Add files using upload-large-folder tool

method_inputs/a1/BOT_MILD_X3_2K_20K/r00000000/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 39330,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_MILD_X3_2K_20K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 0,
+ "cache_sha256": "87ffb5e4008f3e0e2be26688530e5947a490ef57f865d704f9d019500792f492",
+ "canonical_id": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df:00000000",
+ "columns": [
+  39,
+  36,
+  24,
+  55,
+  28,
+  14,
+  34,
+  4,
+  30,
+  50,
+  35,
+  49,
+  33,
+  21,
+  53,
+  22,
+  45,
+  58,
+  42,
+  31,
+  6,
+  20,
+  25,
+  38,
+  27,
+  60,
+  62,
+  5,
+  3,
+  32,
+  11,
+  51
+ ],
+ "contig": "region_0",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "914511afce0625caef6d9c13b450acd53c9557ce33acfaa737ecdd66a8e5adc8",
+  "phlash_contig.npz": "6c89b8df72226d2f5e7fa7cbad0673f325da7e9e7b4892ad8fdadb3716c6e14f",
+  "sfs_unfolded.npy": "2f2d82da40be6c9e6a29de01ba38b661ed6876e978274ace69f2964269031c1f",
+  "view.bcf": "723265cf8cd76bba475ab412d402ea41d772cd4b9ef453bace3656395a129e70",
+  "view.bcf.csi": "4a99877630211fbfe7ffde9db5b28175babe8e051b323f9b2309fe5ff126ab8e"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_MILD_X3_2K_20K/samples/.fragments/fragment_00000000.npz",
+ "fragment_sha256": "d5d65c111c7bd68ebcc897dbefa50679164760f0196652b2297f717690ea898e",
+ "ladder_columns": [
+  39,
+  36,
+  24,
+  55,
+  28,
+  14,
+  34,
+  4,
+  30,
+  50,
+  35,
+  49,
+  33,
+  21,
+  53,
+  22,
+  45,
+  58,
+  42,
+  31,
+  6,
+  20,
+  25,
+  38,
+  27,
+  60,
+  62,
+  5,
+  3,
+  32,
+  11,
+  51
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 39330,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 48296,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  6980,
+  6936,
+  6538,
+  6700,
+  6585,
+  5745,
+  6600,
+  6985,
+  6851,
+  6460,
+  6486,
+  6963,
+  6552,
+  7104,
+  6602,
+  6624,
+  7002,
+  6419,
+  6665,
+  6507,
+  6580,
+  6438,
+  6272,
+  7159,
+  6855,
+  6403,
+  6247,
+  6634,
+  6404,
+  5978,
+  6800,
+  5821
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 0,
+ "sample_id": "sim_00000000",
+ "sample_index": 0,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 39330,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "e343ffdbc2967d1d5cc771c82c53a99a044d1ae3f83866c041a2d414cdbdddb3",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T11:04:02Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_MILD_X3_2K_20K/r00000000/v0_n32.json

@@ -0,0 +1,36 @@
+{
+ "canonical_id": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df:00000000",
+ "checks": {
+  "S_matches": true,
+  "afs_is_sfs_interior": true,
+  "big_endian_differs": true,
+  "bit_rule_matches_little_endian": true,
+  "cache_folded_sfs_matches": true,
+  "cache_folded_sfs_max_abs_diff": 3.637978807091713e-12,
+  "cache_implied_S": 39330.0,
+  "cache_ladder_matches": true,
+  "cache_nw_anchor_matches_S": true,
+  "cache_sequence_length": true,
+  "cache_target_bitwise": true,
+  "columns_follow_ladder_rule": true,
+  "contig_header": true,
+  "file_shas_match_meta": true,
+  "het_matrix_matches_bcf": true,
+  "het_matrix_shape": true,
+  "ladder_matches_recomputed_level_columns": true,
+  "ladder_not_sorted": true,
+  "multihetsep_matches_awk_port": true,
+  "multihetsep_matches_script": true,
+  "multihetsep_script_ran": true,
+  "multihetsep_script_required_and_ran": true,
+  "pos_unique_in_range": true,
+  "samples_match": true,
+  "sfs_matches_bcf": true,
+  "single_contig": true,
+  "view_S": 39330
+ },
+ "n": 32,
+ "passed": true,
+ "schema": "bench_h2h.v0.v1",
+ "utc": "2026-09-16T11:04:03Z"
+}

method_inputs/a1/BOT_MILD_X3_2K_20K/r00000002/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 40498,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_MILD_X3_2K_20K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 2,
+ "cache_sha256": "87ffb5e4008f3e0e2be26688530e5947a490ef57f865d704f9d019500792f492",
+ "canonical_id": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df:00000002",
+ "columns": [
+  23,
+  43,
+  14,
+  34,
+  49,
+  22,
+  60,
+  41,
+  53,
+  4,
+  28,
+  56,
+  37,
+  7,
+  11,
+  20,
+  51,
+  62,
+  30,
+  6,
+  18,
+  1,
+  36,
+  2,
+  8,
+  38,
+  16,
+  29,
+  47,
+  54,
+  42,
+  15
+ ],
+ "contig": "region_2",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "f21975440e5c06ddd76071e4f5d8c363ba28d33745aee5898c1c8caf62776b37",
+  "phlash_contig.npz": "37db1f10206d15cccea63bd4e9039e1beb5ea3446c430f865259342f6d24ab88",
+  "sfs_unfolded.npy": "96a75bf2bb2c420f5d379b008e1912db962c16f5340cbc67379956184bd03303",
+  "view.bcf": "4848083db10eea4f8a2d5d033085d1558655244066dd114f1b5826ef0722fd91",
+  "view.bcf.csi": "11c13d3a44c38f4c14f7d7cc3ed2adada8d8d9f439903fd050faade8fe07a16f"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_MILD_X3_2K_20K/samples/.fragments/fragment_00000000.npz",
+ "fragment_sha256": "d5d65c111c7bd68ebcc897dbefa50679164760f0196652b2297f717690ea898e",
+ "ladder_columns": [
+  23,
+  43,
+  14,
+  34,
+  49,
+  22,
+  60,
+  41,
+  53,
+  4,
+  28,
+  56,
+  37,
+  7,
+  11,
+  20,
+  51,
+  62,
+  30,
+  6,
+  18,
+  1,
+  36,
+  2,
+  8,
+  38,
+  16,
+  29,
+  47,
+  54,
+  42,
+  15
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 40498,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 49834,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  6746,
+  6394,
+  6717,
+  6861,
+  6739,
+  6493,
+  6751,
+  6422,
+  6515,
+  6179,
+  6378,
+  6534,
+  6576,
+  4801,
+  6409,
+  6922,
+  6679,
+  6571,
+  6967,
+  6466,
+  6514,
+  6581,
+  6621,
+  6526,
+  6787,
+  6553,
+  6847,
+  6261,
+  6650,
+  6874,
+  6743,
+  6575
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 2,
+ "sample_id": "sim_00000002",
+ "sample_index": 2,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 40498,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "e343ffdbc2967d1d5cc771c82c53a99a044d1ae3f83866c041a2d414cdbdddb3",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T11:04:06Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_MILD_X3_2K_20K/r00000002/v0_n32.json

