@jbrowse/plugin-spreadsheet-view 2.6.1

package/src/SpreadsheetView/importAdapters/__snapshots__/STARFusionImport.test.ts.snap

@@ -0,0 +1,2354 @@
+// Jest Snapshot v1, https://goo.gl/fbAQLP
+
+exports[`starfusion import 1`] = `
+{
+  "assemblyName": "fogbat",
+  "columnDisplayOrder": [
+    0,
+    1,
+    2,
+    3,
+    4,
+    5,
+    6,
+    7,
+    8,
+    9,
+    10,
+    11,
+    12,
+    13,
+    14,
+  ],
+  "columns": [
+    {
+      "dataType": {
+        "type": "Text",
+      },
+      "name": "FusionName",
+    },
+    {
+      "dataType": {
+        "type": "Number",
+      },
+      "name": "JunctionReadCount",
+    },
+    {
+      "dataType": {
+        "type": "Number",
+      },
+      "name": "SpanningFragCount",
+    },
+    {
+      "dataType": {
+        "type": "Text",
+      },
+      "name": "SpliceType",
+    },
+    {
+      "dataType": {
+        "type": "Text",
+      },
+      "name": "LeftGene",
+    },
+    {
+      "dataType": {
+        "type": "Text",
+      },
+      "name": "LeftBreakpoint",
+    },
+    {
+      "dataType": {
+        "type": "Text",
+      },
+      "name": "RightGene",
+    },
+    {
+      "dataType": {
+        "type": "Text",
+      },
+      "name": "RightBreakpoint",
+    },
+    {
+      "dataType": {
+        "type": "Text",
+      },
+      "name": "LargeAnchorSupport",
+    },
+    {
+      "dataType": {
+        "type": "Number",
+      },
+      "name": "FFPM",
+    },
+    {
+      "dataType": {
+        "type": "Text",
+      },
+      "name": "LeftBreakDinuc",
+    },
+    {
+      "dataType": {
+        "type": "Number",
+      },
+      "name": "LeftBreakEntropy",
+    },
+    {
+      "dataType": {
+        "type": "Text",
+      },
+      "name": "RightBreakDinuc",
+    },
+    {
+      "dataType": {
+        "type": "Number",
+      },
+      "name": "RightBreakEntropy",
+    },
+    {
+      "dataType": {
+        "type": "Text",
+      },
+      "name": "annots",
+    },
+  ],
+  "hasColumnNames": true,
+  "rowSet": {
+    "isLoaded": true,
+    "rows": [
+      {
+        "cells": [
+          {
+            "columnNumber": 0,
+            "text": "THRA--AC090627.1",
+          },
+          {
+            "columnNumber": 1,
+            "text": "27",
+          },
+          {
+            "columnNumber": 2,
+            "text": "93",
+          },
+          {
+            "columnNumber": 3,
+            "text": "ONLY_REF_SPLICE",
+          },
+          {
+            "columnNumber": 4,
+            "text": "THRA^ENSG00000126351.8",
+          },
+          {
+            "columnNumber": 5,
+            "text": "chr17:38243106:+",
+          },
+          {
+            "columnNumber": 6,
+            "text": "AC090627.1^ENSG00000235300.3",
+          },
+          {
+            "columnNumber": 7,
+            "text": "chr17:46371709:+",
+          },
+          {
+            "columnNumber": 8,
+            "text": "YES_LDAS",
+          },
+          {
+            "columnNumber": 9,
+            "text": "23875.8456",
+          },
+          {
+            "columnNumber": 10,
+            "text": "GT",
+          },
+          {
+            "columnNumber": 11,
+            "text": "1.8892",
+          },
+          {
+            "columnNumber": 12,
+            "text": "AG",
+          },
+          {
+            "columnNumber": 13,
+            "text": "1.9656",
+          },
+          {
+            "columnNumber": 14,
+            "text": "["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr17:8.12Mb]"]",
+          },
+        ],
+        "extendedData": {
+          "feature": {
+            "FFPM": 23875.8456,
+            "FusionName": "THRA--AC090627.1",
+            "JunctionReadCount": 27,
+            "LargeAnchorSupport": "YES_LDAS",
+            "LeftBreakDinuc": "GT",
+            "LeftBreakEntropy": 1.8892,
+            "LeftGene": "THRA^ENSG00000126351.8",
+            "RightBreakDinuc": "AG",
+            "RightBreakEntropy": 1.9656,
+            "RightGene": "AC090627.1^ENSG00000235300.3",
+            "SpanningFragCount": 93,
+            "SpliceType": "ONLY_REF_SPLICE",
+            "annots": "["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr17:8.12Mb]"]",
+            "end": 38243106,
+            "mate": {
