0.0079, 315, .nan, .nan] + - [7.75, 0.0079, 317, .nan, .nan] + - [7.8, 0.008, 319, .nan, .nan] + - [7.85, 0.008, 321, .nan, .nan] + - [7.9, 0.0081, 323, .nan, .nan] + - [7.95, 0.0081, 325, .nan, .nan] + - [8.0, 0.0082, 327, .nan, .nan] + - [8.05, 0.0082, 329, .nan, .nan] + - [8.1, 0.0083, 332, .nan, .nan] + - [8.15, 0.0084, 334, .nan, .nan] + - [8.2, 0.0084, 336, .nan, .nan] + - [8.25, 0.0085, 338, .nan, .nan] + - [8.3, 0.0085, 340, .nan, .nan] + - [8.35, 0.0086, 342, .nan, .nan] + - [8.4, 0.0086, 344, .nan, .nan] + - [8.45, 0.0087, 346, .nan, .nan] + - [8.5, 0.0087, 348, .nan, .nan] + - [8.55, 0.0088, 350, .nan, .nan] + - [8.6, 0.0088, 352, .nan, .nan] + - [8.65, 0.0089, 354, .nan, .nan] + - [8.7, 0.0089, 356, .nan, .nan] + - [8.75, 0.009, 358, .nan, .nan] + - [8.8, 0.009, 360, .nan, .nan] + - [8.85, 0.0091, 362, .nan, .nan] + - [8.9, 0.0091, 364, .nan, .nan] + - [8.95, 0.0092, 366, .nan, .nan] + - [9.0, 0.0092, 368, .nan, .nan] + - [9.05, 0.0093, 370, .nan, .nan] + - [9.1, 0.0093, 373, .nan, .nan] + - [9.15, 0.0094, 375, .nan, .nan] + - [9.2, 0.0095, 377, .nan, .nan] + - [9.25, 0.0095, 379, .nan, .nan] + - [9.3, 0.0096, 381, .nan, .nan] + - [9.35, 0.0096, 383, .nan, .nan] + - [9.4, 0.0097, 385, .nan, .nan] + - [9.45, 0.0097, 387, .nan, .nan] + - [9.5, 0.0098, 389, .nan, .nan] + - [9.55, 0.0098, 391, .nan, .nan] + - [9.6, 0.0099, 393, .nan, .nan] + - [9.65, 0.0099, 395, .nan, .nan] + - [9.7, 0.01, 397, .nan, .nan] + - [9.75, 0.01, 399, .nan, .nan] + - [9.8, 0.0101, 401, .nan, .nan] + - [9.85, 0.0101, 403, .nan, .nan] + - [9.9, 0.0102, 405, .nan, .nan] + - [9.95, 0.0102, 407, .nan, .nan] + - [10.0, 0.0103, 409, .nan, .nan] + - minimum_coverage: 3 + asymptote(1000t): 29 + data: + - [0.0, 0.0, 0, .nan, .nan] + - [0.05, 0.0, 0, .nan, .nan] + - [0.1, 0.0, 0, .nan, .nan] + - [0.15, 0.0, 0, .nan, .nan] + - [0.2, 0.0, 0, .nan, .nan] + - [0.25, 0.0, 0, .nan, .nan] + - [0.3, 0.0, 0, .nan, .nan] + - [0.35, 0.0, 0, .nan, .nan] + - [0.4, 0.0, 0, .nan, .nan] + - [0.45, 0.0, 0, .nan, .nan] + - [0.5, 0.0, 0, .nan, .nan] + - [0.55, 0.0, 0, .nan, .nan] + - [0.6, 0.0, 0, .nan, .nan] + - [0.65, 0.0, 0, .nan, .nan] + - [0.7, 0.0, 0, .nan, .nan] + - [0.75, 0.0, 0, .nan, .nan] + - [0.8, 0.0, 0, .nan, .nan] + - [0.85, 0.0, 0, .nan, .nan] + - [0.9, 0.0, 0, .nan, .nan] + - [0.95, 0.0, 0, .nan, .nan] + - [1.0, 0.0, 0, .nan, .nan] + - [1.05, 0.0, 