@@ -0,0 +1,36 @@
+{
+ "canonical_id": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df:00000002",
+ "checks": {
+  "S_matches": true,
+  "afs_is_sfs_interior": true,
+  "big_endian_differs": true,
+  "bit_rule_matches_little_endian": true,
+  "cache_folded_sfs_matches": true,
+  "cache_folded_sfs_max_abs_diff": 5.4569682106375694e-12,
+  "cache_implied_S": 40498.0,
+  "cache_ladder_matches": true,
+  "cache_nw_anchor_matches_S": true,
+  "cache_sequence_length": true,
+  "cache_target_bitwise": true,
+  "columns_follow_ladder_rule": true,
+  "contig_header": true,
+  "file_shas_match_meta": true,
+  "het_matrix_matches_bcf": true,
+  "het_matrix_shape": true,
+  "ladder_matches_recomputed_level_columns": true,
+  "ladder_not_sorted": true,
+  "multihetsep_matches_awk_port": true,
+  "multihetsep_matches_script": true,
+  "multihetsep_script_ran": true,
+  "multihetsep_script_required_and_ran": true,
+  "pos_unique_in_range": true,
+  "samples_match": true,
+  "sfs_matches_bcf": true,
+  "single_contig": true,
+  "view_S": 40498
+ },
+ "n": 32,
+ "passed": true,
+ "schema": "bench_h2h.v0.v1",
+ "utc": "2026-09-16T11:04:07Z"
+}

method_inputs/a1/BOT_MILD_X3_2K_20K/r00000003/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 38679,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_MILD_X3_2K_20K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 3,
+ "cache_sha256": "87ffb5e4008f3e0e2be26688530e5947a490ef57f865d704f9d019500792f492",
+ "canonical_id": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df:00000003",
+ "columns": [
+  35,
+  55,
+  48,
+  11,
+  30,
+  28,
+  53,
+  15,
+  31,
+  60,
+  40,
+  52,
+  61,
+  57,
+  0,
+  13,
+  14,
+  32,
+  6,
+  54,
+  37,
+  17,
+  9,
+  47,
+  23,
+  42,
+  22,
+  12,
+  36,
+  24,
+  50,
+  51
+ ],
+ "contig": "region_3",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "c9273afbab0be3ec4ce12866d18a45e168d645ac2d173735b6c5cdd4a518fbd0",
+  "phlash_contig.npz": "ba366b23368049b30d42dacfa3004edff021d727dd5993af7a3e9857b80d998a",
+  "sfs_unfolded.npy": "b3c9d6c469b81cb2561b5959ef6c6584a7f92e4d584f23434b8d7c03116ba0cf",
+  "view.bcf": "738127cb2460f20b52ed8842f83b122871e9872fe133bc01a75205917bd66223",
+  "view.bcf.csi": "7e4246bce9b74284d084bfc9cc1b53e313b0cd1b2c802778902445b9bc0b202b"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_MILD_X3_2K_20K/samples/.fragments/fragment_00000000.npz",
+ "fragment_sha256": "d5d65c111c7bd68ebcc897dbefa50679164760f0196652b2297f717690ea898e",
+ "ladder_columns": [
+  35,
+  55,
+  48,
+  11,
+  30,
+  28,
+  53,
+  15,
+  31,
+  60,
+  40,
+  52,
+  61,
+  57,
+  0,
+  13,
+  14,
+  32,
+  6,
+  54,
+  37,
+  17,
+  9,
+  47,
+  23,
+  42,
+  22,
+  12,
+  36,
+  24,
+  50,
+  51
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 38679,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 48658,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  6606,
+  6613,
+  6232,
+  6744,
+  6417,
+  6551,
+  6746,
+  6254,
+  6847,
+  6540,
+  6783,
+  6507,
+  6481,
+  6642,
+  6386,
+  7058,
+  6528,
+  6726,
+  6544,
+  6343,
+  6265,
+  6590,
+  6220,
+  6030,
+  6723,
+  6696,
+  6707,
+  6514,
+  6723,
+  6719,
+  6725,
+  6612
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 3,
+ "sample_id": "sim_00000003",
+ "sample_index": 3,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 38679,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "e343ffdbc2967d1d5cc771c82c53a99a044d1ae3f83866c041a2d414cdbdddb3",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T11:04:08Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_MILD_X3_2K_20K/r00000003/v0_n32.json

@@ -0,0 +1,36 @@
+{
+ "canonical_id": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df:00000003",
+ "checks": {
+  "S_matches": true,
+  "afs_is_sfs_interior": true,
+  "big_endian_differs": true,
+  "bit_rule_matches_little_endian": true,
+  "cache_folded_sfs_matches": true,
+  "cache_folded_sfs_max_abs_diff": 1.8189894035458565e-12,
+  "cache_implied_S": 38679.0,
+  "cache_ladder_matches": true,
+  "cache_nw_anchor_matches_S": true,
+  "cache_sequence_length": true,
+  "cache_target_bitwise": true,
+  "columns_follow_ladder_rule": true,
+  "contig_header": true,
+  "file_shas_match_meta": true,
+  "het_matrix_matches_bcf": true,
+  "het_matrix_shape": true,
+  "ladder_matches_recomputed_level_columns": true,
+  "ladder_not_sorted": true,
+  "multihetsep_matches_awk_port": true,
+  "multihetsep_matches_script": true,
+  "multihetsep_script_ran": true,
+  "multihetsep_script_required_and_ran": true,
+  "pos_unique_in_range": true,
+  "samples_match": true,
+  "sfs_matches_bcf": true,
+  "single_contig": true,
+  "view_S": 38679
+ },
+ "n": 32,
+ "passed": true,
+ "schema": "bench_h2h.v0.v1",
+ "utc": "2026-09-16T11:04:10Z"
+}

