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Prepare for public release on Gitea: simurgarray package names, community files, Gitea templates, pseudonymised P6 probe names
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kemal committed 2026-09-30 12:09:13 +01:00
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docs/validation/P6.md
+4 -1
View File
@@ -50,7 +50,7 @@ GTCtoVCF 1.2.1 run under Python 3 with two local compatibility patches (K-022),
|---|---|---|
| identical calls | 23 656 575 | |
| identical no-calls | 109 760 | |
| `oracle_site_includes_probes_we_skip` | 2 917 | GTCtoVCF merges intensity-only CNV probes (e.g. `ilmnseq_CYP2C8_…_CNV`) into SNV sites; their alleles make its call ambiguous. SimurgArray skips intensity-only loci (OUT-019) |
| `oracle_site_includes_probes_we_skip` | 2 917 | GTCtoVCF merges intensity-only CNV probes into SNV sites; their alleles make its call ambiguous. SimurgArray skips intensity-only loci (OUT-019) |
| `oracle_opposite_strand_indel_bug` | 177 | `[I/D]` and `[D/I]` duplicate indel probes all heterozygous: we write `0/1`, GTCtoVCF 1.2.1 `./.` — the reference bug named in OUT-020/EDGE-012 |
| `grouping_differs` | 155 | indel probes designed 1–3 bp apart normalise to the same variant: we merge them (OUT-030), GTCtoVCF groups by manifest position; the probes disagree, so the merged site is missing |
| `ours_missing_het_in_haploid` | 17 | OUT-018 |
@@ -84,3 +84,6 @@ has the dash on the right (patched to skip instead of crash), which SimurgArray
| `--merge-snv-indel` (OUT-021, EDGE-013) | 1 GSA sample; `bcftools norm -c e -f` | 677 SNV+indel positions merged (635 796 → 635 119 records), 0 REF mismatches; unit test of the combined genotypes |
| `--auxiliary-loci` (OUT-035, EDGE-015) | unit tests for every rule (a)–(e) and a minus-strand design; 3 real probes (plus and minus designs) redefined as MNVs | records replaced, genotypes preserved, 0 REF mismatches |
| `export plink --format pgen|both` (plan §8.4) | `plink2 --pfile` on our `.pgen` → `.bed` | byte-identical to our own `.bed` (637 397 variants), no plink2 warnings |
The example rows in `P6_gsa36_vs_gtc2vcf.json` and `P6_gsa36_vs_gtctovcf.json` show probe names as stable
pseudonyms (`locus_NNNN`); sample IDs, positions, alleles and all counts are the original values.
docs/validation/P6_gsa36_vs_gtc2vcf.json
+87 -86
View File
@@ -6,26 +6,26 @@
"probes_in_merged_records": 5000,
"probes_only_in_oracle": 22449,
"only_in_oracle_examples": [
"10:135332149_CNV_CYP2E1",
"10:135332539_CNV_CYP2E1",
"10:135332749_CNV_CYP2E1",
"10:135333169_CNV_CYP2E1",