+              "end": 46371709,
+              "refName": "chr17",
+              "start": 46371709,
+              "strand": 1,
+            },
+            "refName": "chr17",
+            "start": 38243106,
+            "strand": 1,
+            "uniqueId": "sf-1",
+          },
+        },
+        "id": "1",
+      },
+      {
+        "cells": [
+          {
+            "columnNumber": 0,
+            "text": "THRA--AC090627.1",
+          },
+          {
+            "columnNumber": 1,
+            "text": "5",
+          },
+          {
+            "columnNumber": 2,
+            "text": "93",
+          },
+          {
+            "columnNumber": 3,
+            "text": "ONLY_REF_SPLICE",
+          },
+          {
+            "columnNumber": 4,
+            "text": "THRA^ENSG00000126351.8",
+          },
+          {
+            "columnNumber": 5,
+            "text": "chr17:38243106:+",
+          },
+          {
+            "columnNumber": 6,
+            "text": "AC090627.1^ENSG00000235300.3",
+          },
+          {
+            "columnNumber": 7,
+            "text": "chr17:46384693:+",
+          },
+          {
+            "columnNumber": 8,
+            "text": "YES_LDAS",
+          },
+          {
+            "columnNumber": 9,
+            "text": "19498.6072",
+          },
+          {
+            "columnNumber": 10,
+            "text": "GT",
+          },
+          {
+            "columnNumber": 11,
+            "text": "1.8892",
+          },
+          {
+            "columnNumber": 12,
+            "text": "AG",
+          },
+          {
+            "columnNumber": 13,
+            "text": "1.4295",
+          },
+          {
+            "columnNumber": 14,
+            "text": "["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr17:8.12Mb]"]",
+          },
+        ],
+        "extendedData": {
+          "feature": {
+            "FFPM": 19498.6072,
+            "FusionName": "THRA--AC090627.1",
+            "JunctionReadCount": 5,
+            "LargeAnchorSupport": "YES_LDAS",
+            "LeftBreakDinuc": "GT",
+            "LeftBreakEntropy": 1.8892,
+            "LeftGene": "THRA^ENSG00000126351.8",
+            "RightBreakDinuc": "AG",
+            "RightBreakEntropy": 1.4295,
+            "RightGene": "AC090627.1^ENSG00000235300.3",
+            "SpanningFragCount": 93,
+            "SpliceType": "ONLY_REF_SPLICE",
+            "annots": "["CCLE","FA_CancerSupp","INTRACHROMOSOMAL[chr17:8.12Mb]"]",
+            "end": 38243106,
+            "mate": {
+              "end": 46384693,
+              "refName": "chr17",
+              "start": 46384693,
+              "strand": 1,
+            },
+            "refName": "chr17",
+            "start": 38243106,
+            "strand": 1,
+            "uniqueId": "sf-2",
+          },
+        },
+        "id": "2",
+      },
+      {
+        "cells": [
+          {
+            "columnNumber": 0,
+            "text": "ACACA--STAC2",
+          },
+          {
+            "columnNumber": 1,
+            "text": "12",
+          },
+          {
+            "columnNumber": 2,
+            "text": "52",
+          },
+          {
+            "columnNumber": 3,
+            "text": "ONLY_REF_SPLICE",
+          },
+          {
+            "columnNumber": 4,
+            "text": "ACACA^ENSG00000132142.15",
+          },
+          {
+            "columnNumber": 5,
+            "text": "chr17:35479453:-",
+          },
+          {
+            "columnNumber": 6,
+            "text": "STAC2^ENSG00000141750.6",
+          },
+          {
+            "columnNumber": 7,
+            "text": "chr17:37374426:-",
+          },
+          {
+            "columnNumber": 8,
+            "text": "YES_LDAS",
+          },
+          {
+            "columnNumber": 9,
+            "text": "12733.7844",
+          },
+          {
+            "columnNumber": 10,
+            "text": "GT",
+          },
+          {
+            "columnNumber": 11,
+            "text": "1.9656",
+          },
+          {
+            "columnNumber": 12,
+            "text": "AG",
+          },
+          {
+            "columnNumber": 13,
+            "text": "1.9656",
+          },
+          {
+            "columnNumber": 14,
+            "text": "["ChimerSeq","CCLE","Klijn_CellLines","FA_CancerSupp","INTRACHROMOSOMAL[chr17:1.60Mb]"]",