method_inputs/a1/BOT_MILD_X3_2K_20K/r00000004/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 39424,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_MILD_X3_2K_20K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 4,
+ "cache_sha256": "87ffb5e4008f3e0e2be26688530e5947a490ef57f865d704f9d019500792f492",
+ "canonical_id": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df:00000004",
+ "columns": [
+  22,
+  50,
+  14,
+  5,
+  54,
+  46,
+  8,
+  19,
+  52,
+  6,
+  2,
+  4,
+  25,
+  9,
+  17,
+  57,
+  44,
+  62,
+  29,
+  18,
+  26,
+  40,
+  28,
+  34,
+  23,
+  49,
+  35,
+  41,
+  37,
+  13,
+  48,
+  12
+ ],
+ "contig": "region_4",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "fe7c56f60a42b92422fa2a84f5a49ffef8ea91a9e22841d72685365d9f6eaa00",
+  "phlash_contig.npz": "954858d40f65e63138771ed780226b8f7c7759da79f9968b80aac63075d5d006",
+  "sfs_unfolded.npy": "1e1ca71e0562ed26f41784e61a8b9e525c3cabbaeaaf77b1dd7d4d735da4ec46",
+  "view.bcf": "08ba6bf5427530b511203cf95291eff928786ebdd3aa190b80cf50501555ce5f",
+  "view.bcf.csi": "4ec4d8abc66d74813222aadb084cc2b823aef897f0c0cac35b378361e065571d"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_MILD_X3_2K_20K/samples/.fragments/fragment_00000001.npz",
+ "fragment_sha256": "8ffe1f809130587976a8fedd7d79b87694c3c89723aeebe998fdaa8c4791d944",
+ "ladder_columns": [
+  22,
+  50,
+  14,
+  5,
+  54,
+  46,
+  8,
+  19,
+  52,
+  6,
+  2,
+  4,
+  25,
+  9,
+  17,
+  57,
+  44,
+  62,
+  29,
+  18,
+  26,
+  40,
+  28,
+  34,
+  23,
+  49,
+  35,
+  41,
+  37,
+  13,
+  48,
+  12
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 39424,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 49047,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  6765,
+  6457,
+  6724,
+  6773,
+  6409,
+  6569,
+  6692,
+  6792,
+  6741,
+  6515,
+  6793,
+  6592,
+  6599,
+  6623,
+  6504,
+  6357,
+  6644,
+  6654,
+  6308,
+  6258,
+  6806,
+  6496,
+  6442,
+  6686,
+  6328,
+  6202,
+  6168,
+  6620,
+  6357,
+  6174,
+  6349,
+  6608
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 0,
+ "sample_id": "sim_00000004",
+ "sample_index": 4,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 39424,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "e343ffdbc2967d1d5cc771c82c53a99a044d1ae3f83866c041a2d414cdbdddb3",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T11:04:10Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_MILD_X3_2K_20K/r00000004/v0_n32.json

@@ -0,0 +1,36 @@
+{
+ "canonical_id": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df:00000004",
+ "checks": {
+  "S_matches": true,
+  "afs_is_sfs_interior": true,
+  "big_endian_differs": true,
+  "bit_rule_matches_little_endian": true,
+  "cache_folded_sfs_matches": true,
+  "cache_folded_sfs_max_abs_diff": 1.8189894035458565e-12,
+  "cache_implied_S": 39424.0,
+  "cache_ladder_matches": true,
+  "cache_nw_anchor_matches_S": true,
+  "cache_sequence_length": true,
+  "cache_target_bitwise": true,
+  "columns_follow_ladder_rule": true,
+  "contig_header": true,
+  "file_shas_match_meta": true,
+  "het_matrix_matches_bcf": true,
+  "het_matrix_shape": true,
+  "ladder_matches_recomputed_level_columns": true,
+  "ladder_not_sorted": true,
+  "multihetsep_matches_awk_port": true,
+  "multihetsep_matches_script": true,
+  "multihetsep_script_ran": true,
+  "multihetsep_script_required_and_ran": true,
+  "pos_unique_in_range": true,
+  "samples_match": true,
+  "sfs_matches_bcf": true,
+  "single_contig": true,
+  "view_S": 39424
+ },
+ "n": 32,
+ "passed": true,
+ "schema": "bench_h2h.v0.v1",
+ "utc": "2026-09-16T11:04:12Z"
+}

method_inputs/a1/BOT_MILD_X3_2K_20K/r00000005/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 40139,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_MILD_X3_2K_20K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 5,
+ "cache_sha256": "87ffb5e4008f3e0e2be26688530e5947a490ef57f865d704f9d019500792f492",
+ "canonical_id": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df:00000005",
+ "columns": [
+  8,
+  63,
+  60,
+  62,
+  34,
+  10,
+  2,
+  33,
+  23,
+  9,
+  28,
+  49,
+  0,
+  14,
+  30,
+  3,
+  13,
+  41,
+  43,
+  58,
+  6,
+  29,
+  39,
+  4,
+  46,
+  45,
+  48,
+  38,
+  31,
+  11,
+  1,
+  24
+ ],
+ "contig": "region_5",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "a6e205125e898f8fb40d32413d0f8269d69ac838d66e83a0b760cc0237ca47e1",
+  "phlash_contig.npz": "0fc17bc56e9e079a1fb0871f0421aca9abcd1e3440441e9d4d038e257cf35e19",
+  "sfs_unfolded.npy": "827d24890d50d020018ce17fb8d29230cf3ebffa258f927bf88976f961822afb",
+  "view.bcf": "6a715b2c10bde7cfe9f07b5dde3f7208bacb48d8f89da2f9e7344328720edf9f",
+  "view.bcf.csi": "c7f10b8e35f26a75179163e21f26cbf8939d9f910a523e3d43bb0b18bc76c3d7"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_MILD_X3_2K_20K/samples/.fragments/fragment_00000001.npz",
+ "fragment_sha256": "8ffe1f809130587976a8fedd7d79b87694c3c89723aeebe998fdaa8c4791d944",
+ "ladder_columns": [
+  8,
+  63,
+  60,
+  62,
+  34,
+  10,
+  2,
+  33,
+  23,
+  9,
+  28,
+  49,
+  0,
+  14,
+  30,
+  3,
+  13,
+  41,
+  43,
+  58,
+  6,
+  29,
+  39,
+  4,
+  46,
+  45,
+  48,
+  38,
+  31,
+  11,
+  1,
+  24
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 40139,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 49329,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  6405,
+  6698,
+  6283,
+  7033,
+  7049,
+  6729,
+  6759,
+  6666,
+  5482,
+  6835,
+  6433,
+  6380,
+  6787,
+  6800,
+  6724,
+  6642,
+  6850,
+  6647,
+  6816,
+  6700,
+  7317,
+  6753,
+  6531,
+  6714,
+  6967,
+  6955,
+  6711,
+  6833,
+  7063,
+  6553,
+  6682,
+  6686
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 1,
+ "sample_id": "sim_00000005",
+ "sample_index": 5,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 40139,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "e343ffdbc2967d1d5cc771c82c53a99a044d1ae3f83866c041a2d414cdbdddb3",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T11:04:12Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_MILD_X3_2K_20K/r00000007/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 40351,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_MILD_X3_2K_20K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 7,
+ "cache_sha256": "87ffb5e4008f3e0e2be26688530e5947a490ef57f865d704f9d019500792f492",
+ "canonical_id": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df:00000007",
+ "columns": [
+  31,
+  20,
+  55,
+  28,
+  11,
+  48,
+  57,
+  6,
+  42,
+  23,
+  21,
+  26,
+  58,
+  10,
+  1,
+  45,
+  37,
+  54,
+  49,
+  47,
+  62,
+  34,
+  33,
+  61,
+  59,
+  43,
+  40,
+  12,
+  8,
+  7,
+  25,
+  50
+ ],
+ "contig": "region_7",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "7346ccd17b0e2a7fcd9f4f70f1748146206e53352ac12b304e3fb7a27c8c2459",
+  "phlash_contig.npz": "32f6d4267d41ac719e17911ad6e9ebb9b982d97e815ff46d261576c6da26ff2f",
+  "sfs_unfolded.npy": "0f3ccb216bc129c2947c8be3b8d55efbbc54a24eb04f6b5ba1500ba4d7375d5f",
+  "view.bcf": "2445dea4b78fa02d429182a6f72f0857bed0c0fa719b409e61b97346c4420c76",
+  "view.bcf.csi": "3db30e6d689ab0576ffe6afa585095ea122995afaa6ee157a2bd3ea58780bf29"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_MILD_X3_2K_20K/samples/.fragments/fragment_00000001.npz",
+ "fragment_sha256": "8ffe1f809130587976a8fedd7d79b87694c3c89723aeebe998fdaa8c4791d944",
+ "ladder_columns": [
+  31,
+  20,
+  55,
+  28,
+  11,
+  48,
+  57,
+  6,
+  42,
+  23,
+  21,
+  26,
+  58,
+  10,
+  1,
+  45,
+  37,
+  54,
+  49,
+  47,
+  62,
+  34,
+  33,
+  61,
+  59,
+  43,
+  40,
+  12,
+  8,
+  7,
+  25,
+  50
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 40351,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 49208,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  6670,
+  6405,
+  6689,
+  6885,
+  6531,
+  6731,
+  6717,
+  6733,
+  6801,
+  6999,
+  6739,
+  6530,
+  6787,
+  6387,
+  6380,
+  6209,
+  6258,
+  6619,
+  6172,
+  6671,
+  6626,
+  6309,
+  6692,
+  6728,
+  7292,
+  6998,
+  6825,
+  6639,
+  6562,
+  6841,
+  6992,
+  6391
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 3,
+ "sample_id": "sim_00000007",
+ "sample_index": 7,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 40351,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "e343ffdbc2967d1d5cc771c82c53a99a044d1ae3f83866c041a2d414cdbdddb3",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T11:04:16Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_MILD_X3_2K_20K/r00000007/v0_n32.json