"10:135333379_CNV_CYP2E1",
"10:135333589_CNV_CYP2E1",
"10:135333799_CNV_CYP2E1",
"10:135334009_CNV_CYP2E1",
"10:135334009_CNV_CYP2E1_ilmndup1",
"10:135334219_CNV_CYP2E1",
"10:135334429_CNV_CYP2E1",
"10:135334639_CNV_CYP2E1",
"10:135334849_CNV_CYP2E1",
"10:135335059_CNV_CYP2E1",
"10:135335569_CNV_CYP2E1",
"10:135335569_CNV_CYP2E1_ilmndup1",
"10:135335869_CNV_CYP2E1",
"10:135335869_CNV_CYP2E1_ilmndup1",
"10:135336079_CNV_CYP2E1",
"10:135336289_CNV_CYP2E1"
"locus_0001",
"locus_0002",
"locus_0003",
"locus_0004",
"locus_0005",
"locus_0006",
"locus_0007",
"locus_0008",
"locus_0009",
"locus_0010",
"locus_0011",
"locus_0012",
"locus_0013",
"locus_0014",
"locus_0015",
"locus_0016",
"locus_0017",
"locus_0018",
"locus_0019",
"locus_0020"
],
"categories": {
"grouping_differs": 6424,
@@ -39,7 +39,7 @@
"grouping_differs": [
[
"207895980019_R14C03",
"ilmnseq_rs2013249.2_F2BT",
"locus_0021",
[
"1",
"19287570",
@@ -57,7 +57,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs201615754.1_F2BT",
"locus_0022",
[
"1",
"97515784",
@@ -75,7 +75,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs201615754.2_F2BT",
"locus_0023",
[
"1",
"97515784",
@@ -93,7 +93,7 @@
],
[
"207895980019_R14C03",
"rs201615754",
"locus_0024",
[
"1",
"97515784",
@@ -111,7 +111,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs168107.1_ilmnrev_F2BT",
"locus_0025",
[
"1",
"108937356",
@@ -129,7 +129,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs168107.2_ilmnfwd_F2BT",
"locus_0026",
[
"1",
"108937356",
@@ -147,7 +147,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs168107.2_ilmnrev_F2BT",
"locus_0027",
[
"1",
"108937356",
@@ -165,7 +165,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs4648276.2_F2BT",
"locus_0028",
[
"1",
"186676356",
@@ -183,7 +183,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs4648276_ilmnfwd_F2BT",
"locus_0029",
[
"1",
"186676356",
@@ -201,7 +201,7 @@
],
[
"207895980019_R14C03",
"rs4648276",
"locus_0030",
[
"1",
"186676356",
@@ -219,7 +219,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs1819741.1_F2BT",
"locus_0031",
[
"1",
"192815708",
@@ -237,7 +237,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs2777511.1_ilmnfwd_F2BT",
"locus_0032",
[
"10",
"33785635",
@@ -255,7 +255,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs2777511.1_ilmnrev_F2BT",
"locus_0033",
[
"10",
"33785635",
@@ -273,7 +273,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs2777511.2_ilmnrev_F2BT",
"locus_0034",
[
"10",
"33785635",
@@ -291,7 +291,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs11819745.2_F2BT",
"locus_0035",
[
"10",
"37501484",