+          },
+        ],
+        "extendedData": {
+          "feature": {
+            "FFPM": 12733.7844,
+            "FusionName": "ACACA--STAC2",
+            "JunctionReadCount": 12,
+            "LargeAnchorSupport": "YES_LDAS",
+            "LeftBreakDinuc": "GT",
+            "LeftBreakEntropy": 1.9656,
+            "LeftGene": "ACACA^ENSG00000132142.15",
+            "RightBreakDinuc": "AG",
+            "RightBreakEntropy": 1.9656,
+            "RightGene": "STAC2^ENSG00000141750.6",
+            "SpanningFragCount": 52,
+            "SpliceType": "ONLY_REF_SPLICE",
+            "annots": "["ChimerSeq","CCLE","Klijn_CellLines","FA_CancerSupp","INTRACHROMOSOMAL[chr17:1.60Mb]"]",
+            "end": 35479453,
+            "mate": {
+              "end": 37374426,
+              "refName": "chr17",
+              "start": 37374426,
+              "strand": -1,
+            },
+            "refName": "chr17",
+            "start": 35479453,
+            "strand": -1,
+            "uniqueId": "sf-3",
+          },
+        },
+        "id": "3",
+      },
+      {
+        "cells": [
+          {
+            "columnNumber": 0,
+            "text": "RPS6KB1--SNF8",
+          },
+          {
+            "columnNumber": 1,
+            "text": "10",
+          },
+          {
+            "columnNumber": 2,
+            "text": "43",
+          },
+          {
+            "columnNumber": 3,
+            "text": "ONLY_REF_SPLICE",
+          },
+          {
+            "columnNumber": 4,
+            "text": "RPS6KB1^ENSG00000108443.9",
+          },
+          {
+            "columnNumber": 5,
+            "text": "chr17:57970686:+",
+          },
+          {
+            "columnNumber": 6,
+            "text": "SNF8^ENSG00000159210.5",
+          },
+          {
+            "columnNumber": 7,
+            "text": "chr17:47021337:-",
+          },
+          {
+            "columnNumber": 8,
+            "text": "YES_LDAS",
+          },
+          {
+            "columnNumber": 9,
+            "text": "10545.1651",
+          },
+          {
+            "columnNumber": 10,
+            "text": "GT",
+          },
+          {
+            "columnNumber": 11,
+            "text": "1.3753",
+          },
+          {
+            "columnNumber": 12,
+            "text": "AG",
+          },
+          {
+            "columnNumber": 13,
+            "text": "1.8323",
+          },
+          {
+            "columnNumber": 14,
+            "text": "["Klijn_CellLines","FA_CancerSupp","ChimerSeq","CCLE","INTRACHROMOSOMAL[chr17:10.95Mb]"]",
+          },
+        ],
+        "extendedData": {
+          "feature": {
+            "FFPM": 10545.1651,
+            "FusionName": "RPS6KB1--SNF8",
+            "JunctionReadCount": 10,
+            "LargeAnchorSupport": "YES_LDAS",
+            "LeftBreakDinuc": "GT",
+            "LeftBreakEntropy": 1.3753,
+            "LeftGene": "RPS6KB1^ENSG00000108443.9",
+            "RightBreakDinuc": "AG",
+            "RightBreakEntropy": 1.8323,
+            "RightGene": "SNF8^ENSG00000159210.5",
+            "SpanningFragCount": 43,
+            "SpliceType": "ONLY_REF_SPLICE",
+            "annots": "["Klijn_CellLines","FA_CancerSupp","ChimerSeq","CCLE","INTRACHROMOSOMAL[chr17:10.95Mb]"]",
+            "end": 57970686,
+            "mate": {
+              "end": 47021337,
+              "refName": "chr17",
+              "start": 47021337,
+              "strand": -1,
+            },
+            "refName": "chr17",
+            "start": 57970686,
+            "strand": 1,
+            "uniqueId": "sf-4",
+          },
+        },
+        "id": "4",
+      },
+      {
+        "cells": [
+          {
+            "columnNumber": 0,
+            "text": "TOB1--SYNRG",
+          },
+          {
+            "columnNumber": 1,
+            "text": "8",
+          },
+          {
+            "columnNumber": 2,
+            "text": "30",
+          },
+          {
+            "columnNumber": 3,
+            "text": "ONLY_REF_SPLICE",
+          },
+          {
+            "columnNumber": 4,
+            "text": "TOB1^ENSG00000141232.4",
+          },
+          {
+            "columnNumber": 5,
+            "text": "chr17:48943419:-",
+          },