@@ -0,0 +1,36 @@
+{
+ "canonical_id": "0e0fb54329ab707eab03d5a2cbfc55fa78f0f3a0885dd02a14ad0066732e30df:00000007",
+ "checks": {
+  "S_matches": true,
+  "afs_is_sfs_interior": true,
+  "big_endian_differs": true,
+  "bit_rule_matches_little_endian": true,
+  "cache_folded_sfs_matches": true,
+  "cache_folded_sfs_max_abs_diff": 1.8189894035458565e-12,
+  "cache_implied_S": 40351.0,
+  "cache_ladder_matches": true,
+  "cache_nw_anchor_matches_S": true,
+  "cache_sequence_length": true,
+  "cache_target_bitwise": true,
+  "columns_follow_ladder_rule": true,
+  "contig_header": true,
+  "file_shas_match_meta": true,
+  "het_matrix_matches_bcf": true,
+  "het_matrix_shape": true,
+  "ladder_matches_recomputed_level_columns": true,
+  "ladder_not_sorted": true,
+  "multihetsep_matches_awk_port": true,
+  "multihetsep_matches_script": true,
+  "multihetsep_script_ran": true,
+  "multihetsep_script_required_and_ran": true,
+  "pos_unique_in_range": true,
+  "samples_match": true,
+  "sfs_matches_bcf": true,
+  "single_contig": true,
+  "view_S": 40351
+ },
+ "n": 32,
+ "passed": true,
+ "schema": "bench_h2h.v0.v1",
+ "utc": "2026-09-16T11:04:18Z"
+}

method_inputs/a1/BOT_X10_1K/r00000000/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 56657,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_X10_1K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 0,
+ "cache_sha256": "688854533044cd063dbfdc2f3f0e3f7f63a813f1e6f11f8c765be09227bbcc3e",
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000000",
+ "columns": [
+  39,
+  36,
+  24,
+  55,
+  28,
+  14,
+  34,
+  4,
+  30,
+  50,
+  35,
+  49,
+  33,
+  21,
+  53,
+  22,
+  45,
+  58,
+  42,
+  31,
+  6,
+  20,
+  25,
+  38,
+  27,
+  60,
+  62,
+  5,
+  3,
+  32,
+  11,
+  51
+ ],
+ "contig": "region_0",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "a7142f905c9848946b20c399ac2524fd6775208568a0be5ed4ec97e68a7703af",
+  "phlash_contig.npz": "c78e6a67f1dcbb7b16a63c7526459330066804ef34035fb3e6c8137bf2b489c1",
+  "sfs_unfolded.npy": "f6e6ce8517959b0ec78183f86a766144a89a6cabb948e88123f0f33685aaefa1",
+  "view.bcf": "9272d182358374ed5074455e0ad75ea2a95c6f65ec7fba2f654d4567070ff58e",
+  "view.bcf.csi": "623dc5eff4262d2158dd2b1e60ef279577e566aa7162f0d7c46fe803fe81a7bc"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_X10_1K/samples/.fragments/fragment_00000000.npz",
+ "fragment_sha256": "7e788e9aed078cd8d6f10ff85d8c9e0f669e330dce2f8a2068bedb606450729f",
+ "ladder_columns": [
+  39,
+  36,
+  24,
+  55,
+  28,
+  14,
+  34,
+  4,
+  30,
+  50,
+  35,
+  49,
+  33,
+  21,
+  53,
+  22,
+  45,
+  58,
+  42,
+  31,
+  6,
+  20,
+  25,
+  38,
+  27,
+  60,
+  62,
+  5,
+  3,
+  32,
+  11,
+  51
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 56657,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 65219,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  13683,
+  13786,
+  13302,
+  13612,
+  13257,
+  13806,
+  13633,
+  14392,
+  13167,
+  14284,
+  13178,
+  13146,
+  13427,
+  14228,
+  14262,
+  13165,
+  13134,
+  13778,
+  13848,
+  12461,
+  14127,
+  12657,
+  13356,
+  12735,
+  13807,
+  14931,
+  13581,
+  13400,
+  13758,
+  14188,
+  13945,
+  12851
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 0,
+ "sample_id": "sim_00000000",
+ "sample_index": 0,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 56657,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "159975e92501d69b57b0a112d95a0b3a13aca0517b58d84eeec75c3ec69a763a",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T10:58:27Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_X10_1K/r00000000/v0_n32.json

