@genome-spy/core 0.31.2 → 0.32.0

package/dist/schema.json

@@ -306,6 +306,36 @@
       ],
       "type": "object"
     },
+    "BamData": {
+      "additionalProperties": false,
+      "properties": {
+        "channel": {
+          "$ref": "#/definitions/PrimaryPositionalChannel",
+          "description": "Which channel's scale domain to monitor.\n\n__Default value:__ `\"x\"`"
+        },
+        "indexUrl": {
+          "description": "URL of the index file.\n\n__Default value:__ `url` + `\".bai\"`.",
+          "type": "string"
+        },
+        "type": {
+          "const": "bam",
+          "type": "string"
+        },
+        "url": {
+          "description": "URL of the BigBed file.",
+          "type": "string"
+        },
+        "windowSize": {
+          "description": "Size of each chunk when fetching the BigBed file. Data is only fetched when the length of the visible domain smaller than the window size.\n\n__Default value:__ `10000`",
+          "type": "number"
+        }
+      },
+      "required": [
+        "type",
+        "url"
+      ],
+      "type": "object"
+    },
     "Baseline": {
       "enum": [
         "top",
@@ -315,6 +345,58 @@
       ],
       "type": "string"
     },
+    "BigBedData": {
+      "additionalProperties": false,
+      "properties": {
+        "channel": {
+          "$ref": "#/definitions/PrimaryPositionalChannel",
+          "description": "Which channel's scale domain to monitor.\n\n__Default value:__ `\"x\"`"
+        },
+        "type": {
+          "const": "bigbed",
+          "type": "string"
+        },
+        "url": {
+          "description": "URL of the BigBed file.",
+          "type": "string"
+        },
+        "windowSize": {
+          "description": "Size of each chunk when fetching the BigBed file. Data is only fetched when the length of the visible domain smaller than the window size.\n\n__Default value:__ `1000000`",
+          "type": "number"
+        }
+      },
+      "required": [
+        "type",
+        "url"
+      ],
+      "type": "object"
+    },
+    "BigWigData": {
+      "additionalProperties": false,
+      "properties": {
+        "channel": {
+          "$ref": "#/definitions/PrimaryPositionalChannel",
+          "description": "Which channel's scale domain to monitor.\n\n__Default value:__ `\"x\"`"
+        },
+        "pixelsPerBin": {
+          "description": "The approximate minimum width of each data bin, in pixels.\n\n__Default value:__ `2`",
+          "type": "number"
+        },
+        "type": {
+          "const": "bigwig",
+          "type": "string"
+        },
+        "url": {
+          "description": "URL of the BigWig file.",
+          "type": "string"
+        }
+      },
+      "required": [
+        "type",
+        "url"
+      ],
+      "type": "object"
+    },
     "Channel": {
       "anyOf": [
         {
@@ -827,7 +909,7 @@
           "$ref": "#/definitions/DynamicCallbackData"
         },
         {
-          "$ref": "#/definitions/DynamicData"
+          "$ref": "#/definitions/LazyData"
         }
       ]
     },
@@ -883,28 +965,6 @@
       ],
       "type": "object"
     },
-    "DynamicData": {
-      "additionalProperties": false,
-      "properties": {
-        "dynamic": {
-          "$ref": "#/definitions/DynamicDataParams"
-        }
-      },
-      "required": [
-        "dynamic"
-      ],
-      "type": "object"
-    },
-    "DynamicDataParams": {
-      "anyOf": [
-        {
-          "$ref": "#/definitions/AxisTicksData"
-        },
-        {
-          "$ref": "#/definitions/AxisGenomeData"
-        }
-      ]
-    },
     "DynamicOpacity": {
       "additionalProperties": false,
       "description": "DynamicOpacity specifies a zoom-dependent behavior for view opacity. The opacity is interpolated between the specified stops.",
@@ -1538,6 +1598,36 @@
       ],
       "type": "object"
     },
+    "IndexedFastaData": {
+      "additionalProperties": false,
+      "properties": {
+        "channel": {
+          "$ref": "#/definitions/PrimaryPositionalChannel",
+          "description": "Which channel's scale domain to monitor.\n\n__Default value:__ `\"x\"`"
+        },
+        "indexUrl": {
+          "description": "URL of the index file.\n\n__Default value:__ `url` + `\".fai\"`.",
+          "type": "string"
+        },
+        "type": {
+          "const": "indexedFasta",
+          "type": "string"
+        },
+        "url": {
+          "description": "URL of the fasta file.",
+          "type": "string"
+        },
+        "windowSize": {
+          "description": "Size of each chunk when fetching the fasta file. Data is only fetched when the length of the visible domain smaller than the window size.\n\n__Default value:__ `7000`",
+          "type": "number"
+        }
+      },
+      "required": [
+        "type",
+        "url"
+      ],
+      "type": "object"
+    },
     "InlineData": {
       "additionalProperties": false,
       "properties": {
@@ -1777,6 +1867,40 @@
       ],
       "type": "object"
     },
+    "LazyData": {
+      "additionalProperties": false,
+      "properties": {
+        "lazy": {
+          "$ref": "#/definitions/LazyDataParams"
+        }
+      },
+      "required": [
+        "lazy"
+      ],
+      "type": "object"
+    },
+    "LazyDataParams": {
+      "anyOf": [
+        {
+          "$ref": "#/definitions/AxisTicksData"
+        },
+        {
+          "$ref": "#/definitions/AxisGenomeData"
+        },
+        {
+          "$ref": "#/definitions/IndexedFastaData"
+        },
+        {
+          "$ref": "#/definitions/BigWigData"
+        },
+        {
+          "$ref": "#/definitions/BigBedData"
+        },
+        {
+          "$ref": "#/definitions/BamData"
+        }
+      ]
+    },
     "LinearizeGenomicCoordinateParams": {
       "additionalProperties": false,
       "properties": {

package/package.json

@@ -7,7 +7,7 @@
   },
   "contributors": [],
   "license": "MIT",
-  "version": "0.31.2",
+  "version": "0.32.0",
   "main": "dist/index.js",
   "module": "dist/index.es.js",
   "exports": {
@@ -37,12 +37,17 @@
     "build:schema": "mkdir -p dist && ts-json-schema-generator --path 'src/spec/*.ts' --type RootSpec > dist/schema.json"
   },
   "dependencies": {
+    "@gmod/bam": "^1.1.18",
+    "@gmod/bbi": "^4.0.0",
+    "@gmod/bed": "^2.1.2",
+    "@gmod/indexedfasta": "^2.0.4",
     "@types/d3-array": "^3.0.2",
     "@types/d3-dsv": "^3.0.0",
     "@types/d3-ease": "^3.0.0",
     "@types/d3-format": "^3.0.1",
     "@types/d3-interpolate": "^3.0.1",
     "@types/d3-scale": "^4.0.2",
+    "buffer": "^6.0.3",
     "d3-array": "^3.1.1",
     "d3-color": "^3.0.1",
     "d3-ease": "^3.0.1",
@@ -56,5 +61,5 @@
     "vega-scale": "^7.1.1",
     "vega-util": "^1.16.0"
   },
-  "gitHead": "c29482b83972de8f18b0283b3a93f8dbcbb6af9d"
+  "gitHead": "09fe8c737a955ef4351be6f4c6a5d1c18c8be237"
 }

package/LICENSE

@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2018-2023 Kari Lavikka
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.