+          {
+            "columnNumber": 6,
+            "text": "SYNRG^ENSG00000006114.11",
+          },
+          {
+            "columnNumber": 7,
+            "text": "chr17:35880751:-",
+          },
+          {
+            "columnNumber": 8,
+            "text": "YES_LDAS",
+          },
+          {
+            "columnNumber": 9,
+            "text": "7560.6844",
+          },
+          {
+            "columnNumber": 10,
+            "text": "GT",
+          },
+          {
+            "columnNumber": 11,
+            "text": "1.4566",
+          },
+          {
+            "columnNumber": 12,
+            "text": "AG",
+          },
+          {
+            "columnNumber": 13,
+            "text": "1.8892",
+          },
+          {
+            "columnNumber": 14,
+            "text": "["FA_CancerSupp","CCLE","INTRACHROMOSOMAL[chr17:12.97Mb]"]",
+          },
+        ],
+        "extendedData": {
+          "feature": {
+            "FFPM": 7560.6844,
+            "FusionName": "TOB1--SYNRG",
+            "JunctionReadCount": 8,
+            "LargeAnchorSupport": "YES_LDAS",
+            "LeftBreakDinuc": "GT",
+            "LeftBreakEntropy": 1.4566,
+            "LeftGene": "TOB1^ENSG00000141232.4",
+            "RightBreakDinuc": "AG",
+            "RightBreakEntropy": 1.8892,
+            "RightGene": "SYNRG^ENSG00000006114.11",
+            "SpanningFragCount": 30,
+            "SpliceType": "ONLY_REF_SPLICE",
+            "annots": "["FA_CancerSupp","CCLE","INTRACHROMOSOMAL[chr17:12.97Mb]"]",
+            "end": 48943419,
+            "mate": {
+              "end": 35880751,
+              "refName": "chr17",
+              "start": 35880751,
+              "strand": -1,
+            },
+            "refName": "chr17",
+            "start": 48943419,
+            "strand": -1,
+            "uniqueId": "sf-5",
+          },
+        },
+        "id": "5",
+      },
+      {
+        "cells": [
+          {
+            "columnNumber": 0,
+            "text": "VAPB--IKZF3",
+          },
+          {
+            "columnNumber": 1,
+            "text": "4",
+          },
+          {
+            "columnNumber": 2,
+            "text": "46",
+          },
+          {
+            "columnNumber": 3,
+            "text": "ONLY_REF_SPLICE",
+          },
+          {
+            "columnNumber": 4,
+            "text": "VAPB^ENSG00000124164.11",
+          },
+          {
+            "columnNumber": 5,
+            "text": "chr20:56964573:+",
+          },
+          {
+            "columnNumber": 6,
+            "text": "IKZF3^ENSG00000161405.12",
+          },
+          {
+            "columnNumber": 7,
+            "text": "chr17:37934020:-",
+          },
+          {
+            "columnNumber": 8,
+            "text": "YES_LDAS",
+          },
+          {
+            "columnNumber": 9,
+            "text": "9948.269",
+          },
+          {
+            "columnNumber": 10,
+            "text": "GT",
+          },
+          {
+            "columnNumber": 11,
+            "text": "1.9656",
+          },
+          {
+            "columnNumber": 12,
+            "text": "AG",
+          },
+          {
+            "columnNumber": 13,
+            "text": "1.7819",
+          },
+          {
+            "columnNumber": 14,
+            "text": "["FA_CancerSupp","Klijn_CellLines","CCLE","ChimerSeq","ChimerPub","INTERCHROMOSOMAL[chr20--chr17]"]",
+          },
+        ],
+        "extendedData": {
+          "feature": {
+            "FFPM": 9948.269,
+            "FusionName": "VAPB--IKZF3",
+            "JunctionReadCount": 4,
+            "LargeAnchorSupport": "YES_LDAS",
+            "LeftBreakDinuc": "GT",
+            "LeftBreakEntropy": 1.9656,
+            "LeftGene": "VAPB^ENSG00000124164.11",
+            "RightBreakDinuc": "AG",
+            "RightBreakEntropy": 1.7819,
+            "RightGene": "IKZF3^ENSG00000161405.12",
+            "SpanningFragCount": 46,
+            "SpliceType": "ONLY_REF_SPLICE",
+            "annots": "["FA_CancerSupp","Klijn_CellLines","CCLE","ChimerSeq","ChimerPub","INTERCHROMOSOMAL[chr20--chr17]"]",
+            "end": 56964573,
+            "mate": {
+              "end": 37934020,
+              "refName": "chr17",
+              "start": 37934020,
+              "strand": -1,