0, .nan, .nan] + - [1.1, 0.0, 0, .nan, .nan] + - [1.15, 0.0, 0, .nan, .nan] + - [1.2, 0.0, 0, .nan, .nan] + - 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[4.55, 0.0, 0, .nan, .nan] + - [4.6, 0.0, 0, .nan, .nan] + - [4.65, 0.0, 0, .nan, .nan] + - [4.7, 0.0, 0, .nan, .nan] + - [4.75, 0.0, 0, .nan, .nan] + - [4.8, 0.0, 0, .nan, .nan] + - [4.85, 0.0, 0, .nan, .nan] + - [4.9, 0.0, 0, .nan, .nan] + - [4.95, 0.0, 0, .nan, .nan] + - [5.0, 0.0, 0, .nan, .nan] + - [5.05, 0.0, 0, .nan, .nan] + - [5.1, 0.0, 0, .nan, .nan] + - [5.15, 0.0, 0, .nan, .nan] + - [5.2, 0.0, 0, .nan, .nan] + - [5.25, 0.0, 0, .nan, .nan] + - [5.3, 0.0, 0, .nan, .nan] + - [5.35, 0.0, 0, .nan, .nan] + - [5.4, 0.0, 0, .nan, .nan] + - [5.45, 0.0, 0, .nan, .nan] + - [5.5, 0.0, 0, .nan, .nan] + - [5.55, 0.0, 0, .nan, .nan] + - [5.6, 0.0, 0, .nan, .nan] + - [5.65, 0.0, 0, .nan, .nan] + - [5.7, 0.0, 0, .nan, .nan] + - [5.75, 0.0, 0, .nan, .nan] + - [5.8, 0.0, 0, .nan, .nan] + - [5.85, 0.0, 0, .nan, .nan] + - [5.9, 0.0, 0, .nan, .nan] + - [5.95, 0.0, 0, .nan, .nan] + - [6.0, 0.0, 0, .nan, .nan] + - [6.05, 0.0, 0, .nan, .nan] + - [6.1, 0.0, 0, .nan, .nan] + - [6.15, 0.0, 0, .nan, .nan] + - [6.2, 0.0, 0, .nan, .nan] + - [6.25, 0.0, 0, .nan, .nan] + - [6.3, 0.0, 0, .nan, .nan] + - [6.35, 0.0, 0, .nan, .nan] + - [6.4, 0.0, 0, .nan, .nan] + - [6.45, 0.0, 0, .nan, .nan] + - [6.5, 0.0, 0, .nan, .nan] + - [6.55, 0.0, 0, .nan, .nan] + - [6.6, 0.0, 0, .nan, .nan] + - [6.65, 0.0, 0, .nan, .nan] + - [6.7, 0.0, 0, .nan, .nan] + - [6.75, 0.0, 0, .nan, .nan] + - [6.8, 0.0, 0, .nan, .nan] + - [6.85, 0.0, 0, .nan, .nan] + - [6.9, 0.0, 0, .nan, .nan] + - [6.95, 0.0, 0, .nan, .nan] + - [7.0, 0.0, 0, .nan, .nan] + - [7.05, 0.0, 0, .nan, .nan] + - [7.1, 0.0, 0, .nan, .nan] + - [7.15, 0.0, 0, .nan, .nan] + - [7.2, 0.0, 0, .nan, .nan] + - [7.25, 0.0, 0, .nan, .nan] + - [7.3, 0.0, 0, .nan, .nan] + - [7.35, 0.0, 0, .nan, .nan] + - [7.4, 0.0, 0, .nan, .nan] + - [7.45, 0.0, 0, .nan, .nan] + - [7.5, 0.0, 0, .nan, .nan] + - [7.55, 0.0, 0, .nan, .nan] + - [7.6, 0.0, 0, .nan, .nan] + - [7.65, 0.0, 0, .nan, .nan] + - [7.7, 0.0, 0, .nan, .nan] + - [7.75, 0.0, 0, .nan, .nan] + - [7.8, 0.0, 0, .nan, .nan] + - [7.85, 0.0, 0, .nan, .nan] + - [7.9, 0.0, 0, .nan, .nan] + - [7.95, 0.0, 0, .nan, .nan] + - [8.0, 0.0, 0, .nan, .nan] + - [8.05, 0.0, 0, .nan, .nan] + - [8.1, 0.0, 0, .nan, .nan] + - [8.15, 