@@ -0,0 +1,36 @@
+{
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000000",
+ "checks": {
+  "S_matches": true,
+  "afs_is_sfs_interior": true,
+  "big_endian_differs": true,
+  "bit_rule_matches_little_endian": true,
+  "cache_folded_sfs_matches": true,
+  "cache_folded_sfs_max_abs_diff": 1.8189894035458565e-12,
+  "cache_implied_S": 56657.00000000001,
+  "cache_ladder_matches": true,
+  "cache_nw_anchor_matches_S": true,
+  "cache_sequence_length": true,
+  "cache_target_bitwise": true,
+  "columns_follow_ladder_rule": true,
+  "contig_header": true,
+  "file_shas_match_meta": true,
+  "het_matrix_matches_bcf": true,
+  "het_matrix_shape": true,
+  "ladder_matches_recomputed_level_columns": true,
+  "ladder_not_sorted": true,
+  "multihetsep_matches_awk_port": true,
+  "multihetsep_matches_script": true,
+  "multihetsep_script_ran": true,
+  "multihetsep_script_required_and_ran": true,
+  "pos_unique_in_range": true,
+  "samples_match": true,
+  "sfs_matches_bcf": true,
+  "single_contig": true,
+  "view_S": 56657
+ },
+ "n": 32,
+ "passed": true,
+ "schema": "bench_h2h.v0.v1",
+ "utc": "2026-09-16T10:58:31Z"
+}

method_inputs/a1/BOT_X10_1K/r00000001/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 57634,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_X10_1K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 1,
+ "cache_sha256": "688854533044cd063dbfdc2f3f0e3f7f63a813f1e6f11f8c765be09227bbcc3e",
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000001",
+ "columns": [
+  16,
+  57,
+  22,
+  43,
+  38,
+  41,
+  39,
+  2,
+  35,
+  59,
+  51,
+  30,
+  36,
+  32,
+  40,
+  26,
+  20,
+  45,
+  47,
+  33,
+  6,
+  37,
+  34,
+  23,
+  1,
+  4,
+  58,
+  52,
+  14,
+  7,
+  49,
+  62
+ ],
+ "contig": "region_1",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "a085a1f06414cb74512a70adf9118d330491d9df151c9c53c5f8cd1d1b83b045",
+  "phlash_contig.npz": "0b89f622f5b91e0ad7be0a71ebd1afc4b6ef1d1ce5c5e8dde6d374eb03b36fdf",
+  "sfs_unfolded.npy": "e0425f45f7dfd1d14ca533f689da5878c68bbca882f970e49f4a8c71db7ea0f6",
+  "view.bcf": "9313efb54d5f9c573a27efe5cc372e18ed3722364b6d95d740f17e55d63b7bc8",
+  "view.bcf.csi": "90d1c365c4108e81e5daf93aa22ee99062ac635499f48b4f330674029c37443a"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_X10_1K/samples/.fragments/fragment_00000000.npz",
+ "fragment_sha256": "7e788e9aed078cd8d6f10ff85d8c9e0f669e330dce2f8a2068bedb606450729f",
+ "ladder_columns": [
+  16,
+  57,
+  22,
+  43,
+  38,
+  41,
+  39,
+  2,
+  35,
+  59,
+  51,
+  30,
+  36,
+  32,
+  40,
+  26,
+  20,
+  45,
+  47,
+  33,
+  6,
+  37,
+  34,
+  23,
+  1,
+  4,
+  58,
+  52,
+  14,
+  7,
+  49,
+  62
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 57634,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 66079,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  13711,
+  13336,
+  13241,
+  13157,
+  12442,
+  13220,
+  13609,
+  13136,
+  14241,
+  11925,
+  14250,
+  13728,
+  14251,
+  13496,
+  13622,
+  13376,
+  13599,
+  13696,
+  12449,
+  13410,
+  13026,
+  13772,
+  13200,
+  13673,
+  13542,
+  12617,
+  11891,
+  11968,
+  12791,
+  13855,
+  12630,
+  12580
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 1,
+ "sample_id": "sim_00000001",
+ "sample_index": 1,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 57634,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "159975e92501d69b57b0a112d95a0b3a13aca0517b58d84eeec75c3ec69a763a",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T10:58:32Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_X10_1K/r00000001/v0_n32.json

@@ -0,0 +1,36 @@
+{
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000001",
+ "checks": {
+  "S_matches": true,
+  "afs_is_sfs_interior": true,
+  "big_endian_differs": true,
+  "bit_rule_matches_little_endian": true,
+  "cache_folded_sfs_matches": true,
+  "cache_folded_sfs_max_abs_diff": 5.4569682106375694e-12,
+  "cache_implied_S": 57634.00000000001,
+  "cache_ladder_matches": true,
+  "cache_nw_anchor_matches_S": true,
+  "cache_sequence_length": true,
+  "cache_target_bitwise": true,
+  "columns_follow_ladder_rule": true,
+  "contig_header": true,
+  "file_shas_match_meta": true,
+  "het_matrix_matches_bcf": true,
+  "het_matrix_shape": true,
+  "ladder_matches_recomputed_level_columns": true,
+  "ladder_not_sorted": true,
+  "multihetsep_matches_awk_port": true,
+  "multihetsep_matches_script": true,
+  "multihetsep_script_ran": true,
+  "multihetsep_script_required_and_ran": true,
+  "pos_unique_in_range": true,
+  "samples_match": true,
+  "sfs_matches_bcf": true,
+  "single_contig": true,
+  "view_S": 57634
+ },
+ "n": 32,
+ "passed": true,
+ "schema": "bench_h2h.v0.v1",
+ "utc": "2026-09-16T10:58:36Z"
+}

method_inputs/a1/BOT_X10_1K/r00000002/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 57772,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_X10_1K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 2,
+ "cache_sha256": "688854533044cd063dbfdc2f3f0e3f7f63a813f1e6f11f8c765be09227bbcc3e",
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000002",
+ "columns": [
+  23,
+  43,
+  14,
+  34,
+  49,
+  22,
+  60,
+  41,
+  53,
+  4,
+  28,
+  56,
+  37,
+  7,
+  11,
+  20,
+  51,
+  62,
+  30,
+  6,
+  18,
+  1,
+  36,
+  2,
+  8,
+  38,
+  16,
+  29,
+  47,
+  54,
+  42,
+  15
+ ],
+ "contig": "region_2",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "1cdeb281228af7513a602dc5e56c847a9cb76f575065d0cc9b7fdf0e76f6111b",
+  "phlash_contig.npz": "ce5f5b644dde63f8b76e55c2eae71092ced31c1ba9db6194f13c582392f4399a",
+  "sfs_unfolded.npy": "eede88e32bde938043c9d3052e5284633bf3af3810df5d785add3dbaa018230a",
+  "view.bcf": "2187a5b10e92006c8920d977d64ab69cf55030ba12553f6657f8cfaff2f8ee0f",
+  "view.bcf.csi": "6e39698a2b83d54c2af1db5b7f0b9bf58a4f008861f42e1181b53cdaedbfb64b"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_X10_1K/samples/.fragments/fragment_00000000.npz",
+ "fragment_sha256": "7e788e9aed078cd8d6f10ff85d8c9e0f669e330dce2f8a2068bedb606450729f",
+ "ladder_columns": [
+  23,
+  43,
+  14,
+  34,
+  49,
+  22,
+  60,
+  41,
+  53,
+  4,
+  28,
+  56,
+  37,
+  7,
+  11,
+  20,
+  51,
+  62,
+  30,
+  6,
+  18,
+  1,
+  36,
+  2,
+  8,
+  38,
+  16,
+  29,
+  47,
+  54,
+  42,
+  15
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 57772,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 66602,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  13106,
+  13220,
+  13566,
+  13730,
+  13458,
+  13165,
+  14472,
+  13475,
+  13384,
+  13202,
+  13970,
+  13244,
+  14366,
+  13934,
+  13243,
+  11205,
+  13985,
+  13963,
+  13780,
+  12961,
+  13150,
+  13672,
+  14243,
+  13787,
+  13414,
+  13792,
+  14236,
+  14347,
+  12931,
+  13731,
+  13775,
+  13475
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 2,
+ "sample_id": "sim_00000002",
+ "sample_index": 2,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 57772,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "159975e92501d69b57b0a112d95a0b3a13aca0517b58d84eeec75c3ec69a763a",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T10:58:38Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_X10_1K/r00000002/v0_n32.json