@@ -309,7 +309,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs7091672.2_F2BT",
"locus_0036",
[
"10",
"118836909",
@@ -327,7 +327,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs7091672.3_F2BT",
"locus_0037",
[
"10",
"118836909",
@@ -345,7 +345,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs7091672_ilmnfwd_F2BT",
"locus_0038",
[
"10",
"118836909",
@@ -363,7 +363,7 @@
],
[
"207895980019_R14C03",
"rs7091672",
"locus_0039",
[
"10",
"118836909",
@@ -381,7 +381,7 @@
],
[
"207895980019_R14C03",
"ilmnseq_rs1219648.2_F2BT",
"locus_0040",
[
"10",
"121586676",
@@ -400,7 +400,7 @@
],
"representation_diff": [
[
"IlmnSeq_rs3215400",
"locus_0041",
[
"1",
"20589096",
@@ -415,7 +415,7 @@
]
],
[
"ilmnseq_rs3215400_ilmnrev",
"locus_0042",
[
"1",
"20589096",
@@ -430,7 +430,7 @@
]
],
[
"rs3215400",
"locus_0043",
[
"1",
"20589096",
@@ -445,7 +445,7 @@
]
],
[
"ilmnseq_rs61697860_ilmnfwd",
"locus_0044",
[
"1",
"78303099",
@@ -460,7 +460,7 @@
]
],
[
"ilmnseq_rs35219756_ilmnrev_F2BTindel",
"locus_0045",
[
"1",
"78392093",
@@ -475,7 +475,7 @@
]
],
[
"ilmnseq_rs35081652_ilmnfwd",
"locus_0046",
[
"1",
"78411336",
@@ -490,7 +490,7 @@
]
],
[
"IlmnSeq_rs72549303_IlmnFWD",
"locus_0047",
[
"1",
"97450065",
@@ -505,7 +505,7 @@
]
],
[
"IlmnSeq_rs72549303_IlmnREV",
"locus_0048",
[
"1",
"97450065",
@@ -520,7 +520,7 @@
]
],
[
"ilmnseq_rs72549303",
"locus_0049",
[
"1",
"97450065",
@@ -535,7 +535,7 @@
]
],
[
"ilmnseq_rs72549303_ilmndup1",
"locus_0050",
[
"1",
"97450065",
@@ -550,7 +550,7 @@
]
],
[
"ilmnseq_rs72549303_ilmnfwd_deg3a2b0",
"locus_0051",
[
"1",
"97450065",
@@ -565,7 +565,7 @@
]
],
[
"ilmnseq_rs72549303_ilmnrev_deg3a1b0",
"locus_0052",
[
"1",
"97450065",
@@ -580,7 +580,7 @@
]
],
[
"ilmnseq_rs1184321568",
"locus_0053",
[
"1",
"97593250",
@@ -595,7 +595,7 @@
]
],
[
"ilmnseq_rs1184321568_ilmnfwd",
"locus_0054",
[
"1",
"97593250",
@@ -610,7 +610,7 @@
]
],
[
"ilmnseq_rs1184321568_ilmnfwd_deg3a1b0",
"locus_0055",
[
"1",
"97593250",
@@ -625,7 +625,7 @@
]
],
[
"ilmnseq_rs1184321568_ilmnrev",
"locus_0056",
[
"1",
"97593250",
@@ -640,7 +640,7 @@
]
],
[
"ilmnseq_rs1184321568_ilmnrev_deg3a1b0",
"locus_0057",
[
"1",
"97593250",
@@ -655,7 +655,7 @@
]
],
[
"IlmnSeq_rs72549315_IlmnFWD",
"locus_0058",
[
"1",
"147208902",
@@ -670,7 +670,7 @@
]
],
[
"ilmnseq_rs72549315_ilmnfwd_ilmndup1",
"locus_0059",
[
"1",
"147208902",
@@ -685,7 +685,7 @@
]
],
[
"ilmnseq_rs72549315_ilmnfwd_ilmndup2",
"locus_0060",
[
"1",
"147208902",
@@ -703,7 +703,7 @@
"ours_missing_haploid_Y": [
[
"207895980019_R11C02",
"rs5018209",
"locus_0061",
[
"Y",
"19428214",
@@ -721,7 +721,7 @@
],
[
"207895980035_R10C01",