0.0, 0, .nan, .nan] + - [8.2, 0.0, 0, .nan, .nan] + - [8.25, 0.0, 0, .nan, .nan] + - [8.3, 0.0, 0, .nan, .nan] + - [8.35, 0.0, 0, .nan, .nan] + - [8.4, 0.0, 0, .nan, .nan] + - [8.45, 0.0, 0, .nan, .nan] + - [8.5, 0.0, 0, .nan, .nan] + - [8.55, 0.0, 0, .nan, .nan] + - [8.6, 0.0, 0, .nan, .nan] + - [8.65, 0.0, 0, .nan, .nan] + - [8.7, 0.0, 0, .nan, .nan] + - [8.75, 0.0, 0, .nan, .nan] + - [8.8, 0.0, 0, .nan, .nan] + - [8.85, 0.0, 0, .nan, .nan] + - [8.9, 0.0, 0, .nan, .nan] + - [8.95, 0.0, 0, .nan, .nan] + - [9.0, 0.0, 0, .nan, .nan] + - [9.05, 0.0, 0, .nan, .nan] + - [9.1, 0.0, 0, .nan, .nan] + - [9.15, 0.0, 0, .nan, .nan] + - [9.2, 0.0, 0, .nan, .nan] + - [9.25, 0.0, 0, .nan, .nan] + - [9.3, 0.0, 0, .nan, .nan] + - [9.35, 0.0, 0, .nan, .nan] + - [9.4, 0.0, 0, .nan, .nan] + - [9.45, 0.0, 0, .nan, .nan] + - [9.5, 0.0, 0, .nan, .nan] + - [9.55, 0.0, 0, .nan, .nan] + - [9.6, 0.0, 0, .nan, .nan] + - [9.65, 0.0, 0, .nan, .nan] + - [9.7, 0.0, 0, .nan, .nan] + - [9.75, 0.0, 0, .nan, .nan] + - [9.8, 0.0, 0, .nan, .nan] + - [9.85, 0.0, 0, .nan, .nan] + - [9.9, 0.0, 0, .nan, .nan] + - [9.95, 0.0, 0, .nan, .nan] + - [10.0, 0.0, 0, .nan, .nan] From 4f212ee3fca1b8191ff77a4801ebbd25f1d2555b Mon Sep 17 00:00:00 2001 From: edogiuili Date: Wed, 28 Jan 2026 11:14:49 +0100 Subject: [PATCH 3/3] update test data for methurator v2.1.0 --- .../v2.1.0/gtestimator_command/methurator_summary.yml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/data/modules/methurator/v2.1.0/gtestimator_command/methurator_summary.yml b/data/modules/methurator/v2.1.0/gtestimator_command/methurator_summary.yml index 7e4d1d60..f9e01ce4 100644 --- a/data/modules/methurator/v2.1.0/gtestimator_command/methurator_summary.yml +++ b/data/modules/methurator/v2.1.0/gtestimator_command/methurator_summary.yml @@ -1,6 +1,6 @@ methurator_summary: metadata: - date_generated: '2026-01-27T17:04:56.600219' + date_generated: '2026-01-28T11:12:04.516736' methurator_version: 2.1.0 command: methurator gt_estimator options: @@ -20,6 +20,7 @@ methurator_summary: gt_summary: - Ecoli.csorted_CpG.bedGraph: - minimum_coverage: 1 + reads: 10 asymptote(1000t): 39894 data: - [0.0, 0.0, 0, .nan, .nan] @@ -224,6 +225,7 @@ methurator_summary: - [9.95, 0.0102, 407, .nan, .nan] - [10.0, 0.0103, 409, .nan, .nan] - minimum_coverage: 3 + reads: 10 asymptote(1000t): 29 data: - [0.0, 0.0, 0, .nan, .nan]