@@ -0,0 +1,36 @@
+{
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000002",
+ "checks": {
+  "S_matches": true,
+  "afs_is_sfs_interior": true,
+  "big_endian_differs": true,
+  "bit_rule_matches_little_endian": true,
+  "cache_folded_sfs_matches": true,
+  "cache_folded_sfs_max_abs_diff": 1.8189894035458565e-12,
+  "cache_implied_S": 57772.0,
+  "cache_ladder_matches": true,
+  "cache_nw_anchor_matches_S": true,
+  "cache_sequence_length": true,
+  "cache_target_bitwise": true,
+  "columns_follow_ladder_rule": true,
+  "contig_header": true,
+  "file_shas_match_meta": true,
+  "het_matrix_matches_bcf": true,
+  "het_matrix_shape": true,
+  "ladder_matches_recomputed_level_columns": true,
+  "ladder_not_sorted": true,
+  "multihetsep_matches_awk_port": true,
+  "multihetsep_matches_script": true,
+  "multihetsep_script_ran": true,
+  "multihetsep_script_required_and_ran": true,
+  "pos_unique_in_range": true,
+  "samples_match": true,
+  "sfs_matches_bcf": true,
+  "single_contig": true,
+  "view_S": 57772
+ },
+ "n": 32,
+ "passed": true,
+ "schema": "bench_h2h.v0.v1",
+ "utc": "2026-09-16T10:58:42Z"
+}

method_inputs/a1/BOT_X10_1K/r00000003/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 56277,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_X10_1K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 3,
+ "cache_sha256": "688854533044cd063dbfdc2f3f0e3f7f63a813f1e6f11f8c765be09227bbcc3e",
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000003",
+ "columns": [
+  35,
+  55,
+  48,
+  11,
+  30,
+  28,
+  53,
+  15,
+  31,
+  60,
+  40,
+  52,
+  61,
+  57,
+  0,
+  13,
+  14,
+  32,
+  6,
+  54,
+  37,
+  17,
+  9,
+  47,
+  23,
+  42,
+  22,
+  12,
+  36,
+  24,
+  50,
+  51
+ ],
+ "contig": "region_3",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "5ed3539810ce49cb7657037071ef090c34f73700ddcb91d412bf4495c4cf80b8",
+  "phlash_contig.npz": "fb73feb38e9aa047644adf315795ae09aaead19657a3b5f0a790b3c97513aa76",
+  "sfs_unfolded.npy": "9f92d333305a314b6f8019f5a70b4ec81195c37cf4848433daa77d0b18437c2a",
+  "view.bcf": "54a9ce62db59a51545693850d04ab9f484e570b8107a6a46343fe78e0d275308",
+  "view.bcf.csi": "733b5447a0e95127ef21ae920c78d7f5b08e2be59326af5833e0d338bd67583d"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_X10_1K/samples/.fragments/fragment_00000000.npz",
+ "fragment_sha256": "7e788e9aed078cd8d6f10ff85d8c9e0f669e330dce2f8a2068bedb606450729f",
+ "ladder_columns": [
+  35,
+  55,
+  48,
+  11,
+  30,
+  28,
+  53,
+  15,
+  31,
+  60,
+  40,
+  52,
+  61,
+  57,
+  0,
+  13,
+  14,
+  32,
+  6,
+  54,
+  37,
+  17,
+  9,
+  47,
+  23,
+  42,
+  22,
+  12,
+  36,
+  24,
+  50,
+  51
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 56277,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 64485,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  13062,
+  13273,
+  14196,
+  13764,
+  13455,
+  13321,
+  13233,
+  13448,
+  13657,
+  12733,
+  12367,
+  12987,
+  13435,
+  13663,
+  14118,
+  13257,
+  12813,
+  12691,
+  13043,
+  13818,
+  13057,
+  14525,
+  13009,
+  13406,
+  13723,
+  12824,
+  13104,
+  13836,
+  13298,
+  13430,
+  13926,
+  14023
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 3,
+ "sample_id": "sim_00000003",
+ "sample_index": 3,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 56277,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "159975e92501d69b57b0a112d95a0b3a13aca0517b58d84eeec75c3ec69a763a",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T10:58:44Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_X10_1K/r00000003/v0_n32.json

@@ -0,0 +1,36 @@
+{
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000003",
+ "checks": {
+  "S_matches": true,
+  "afs_is_sfs_interior": true,
+  "big_endian_differs": true,
+  "bit_rule_matches_little_endian": true,
+  "cache_folded_sfs_matches": true,
+  "cache_folded_sfs_max_abs_diff": 9.094947017729282e-13,
+  "cache_implied_S": 56277.0,
+  "cache_ladder_matches": true,
+  "cache_nw_anchor_matches_S": true,
+  "cache_sequence_length": true,
+  "cache_target_bitwise": true,
+  "columns_follow_ladder_rule": true,
+  "contig_header": true,
+  "file_shas_match_meta": true,
+  "het_matrix_matches_bcf": true,
+  "het_matrix_shape": true,
+  "ladder_matches_recomputed_level_columns": true,
+  "ladder_not_sorted": true,
+  "multihetsep_matches_awk_port": true,
+  "multihetsep_matches_script": true,
+  "multihetsep_script_ran": true,
+  "multihetsep_script_required_and_ran": true,
+  "pos_unique_in_range": true,
+  "samples_match": true,
+  "sfs_matches_bcf": true,
+  "single_contig": true,
+  "view_S": 56277
+ },
+ "n": 32,
+ "passed": true,
+ "schema": "bench_h2h.v0.v1",
+ "utc": "2026-09-16T10:58:47Z"
+}