"rs186564287",
"locus_0062",
[
"Y",
"14081208",
@@ -739,7 +739,7 @@
],
[
"207895980019_R12C01",
"ilmnseq_rs538240449",
"locus_0063",
[
"Y",
"12030916",
@@ -757,7 +757,7 @@
],
[
"207895980019_R12C01",
"ilmnseq_rs537620655",
"locus_0064",
[
"Y",
"13331090",
@@ -775,7 +775,7 @@
],
[
"207895980035_R04C03",
"rs13304158",
"locus_0065",
[
"Y",
"9957467",
@@ -793,7 +793,7 @@
],
[
"207895980035_R04C03",
"exm1667692",
"locus_0066",
[
"Y",
"12816261",
@@ -811,7 +811,7 @@
],
[
"207895980019_R03C01",
"rs373082162",
"locus_0067",
[
"Y",
"19466559",
@@ -829,7 +829,7 @@
],
[
"207895980019_R04C01",
"rs4020596",
"locus_0068",
[
"Y",
"5680808",
@@ -847,7 +847,7 @@
],
[
"207895980019_R03C02",
"JHU_Y.14692226",
"locus_0069",
[
"Y",
"12580293",
@@ -867,7 +867,7 @@
"ours_missing_het_in_haploid": [
[
"207895980035_R13C03",
"rs5979572",
"locus_0070",
[
"X",
"7467632",
@@ -885,7 +885,7 @@
],
[
"207895980035_R13C03",
"rs7887088",
"locus_0071",
[
"X",
"7478861",
@@ -903,7 +903,7 @@
],
[
"207895980035_R13C03",
"rs146250304",
"locus_0072",
[
"X",
"68391913",
@@ -921,7 +921,7 @@
],
[
"207895980019_R06C01",
"rs138003892",
"locus_0073",
[
"X",
"33006670",
@@ -939,7 +939,7 @@
],
[
"207895980035_R09C03",
"rs28602676",
"locus_0074",
[
"MT",
"2690",
@@ -957,7 +957,7 @@
],
[
"207895980019_R15C02",
"rs1606778",
"locus_0075",
[
"X",
"79535086",
@@ -975,7 +975,7 @@
],
[
"207895980035_R14C01",
"rs104894858",
"locus_0076",
[
"X",
"120442599",
@@ -993,7 +993,7 @@
],
[
"207895980035_R03C03",
"JHU_X.22234615",
"locus_0077",
[
"X",
"22216499",
@@ -1011,7 +1011,7 @@
],
[
"207895980019_R09C03",
"rs9786566",
"locus_0078",
[
"Y",
"7044951",
@@ -1029,7 +1029,7 @@
],
[
"207895980035_R12C03",
"rs148519285",
"locus_0079",
[
"X",
"20830034",
@@ -1047,7 +1047,7 @@
],
[
"207895980035_R11C03",
"ilmnseq_rs111298280",
"locus_0080",
[
"X",
"91616889",
@@ -1065,7 +1065,7 @@
],
[
"207895980035_R11C03",
"ilmnseq_chrX:154532408_ilmnfwd_ilmndup3",
"locus_0081",
[
"X",
"154532408",
@@ -1083,7 +1083,7 @@
],
[
"207895980042_R15C02",
"ilmnseq_rs553518378",
"locus_0082",
[
"Y",
"15734824",
@@ -1101,7 +1101,7 @@
],
[
"207895980035_R05C03",
"rs12396137",
"locus_0083",
[
"X",
"7462384",
@@ -1119,7 +1119,7 @@
],
[
"207895980035_R05C03",
"rs4830772",
"locus_0084",
[
"X",
"7475195",
@@ -1137,7 +1137,7 @@
],
[
"207895980035_R05C03",
"rs146250304",
"locus_0072",
[
"X",
"68391913",
@@ -1155,5 +1155,6 @@
]
]
},
"unexplained": 0
"unexplained": 0,
"note": "Probe names from the vendor manifest are replaced by stable pseudonyms (locus_NNNN, shared by both oracle files); sample IDs, positions, alleles and all counts are unchanged."