+            },
+            "refName": "chr20",
+            "start": 56964573,
+            "strand": 1,
+            "uniqueId": "sf-6",
+          },
+        },
+        "id": "6",
+      },
+      {
+        "cells": [
+          {
+            "columnNumber": 0,
+            "text": "ZMYND8--CEP250",
+          },
+          {
+            "columnNumber": 1,
+            "text": "2",
+          },
+          {
+            "columnNumber": 2,
+            "text": "44",
+          },
+          {
+            "columnNumber": 3,
+            "text": "ONLY_REF_SPLICE",
+          },
+          {
+            "columnNumber": 4,
+            "text": "ZMYND8^ENSG00000101040.15",
+          },
+          {
+            "columnNumber": 5,
+            "text": "chr20:45852970:-",
+          },
+          {
+            "columnNumber": 6,
+            "text": "CEP250^ENSG00000126001.11",
+          },
+          {
+            "columnNumber": 7,
+            "text": "chr20:34078463:+",
+          },
+          {
+            "columnNumber": 8,
+            "text": "NO_LDAS",
+          },
+          {
+            "columnNumber": 9,
+            "text": "9152.4075",
+          },
+          {
+            "columnNumber": 10,
+            "text": "GT",
+          },
+          {
+            "columnNumber": 11,
+            "text": "1.8295",
+          },
+          {
+            "columnNumber": 12,
+            "text": "AG",
+          },
+          {
+            "columnNumber": 13,
+            "text": "1.8062",
+          },
+          {
+            "columnNumber": 14,
+            "text": "["FA_CancerSupp","CCLE","ChimerSeq","INTRACHROMOSOMAL[chr20:11.74Mb]"]",
+          },
+        ],
+        "extendedData": {
+          "feature": {
+            "FFPM": 9152.4075,
+            "FusionName": "ZMYND8--CEP250",
+            "JunctionReadCount": 2,
+            "LargeAnchorSupport": "NO_LDAS",
+            "LeftBreakDinuc": "GT",
+            "LeftBreakEntropy": 1.8295,
+            "LeftGene": "ZMYND8^ENSG00000101040.15",
+            "RightBreakDinuc": "AG",
+            "RightBreakEntropy": 1.8062,
+            "RightGene": "CEP250^ENSG00000126001.11",
+            "SpanningFragCount": 44,
+            "SpliceType": "ONLY_REF_SPLICE",
+            "annots": "["FA_CancerSupp","CCLE","ChimerSeq","INTRACHROMOSOMAL[chr20:11.74Mb]"]",
+            "end": 45852970,
+            "mate": {
+              "end": 34078463,
+              "refName": "chr20",
+              "start": 34078463,
+              "strand": 1,
+            },
+            "refName": "chr20",
+            "start": 45852970,
+            "strand": -1,
+            "uniqueId": "sf-7",
+          },
+        },
+        "id": "7",
+      },
+      {
+        "cells": [
+          {
+            "columnNumber": 0,
+            "text": "AHCTF1--NAAA",
+          },
+          {
+            "columnNumber": 1,
+            "text": "3",
+          },
+          {
+            "columnNumber": 2,
+            "text": "38",
+          },
+          {
+            "columnNumber": 3,
+            "text": "ONLY_REF_SPLICE",
+          },
+          {
+            "columnNumber": 4,
+            "text": "AHCTF1^ENSG00000153207.10",
+          },
+          {
+            "columnNumber": 5,
+            "text": "chr1:247094880:-",
+          },
+          {
+            "columnNumber": 6,
+            "text": "NAAA^ENSG00000138744.10",
+          },
+          {
+            "columnNumber": 7,
+            "text": "chr4:76846964:-",
+          },
+          {
+            "columnNumber": 8,
+            "text": "YES_LDAS",
+          },
+          {
+            "columnNumber": 9,
+            "text": "8157.5805",
+          },
+          {
+            "columnNumber": 10,
+            "text": "GT",
+          },
+          {
+            "columnNumber": 11,
+            "text": "1.7232",
+          },
+          {
+            "columnNumber": 12,
+            "text": "AG",
+          },
+          {
+            "columnNumber": 13,
+            "text": "1.8062",
+          },
+          {
+            "columnNumber": 14,
+            "text": "["FA_CancerSupp","CCLE","INTERCHROMOSOMAL[chr1--chr4]"]",
+          },
+        ],
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