method_inputs/a1/BOT_X10_1K/r00000004/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 55503,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_X10_1K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 4,
+ "cache_sha256": "688854533044cd063dbfdc2f3f0e3f7f63a813f1e6f11f8c765be09227bbcc3e",
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000004",
+ "columns": [
+  22,
+  50,
+  14,
+  5,
+  54,
+  46,
+  8,
+  19,
+  52,
+  6,
+  2,
+  4,
+  25,
+  9,
+  17,
+  57,
+  44,
+  62,
+  29,
+  18,
+  26,
+  40,
+  28,
+  34,
+  23,
+  49,
+  35,
+  41,
+  37,
+  13,
+  48,
+  12
+ ],
+ "contig": "region_4",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "62a9d1e6950cd6b9a7dbfa50fda9a96578820b3dabc1f371015342988eb205c0",
+  "phlash_contig.npz": "5951266799cfc7361d9e8d16c7d0fc2302486d87af067d1132c302e7fab74f58",
+  "sfs_unfolded.npy": "f14eee39f29220327160dd2b1cb6b1fc7499ac02327a07ce815f1ae3b414d593",
+  "view.bcf": "fc7e2b4373ec833881df4c40cbb9cbd0be55d305330b67df3f14a868ff0567e8",
+  "view.bcf.csi": "464cce494daf0b7a396730b612e1319c28e53513fa0dc80e8bcdf4b2111034ac"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_X10_1K/samples/.fragments/fragment_00000001.npz",
+ "fragment_sha256": "50b76cce2d55af19a51d7f1a1340770703629e1a79725a0ac0218114de100fde",
+ "ladder_columns": [
+  22,
+  50,
+  14,
+  5,
+  54,
+  46,
+  8,
+  19,
+  52,
+  6,
+  2,
+  4,
+  25,
+  9,
+  17,
+  57,
+  44,
+  62,
+  29,
+  18,
+  26,
+  40,
+  28,
+  34,
+  23,
+  49,
+  35,
+  41,
+  37,
+  13,
+  48,
+  12
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 55503,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 64230,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  12517,
+  11994,
+  12503,
+  12099,
+  13322,
+  12995,
+  7662,
+  11980,
+  12888,
+  12903,
+  12645,
+  13073,
+  13247,
+  13358,
+  12944,
+  13347,
+  12936,
+  12734,
+  11514,
+  13243,
+  12916,
+  12543,
+  12618,
+  13914,
+  13063,
+  13263,
+  12919,
+  12290,
+  12946,
+  13049,
+  12841,
+  11859
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 0,
+ "sample_id": "sim_00000004",
+ "sample_index": 4,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 55503,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "159975e92501d69b57b0a112d95a0b3a13aca0517b58d84eeec75c3ec69a763a",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T10:58:49Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_X10_1K/r00000004/v0_n32.json

@@ -0,0 +1,36 @@
+{
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000004",
+ "checks": {
+  "S_matches": true,
+  "afs_is_sfs_interior": true,
+  "big_endian_differs": true,
+  "bit_rule_matches_little_endian": true,
+  "cache_folded_sfs_matches": true,
+  "cache_folded_sfs_max_abs_diff": 5.4569682106375694e-12,
+  "cache_implied_S": 55502.99999999999,
+  "cache_ladder_matches": true,
+  "cache_nw_anchor_matches_S": true,
+  "cache_sequence_length": true,
+  "cache_target_bitwise": true,
+  "columns_follow_ladder_rule": true,
+  "contig_header": true,
+  "file_shas_match_meta": true,
+  "het_matrix_matches_bcf": true,
+  "het_matrix_shape": true,
+  "ladder_matches_recomputed_level_columns": true,
+  "ladder_not_sorted": true,
+  "multihetsep_matches_awk_port": true,
+  "multihetsep_matches_script": true,
+  "multihetsep_script_ran": true,
+  "multihetsep_script_required_and_ran": true,
+  "pos_unique_in_range": true,
+  "samples_match": true,
+  "sfs_matches_bcf": true,
+  "single_contig": true,
+  "view_S": 55503
+ },
+ "n": 32,
+ "passed": true,
+ "schema": "bench_h2h.v0.v1",
+ "utc": "2026-09-16T10:58:53Z"
+}

method_inputs/a1/BOT_X10_1K/r00000005/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 54697,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_X10_1K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 5,
+ "cache_sha256": "688854533044cd063dbfdc2f3f0e3f7f63a813f1e6f11f8c765be09227bbcc3e",
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000005",
+ "columns": [
+  8,
+  63,
+  60,
+  62,
+  34,
+  10,
+  2,
+  33,
+  23,
+  9,
+  28,
+  49,
+  0,
+  14,
+  30,
+  3,
+  13,
+  41,
+  43,
+  58,
+  6,
+  29,
+  39,
+  4,
+  46,
+  45,
+  48,
+  38,
+  31,
+  11,
+  1,
+  24
+ ],
+ "contig": "region_5",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "d9c2820c986722a569c2c4e80deea002fd6828e3a311457881c3f7313ea3ecf6",
+  "phlash_contig.npz": "4591468dbf720bedda4d7d398f1fffe38f94e0099b9c0f20396f46320d7db805",
+  "sfs_unfolded.npy": "ec6e4e321a271b5cd2667b1f18f26142a553f9ad49f8d094244d43d4472cdad3",
+  "view.bcf": "6a86e68471f3f857c03564d2392e5f9b7fd798c10c76024c8a259df5641fc8f0",
+  "view.bcf.csi": "4c1cffc5385660c19c372e592bad46ac741d24c33434af0d217efa574298e236"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_X10_1K/samples/.fragments/fragment_00000001.npz",
+ "fragment_sha256": "50b76cce2d55af19a51d7f1a1340770703629e1a79725a0ac0218114de100fde",
+ "ladder_columns": [
+  8,
+  63,
+  60,
+  62,
+  34,
+  10,
+  2,
+  33,
+  23,
+  9,
+  28,
+  49,
+  0,
+  14,
+  30,
+  3,
+  13,
+  41,
+  43,
+  58,
+  6,
+  29,
+  39,
+  4,
+  46,
+  45,
+  48,
+  38,
+  31,
+  11,
+  1,
+  24
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 54697,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 63679,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  12321,
+  12584,
+  13064,
+  12925,
+  12907,
+  12582,
+  13657,
+  13402,
+  11496,
+  11821,
+  13256,
+  12445,
+  11508,
+  12423,
+  12770,
+  12324,
+  12276,
+  12723,
+  12854,
+  12569,
+  13146,
+  13241,
+  12584,
+  13630,
+  13529,
+  12359,
+  12579,
+  12746,
+  11989,
+  12221,
+  12159,
+  11868
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 1,
+ "sample_id": "sim_00000005",
+ "sample_index": 5,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 54697,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "159975e92501d69b57b0a112d95a0b3a13aca0517b58d84eeec75c3ec69a763a",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T10:58:54Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_X10_1K/r00000005/v0_n32.json

@@ -0,0 +1,36 @@
+{
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000005",
+ "checks": {
+  "S_matches": true,
+  "afs_is_sfs_interior": true,
+  "big_endian_differs": true,
+  "bit_rule_matches_little_endian": true,
+  "cache_folded_sfs_matches": true,
+  "cache_folded_sfs_max_abs_diff": 9.094947017729282e-13,
+  "cache_implied_S": 54697.0,
+  "cache_ladder_matches": true,
+  "cache_nw_anchor_matches_S": true,
+  "cache_sequence_length": true,
+  "cache_target_bitwise": true,
+  "columns_follow_ladder_rule": true,
+  "contig_header": true,
+  "file_shas_match_meta": true,
+  "het_matrix_matches_bcf": true,
+  "het_matrix_shape": true,
+  "ladder_matches_recomputed_level_columns": true,
+  "ladder_not_sorted": true,
+  "multihetsep_matches_awk_port": true,
+  "multihetsep_matches_script": true,
+  "multihetsep_script_ran": true,
+  "multihetsep_script_required_and_ran": true,
+  "pos_unique_in_range": true,
+  "samples_match": true,
+  "sfs_matches_bcf": true,
+  "single_contig": true,
+  "view_S": 54697
+ },
+ "n": 32,
+ "passed": true,
+ "schema": "bench_h2h.v0.v1",
+ "utc": "2026-09-16T10:58:58Z"
+}