}
docs/validation/P6_gsa36_vs_gtctovcf.json
+110 -109
View File
@@ -6,26 +6,26 @@
"probes_in_merged_records": 37785,
"probes_only_in_oracle": 22400,
"only_in_oracle_examples": [
"10:135332149_CNV_CYP2E1",
"10:135332539_CNV_CYP2E1",
"10:135332749_CNV_CYP2E1",
"10:135333169_CNV_CYP2E1",
"10:135333379_CNV_CYP2E1",
"10:135333589_CNV_CYP2E1",
"10:135333799_CNV_CYP2E1",
"10:135334009_CNV_CYP2E1",
"10:135334009_CNV_CYP2E1_ilmndup1",
"10:135334219_CNV_CYP2E1",
"10:135334429_CNV_CYP2E1",
"10:135334639_CNV_CYP2E1",
"10:135334849_CNV_CYP2E1",
"10:135335059_CNV_CYP2E1",
"10:135335569_CNV_CYP2E1",
"10:135335569_CNV_CYP2E1_ilmndup1",
"10:135335869_CNV_CYP2E1",
"10:135335869_CNV_CYP2E1_ilmndup1",
"10:135336079_CNV_CYP2E1",
"10:135336289_CNV_CYP2E1"
"locus_0001",
"locus_0002",
"locus_0003",
"locus_0004",
"locus_0005",
"locus_0006",
"locus_0007",
"locus_0008",
"locus_0009",
"locus_0010",
"locus_0011",
"locus_0012",
"locus_0013",
"locus_0014",
"locus_0015",
"locus_0016",
"locus_0017",
"locus_0018",
"locus_0019",
"locus_0020"
],
"categories": {
"grouping_differs": 155,
@@ -42,7 +42,7 @@
"oracle_site_includes_probes_we_skip": [
[
"207895980019_R03C01",
"ilmnseq_rs529038948_ilmnrev",
"locus_0085",
[
"1",
"201085496",
@@ -60,7 +60,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs529038948_ilmnrev_F2BT",
"locus_0086",
[
"1",
"201085496",
@@ -78,7 +78,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs578144976",
"locus_0087",
[
"10",
"94981305",
@@ -96,7 +96,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs578144976_ilmnfwd_F2BT",
"locus_0088",
[
"10",
"94981305",
@@ -114,7 +114,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs578144976_ilmnrev_F2BT",
"locus_0089",
[
"10",
"94981305",
@@ -132,7 +132,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs2860977_ilmnfwd_F2BT",
"locus_0090",
[
"10",
"95063364",
@@ -150,7 +150,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs11045893_ilmnfwd",
"locus_0091",
[
"12",
"21239885",
@@ -168,7 +168,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_16:55856356",
"locus_0092",
[
"16",
"55822444",
@@ -186,7 +186,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs9947507_ilmnfwd",
"locus_0093",
[
"18",
"657095",
@@ -204,7 +204,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs77654350_ilmnfwd",
"locus_0094",
[
"18",
"664286",
@@ -222,7 +222,7 @@
],
[
"207895980019_R03C01",
"rs150569967",
"locus_0095",
[
"19",
"39244961",
@@ -240,7 +240,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs28416813_ilmnfwd_F2BT",
"locus_0096",
[
"19",
"39245004",
@@ -258,7 +258,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs28416813_ilmnfwd_F2BT_ilmndup1",
"locus_0097",
[
"19",
"39245004",
@@ -276,7 +276,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs28416813_ilmnfwd_F2BT_ilmndup2",
"locus_0098",
[
"19",
"39245004",
@@ -294,7 +294,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs28416813_ilmnrev_F2BT",
"locus_0099",
[
"19",
"39245004",
@@ -312,7 +312,7 @@
],
[
"207895980019_R03C01",
"19:41351926",
"locus_0100",
[
"19",
"40846021",
@@ -330,7 +330,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs114114578_ilmnrev",
"locus_0101",
[
"19",
"40849103",
@@ -348,7 +348,7 @@
],
[
"207895980019_R03C01",
"rs121909682",
"locus_0102",
[
"2",
"85552428",
@@ -366,7 +366,7 @@
],
[
"207895980019_R03C01",
"seq-rs796053097",
"locus_0103",
[
"2",
"166073440",
@@ -384,7 +384,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs574780348_ilmnfwd",
"locus_0104",
[
"22",
"42126481",
@@ -404,7 +404,7 @@
"grouping_differs": [
[
"207895980019_R03C01",
"ilmnseq_rs45460698",
"locus_0105",
[
"11",
"113904829",
@@ -422,7 +422,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs11280056",
"locus_0106",
[
"18",
"673443",
@@ -440,7 +440,7 @@
],
[
"207895980019_R03C01",
"rs16430",
"locus_0107",
[
"18",
"673443",
@@ -458,7 +458,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs45460698",
"locus_0105",
[
"11",
"113904829",
@@ -476,7 +476,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs11280056",
"locus_0106",
[
"18",
"673443",
@@ -494,7 +494,7 @@
],
[
"207895980019_R03C02",
"rs16430",
"locus_0107",
[
"18",
"673443",
@@ -512,7 +512,7 @@
],
[
"207895980019_R04C01",
"ilmnseq_rs45460698",
"locus_0105",
[
"11",
"113904829",
@@ -530,7 +530,7 @@
],
[
"207895980019_R04C01",
"ilmnseq_rs11280056",
"locus_0106",
[
"18",
"673443",
@@ -548,7 +548,7 @@
],
[
"207895980019_R04C01",
"rs16430",
"locus_0107",
[
"18",
"673443",
@@ -566,7 +566,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs45460698",
"locus_0105",
[
"11",
"113904829",
@@ -584,7 +584,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs11280056",
"locus_0106",
[
"18",
"673443",
@@ -602,7 +602,7 @@
],
[
"207895980019_R05C01",
"rs16430",
"locus_0107",
[
"18",
"673443",
@@ -620,7 +620,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs333_ilmnfwd",
"locus_0108",
[
"3",
"46373452",
@@ -638,7 +638,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs333_ilmnfwd_F2BTindel",
"locus_0109",
[
"3",
"46373452",
@@ -656,7 +656,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs333_ilmnrev",
"locus_0110",
[
"3",
"46373452",
@@ -674,7 +674,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs333_ilmnrev_F2BTindel",
"locus_0111",
[
"3",
"46373452",
@@ -692,7 +692,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs35854239_ilmnfwd",
"locus_0112",
[
"6",
"160139865",
@@ -710,7 +710,7 @@
],
[
"207895980019_R05C01",
"ilmnseq_rs36056065",
"locus_0113",
[
"6",
"160139865",
@@ -728,7 +728,7 @@
],
[
"207895980019_R06C01",
"ilmnseq_rs45460698",
"locus_0105",
[
"11",
"113904829",
@@ -746,7 +746,7 @@
],
[
"207895980019_R06C01",
"ilmnseq_rs333_ilmnfwd",
"locus_0108",
[
"3",
"46373452",
@@ -766,7 +766,7 @@
"oracle_opposite_strand_indel_bug": [
[
"207895980019_R03C01",
"ilmnseq_rs3834939",
"locus_0114",
[
"12",
"21334835",
@@ -784,7 +784,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs3834939_ilmnfwd_F2BTindel",
"locus_0115",
[
"12",
"21334835",
@@ -802,7 +802,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs3834939_ilmnrev",
"locus_0116",
[
"12",
"21334835",
@@ -820,7 +820,7 @@
],
[
"207895980019_R03C01",
"rs3834939",
"locus_0117",
[
"12",
"21334835",
@@ -838,7 +838,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs540086241_ilmnfwd_F2BTindel",
"locus_0118",
[
"6",
"33087504",