method_inputs/a1/BOT_X10_1K/r00000006/n32/meta.json

@@ -0,0 +1,249 @@
+{
+ "S": 54595,
+ "arm": "CLEAN",
+ "bcftools_version": "bcftools 1.16-90-gab5de54-dirty",
+ "cache_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/cohort/v2_a1_BOT_X10_1K/chain0_level32/unphased_evidence_cache.npz",
+ "cache_row": 6,
+ "cache_sha256": "688854533044cd063dbfdc2f3f0e3f7f63a813f1e6f11f8c765be09227bbcc3e",
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000006",
+ "columns": [
+  60,
+  11,
+  20,
+  15,
+  58,
+  4,
+  9,
+  46,
+  38,
+  27,
+  16,
+  32,
+  25,
+  29,
+  56,
+  37,
+  40,
+  48,
+  57,
+  0,
+  50,
+  30,
+  5,
+  33,
+  47,
+  6,
+  61,
+  23,
+  8,
+  43,
+  22,
+  34
+ ],
+ "contig": "region_6",
+ "duplicate_pos_rule": "first kept site at a POS is exported; later kept sites at the same POS are dropped",
+ "export_view_sha256": "73ad2d4ff5e65ee72515a48f895f5172ea2f25a017632bbb85ae71789aafb795",
+ "files": {
+  "multihetsep.txt": "31f0274ffc745f9f2e2603e71318320ac7bcaf3fa4cc4f52af540d6b42ce96db",
+  "phlash_contig.npz": "2bf3accb07a04162028d2e51d09b6127db492046490c3002fa902f8a03b47e17",
+  "sfs_unfolded.npy": "ffe094db991e68e166747145ac0e43099499e930805bb4b451794ef56f6d49f9",
+  "view.bcf": "8a98f6bc637a8a567e728f05a5bcd7f5a72e71bdace54e9bbcbb81616c062601",
+  "view.bcf.csi": "72c193c123d9f65eb0a7948ea84ec8d3917d274f3beafd9f08bed381777d2801"
+ },
+ "fragment_path": "/ibex/project/c2041/hany0c/bench_h2h_20260915/data/v2_a1_BOT_X10_1K/samples/.fragments/fragment_00000001.npz",
+ "fragment_sha256": "50b76cce2d55af19a51d7f1a1340770703629e1a79725a0ac0218114de100fde",
+ "ladder_columns": [
+  60,
+  11,
+  20,
+  15,
+  58,
+  4,
+  9,
+  46,
+  38,
+  27,
+  16,
+  32,
+  25,
+  29,
+  56,
+  37,
+  40,
+  48,
+  57,
+  0,
+  50,
+  30,
+  5,
+  33,
+  47,
+  6,
+  61,
+  23,
+  8,
+  43,
+  22,
+  34
+ ],
+ "missing_window_rule": "window -1 iff it holds a kept site with a missing call for that diploid",
+ "mu_for_tools": 1.2500000146076218e-08,
+ "mu_source": "true constant (obs == true in CLEAN)",
+ "n": 32,
+ "n_complete_sites": 54595,
+ "n_duplicate_pos_dropped": 0,
+ "n_panel_sites": 63235,
+ "n_windows": 300000,
+ "obs_map_mean_mu": 1.2500000146076218e-08,
+ "obs_map_mean_r": 9.99999993922529e-09,
+ "per_diploid_het_counts": [
+  12161,
+  13360,
+  12500,
+  13478,
+  13007,
+  13415,
+  12602,
+  12236,
+  12659,
+  12319,
+  12913,
+  13046,
+  13620,
+  12741,
+  13436,
+  11951,
+  12924,
+  13121,
+  12545,
+  13007,
+  12234,
+  12476,
+  13258,
+  13080,
+  11843,
+  12171,
+  12301,
+  13535,
+  13354,
+  12839,
+  12827,
+  13253
+ ],
+ "per_diploid_missing_sites": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "per_diploid_missing_windows": [
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0,
+  0
+ ],
+ "plan_sha256": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc",
+ "r_for_tools": 9.99999993922529e-09,
+ "row_in_fragment": 2,
+ "sample_id": "sim_00000006",
+ "sample_index": 6,
+ "sample_names": [
+  "sample0",
+  "sample1",
+  "sample2",
+  "sample3",
+  "sample4",
+  "sample5",
+  "sample6",
+  "sample7",
+  "sample8",
+  "sample9",
+  "sample10",
+  "sample11",
+  "sample12",
+  "sample13",
+  "sample14",
+  "sample15",
+  "sample16",
+  "sample17",
+  "sample18",
+  "sample19",
+  "sample20",
+  "sample21",
+  "sample22",
+  "sample23",
+  "sample24",
+  "sample25",
+  "sample26",
+  "sample27",
+  "sample28",
+  "sample29",
+  "sample30",
+  "sample31"
+ ],
+ "schema": "bench_h2h.export_view.v1",
+ "sequence_length": 30000000,
+ "sfs_total": 54595,
+ "site_rule": "0 < derived < called over exported haplotypes (rung_site_mask)",
+ "target_sha256": "159975e92501d69b57b0a112d95a0b3a13aca0517b58d84eeec75c3ec69a763a",
+ "true_mu": 1.2500000146076218e-08,
+ "true_r": 9.99999993922529e-09,
+ "utc": "2026-09-16T10:58:59Z",
+ "window_size": 100
+}

method_inputs/a1/BOT_X10_1K/r00000006/v0_n32.json

@@ -0,0 +1,36 @@
+{
+ "canonical_id": "69c2952ec112051356e0bc0c56cfc53d13246ef334cf4942f54937de883d1abc:00000006",
+ "checks": {
+  "S_matches": true,
+  "afs_is_sfs_interior": true,
+  "big_endian_differs": true,
+  "bit_rule_matches_little_endian": true,
+  "cache_folded_sfs_matches": true,
+  "cache_folded_sfs_max_abs_diff": 9.094947017729282e-13,
+  "cache_implied_S": 54595.0,
+  "cache_ladder_matches": true,
+  "cache_nw_anchor_matches_S": true,
+  "cache_sequence_length": true,
+  "cache_target_bitwise": true,
+  "columns_follow_ladder_rule": true,
+  "contig_header": true,
+  "file_shas_match_meta": true,
+  "het_matrix_matches_bcf": true,
+  "het_matrix_shape": true,
+  "ladder_matches_recomputed_level_columns": true,
+  "ladder_not_sorted": true,
+  "multihetsep_matches_awk_port": true,
+  "multihetsep_matches_script": true,
+  "multihetsep_script_ran": true,
+  "multihetsep_script_required_and_ran": true,
+  "pos_unique_in_range": true,
+  "samples_match": true,
+  "sfs_matches_bcf": true,
+  "single_contig": true,
+  "view_S": 54595
+ },
+ "n": 32,
+ "passed": true,
+ "schema": "bench_h2h.v0.v1",
+ "utc": "2026-09-16T10:59:03Z"
+}