@@ -856,7 +856,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs540086241_ilmnrev_deg3a2b0",
"locus_0119",
[
"6",
"33087504",
@@ -874,7 +874,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs59782580_ilmnrev_deg3a1b0",
"locus_0120",
[
"7",
"140836521",
@@ -892,7 +892,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs59782580_ilmnrev_F2BTindel",
"locus_0121",
[
"7",
"140836521",
@@ -910,7 +910,7 @@
],
[
"207895980019_R03C01",
"ilmnseq_rs59782580_ilmnrev_F2BTindel_deg3a1b1",
"locus_0122",
[
"7",
"140836521",
@@ -928,7 +928,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs3834939",
"locus_0114",
[
"12",
"21334835",
@@ -946,7 +946,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs3834939_ilmnfwd_F2BTindel",
"locus_0115",
[
"12",
"21334835",
@@ -964,7 +964,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs3834939_ilmnrev",
"locus_0116",
[
"12",
"21334835",
@@ -982,7 +982,7 @@
],
[
"207895980019_R03C02",
"rs3834939",
"locus_0117",
[
"12",
"21334835",
@@ -1000,7 +1000,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs540086241_ilmnfwd_F2BTindel",
"locus_0118",
[
"6",
"33087504",
@@ -1018,7 +1018,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs540086241_ilmnrev_deg3a2b0",
"locus_0119",
[
"6",
"33087504",
@@ -1036,7 +1036,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs59782580_ilmnrev_deg3a1b0",
"locus_0120",
[
"7",
"140836521",
@@ -1054,7 +1054,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs59782580_ilmnrev_F2BTindel",
"locus_0121",
[
"7",
"140836521",
@@ -1072,7 +1072,7 @@
],
[
"207895980019_R03C02",
"ilmnseq_rs59782580_ilmnrev_F2BTindel_deg3a1b1",
"locus_0122",
[
"7",
"140836521",
@@ -1090,7 +1090,7 @@
],
[
"207895980019_R04C01",
"ilmnseq_rs3834939",
"locus_0114",
[
"12",
"21334835",
@@ -1108,7 +1108,7 @@
],
[
"207895980019_R04C01",
"ilmnseq_rs3834939_ilmnfwd_F2BTindel",
"locus_0115",
[
"12",
"21334835",
@@ -1128,7 +1128,7 @@
"ours_missing_haploid_Y": [
[
"207895980019_R03C01",
"rs373082162",
"locus_0067",
[
"Y",
"19466559",
@@ -1146,7 +1146,7 @@
],
[
"207895980019_R03C02",
"JHU_Y.14692226",
"locus_0069",
[
"Y",
"12580293",
@@ -1164,7 +1164,7 @@
],
[
"207895980019_R04C01",
"rs4020596",
"locus_0068",
[
"Y",
"5680808",
@@ -1182,7 +1182,7 @@
],
[
"207895980019_R11C02",
"rs5018209",
"locus_0061",
[
"Y",
"19428214",
@@ -1200,7 +1200,7 @@
],
[
"207895980019_R12C01",
"ilmnseq_rs538240449",
"locus_0063",
[
"Y",
"12030916",
@@ -1218,7 +1218,7 @@
],
[
"207895980019_R12C01",
"ilmnseq_rs537620655",
"locus_0064",
[
"Y",
"13331090",
@@ -1236,7 +1236,7 @@
],
[
"207895980035_R04C03",
"rs13304158",
"locus_0065",
[
"Y",
"9957467",
@@ -1254,7 +1254,7 @@
],
[
"207895980035_R04C03",
"exm1667692",
"locus_0066",
[
"Y",
"12816261",
@@ -1272,7 +1272,7 @@
],
[
"207895980035_R10C01",
"rs186564287",
"locus_0062",
[
"Y",
"14081208",
@@ -1292,7 +1292,7 @@
"ours_missing_het_in_haploid": [
[
"207895980019_R06C01",
"rs138003892",
"locus_0073",
[
"X",
"33006670",
@@ -1310,7 +1310,7 @@
],
[
"207895980019_R09C03",
"JHU_Y.6912991",
"locus_0123",
[
"Y",
"7044951",
@@ -1328,7 +1328,7 @@
],
[
"207895980019_R09C03",
"rs9786566",
"locus_0078",
[
"Y",
"7044951",
@@ -1346,7 +1346,7 @@
],
[
"207895980019_R15C02",
"rs1606778",
"locus_0075",
[
"X",
"79535086",
@@ -1364,7 +1364,7 @@
],
[
"207895980035_R03C03",
"JHU_X.22234615",
"locus_0077",
[
"X",
"22216499",
@@ -1382,7 +1382,7 @@
],
[
"207895980035_R05C03",
"rs12396137",
"locus_0083",
[
"X",
"7462384",
@@ -1400,7 +1400,7 @@
],
[
"207895980035_R05C03",
"rs4830772",
"locus_0084",
[
"X",
"7475195",
@@ -1418,7 +1418,7 @@
],
[
"207895980035_R05C03",
"rs146250304",
"locus_0072",
[
"X",
"68391913",
@@ -1436,7 +1436,7 @@
],
[
"207895980035_R09C03",
"rs28602676",
"locus_0074",
[
"MT",
"2690",
@@ -1454,7 +1454,7 @@
],
[
"207895980035_R11C03",
"ilmnseq_rs111298280",
"locus_0080",
[
"X",
"91616889",
@@ -1472,7 +1472,7 @@
],
[
"207895980035_R12C03",
"rs148519285",
"locus_0079",
[
"X",
"20830034",
@@ -1490,7 +1490,7 @@
],
[
"207895980035_R13C03",
"rs5979572",
"locus_0070",
[
"X",
"7467632",
@@ -1508,7 +1508,7 @@
],
[
"207895980035_R13C03",
"exm2273083",
"locus_0124",
[
"X",
"7478861",
@@ -1526,7 +1526,7 @@
],
[
"207895980035_R13C03",
"rs7887088",
"locus_0071",
[
"X",
"7478861",
@@ -1544,7 +1544,7 @@
],
[
"207895980035_R13C03",
"rs146250304",
"locus_0072",
[
"X",
"68391913",
@@ -1562,7 +1562,7 @@
],
[
"207895980035_R14C01",
"rs104894858",
"locus_0076",
[
"X",
"120442599",
@@ -1580,7 +1580,7 @@
],
[
"207895980042_R15C02",
"ilmnseq_rs553518378",
"locus_0082",
[
"Y",
"15734824",
@@ -1600,7 +1600,7 @@
"oracle_diploid_candidates_in_haploid_context": [
[
"207895980035_R11C03",
"ilmnseq_rs144970500.1_F2BT",
"locus_0125",
[
"X",
"22890860",
@@ -1618,7 +1618,7 @@
],
[
"207895980035_R11C03",
"ilmnseq_rs144970500.2_F2BT",
"locus_0126",
[
"X",
"22890860",
@@ -1636,5 +1636,6 @@
]
]
},
"unexplained": 0
"unexplained": 0,
"note": "Probe names from the vendor manifest are replaced by stable pseudonyms (locus_NNNN, shared by both oracle files); sample IDs, positions, alleles and all counts are unchanged."
}
docs/validation/P9.md
+1 -1
View File
@@ -79,4 +79,4 @@ Manifest loading: GSA 13 s → 3 s, Omni2.5 53 s → 13 s, GDA 40 s → 10 s (Pi
* Remaining per-sample time with the kernels (Pi, 1.1 s): normalization fit 0.53 s (many small robust fits per bin),
calling 0.24 s, normalize/polar 0.08 s, raw X/Y 0.06 s. A full Rust normalization fit is the next step if needed.
* Pi thread scaling is poor (36 samples, 3 workers ≈ 1.7× one core): the Pi 5's memory bandwidth, not the code.
* CI (`.github/workflows/ci.yml`) builds the extension and runs the unit tests with and without it.
* CI (`.gitea/workflows/ci.yml`) builds the extension and runs the unit tests with and without it.
docs/validation/V2_arraytrain.md
+1 -1
View File
@@ -39,7 +39,7 @@ A per-locus diagnosis on chr22 compared our trained clusters, the vendor cluster
- **2-cluster loci were the problem.** There, v1 made 1418 errors against the vendor's 186.
- **The cause was the fixed θ windows.** Many loci are compressed or asymmetric in θ; for example the vendor file
has AA 0.05 / AB 0.27 / BB 0.45, or AA 0.37 / AB 0.68 / BB 0.96. With fixed windows such loci were mislabelled:
GSA-rs2003814 (truth 14 AB + 66 BB) was clustered as AA + AB.
rs2003814 (truth 14 AB + 66 BB) was clustered as AA + AB.
v2 (`src/simurg/train/clusters.py`) replaces this with: