Updates

GMOD · Nov 23, 2024 · 50bda9e · 50bda9e
1 parent 9c5b563
commit 50bda9e
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Showing 5 changed files with 117 additions and 86 deletions.
diff --git a/plugins/variants/src/LinearVariantMatrixRenderer/LinearVariantMatrixRenderer.ts b/plugins/variants/src/LinearVariantMatrixRenderer/LinearVariantMatrixRenderer.ts
@@ -54,7 +54,7 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
       let c2 = 0
       const samp = feat.get('genotypes')
       for (const { name } of sources) {
-        const s = samp[name]!
+        const s = samp.get(name)!
         if (s === '0|0') {
         } else if (s === '1|0' || s === '0|1') {
           c++
@@ -82,7 +82,7 @@ export default class LinearVariantMatrixRenderer extends BoxRendererType {
         for (let j = 0; j < sources.length; j++) {
           const y = (j / sources.length) * canvasHeight
           const { name } = sources[j]!
-          if (samp[name]! === val) {
+          if (samp.get(name)! === val) {
             ctx.rect(x - f2, y - f2, w + f2, h + f2)
           }
         }

diff --git a/...nts/src/LinearVariantMatrixRenderer/components/LinesConnectingMatrixToGenomicPosition.tsx b/...nts/src/LinearVariantMatrixRenderer/components/LinesConnectingMatrixToGenomicPosition.tsx
@@ -12,9 +12,9 @@ import { LinearVariantMatrixDisplayModel } from '../../LinearVariantMatrixDispla
 
 const LinesConnectingMatrixToGenomicPosition = observer(function ({
   model,
-  features,
+  features = [],
 }: {
-  features: Feature[]
+  features?: Feature[]
   model: LinearVariantMatrixDisplayModel
 }) {
   const { assemblyManager } = getSession(model)

diff --git a/plugins/variants/src/VcfFeature/index.ts b/plugins/variants/src/VcfFeature/index.ts
@@ -7,22 +7,33 @@ import { getSOTermAndDescription } from './util'
 type FeatureData = ReturnType<typeof dataFromVariant>
 
 function dataFromVariant(variant: Variant, parser: VCFParser) {
-  const { REF = '', ALT, POS, CHROM, INFO, ID } = variant
+  const { REF = '', ALT, POS, CHROM, ID } = variant
   const start = POS - 1
   const [type, description] = getSOTermAndDescription(REF, ALT, parser)
-  const isTRA = ALT?.includes('<TRA>')
-  const isSymbolic = ALT?.some(f => f.includes('<'))
 
   return {
     refName: CHROM,
     start,
-    end: isSymbolic && INFO.END && !isTRA ? +INFO.END[0] : start + REF.length,
+    end: getEnd(variant),
     description,
     type,
     name: ID?.join(','),
     aliases: ID && ID.length > 1 ? ID.slice(1) : undefined,
   }
 }
+function getEnd(variant: Variant) {
+  const { POS, REF = '', ALT } = variant
+  const isTRA = ALT?.includes('<TRA>')
+  const start = POS - 1
+  const isSymbolic = ALT?.some(f => f.includes('<'))
+  if (isSymbolic) {
+    const info = variant.INFO()
+    if (info.END && !isTRA) {
+      return +info.END[0]
+    }
+  }
+  return start + REF.length
+}
 
 export default class VCFFeature implements Feature {
   private variant: Variant

diff --git a/test_data/config_demo.json b/test_data/config_demo.json
@@ -4860,6 +4860,26 @@
         }
       },
       "assemblyNames": ["hg38"]
+    },
+    {
+      "type": "VariantTrack",
+      "trackId": "out2.vcf",
+      "name": "out2.vcf",
+      "adapter": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "out2.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "out2.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          },
+          "indexType": "TBI"
+        }
+      },
+      "assemblyNames": ["hg38"]
     }
   ],
   "connections": [],

diff --git a/yarn.lock b/yarn.lock
@@ -3378,9 +3378,9 @@
     which "^4.0.0"
 
 "@nx/devkit@>=17.1.2 < 21":
-  version "20.1.2"
-  resolved "https://registry.yarnpkg.com/@nx/devkit/-/devkit-20.1.2.tgz#10280e90aad081d7ba7b9366f4bc0abb46e65397"
-  integrity sha512-MTEWiEST7DhzZ2QmrixLnHfYVDZk7QN9omLL8m+5Etcn/3ZKa1aAo9Amd2MkUM+0MPoTKnxoGdw0fQUpAy21Mg==
+  version "20.1.3"
+  resolved "https://registry.yarnpkg.com/@nx/devkit/-/devkit-20.1.3.tgz#b67fccf91fa5b824131dac86576d41be86939a63"
+  integrity sha512-+bNCRNSHKS7SS4Q2xI/p4hhd4mIibIbeF+hpF3TLO5wxyXbrYGSdhCVK5SwclwWUN/KhcKQjOrVGW5CKAm7HAw==
   dependencies:
     ejs "^3.1.7"
     enquirer "~2.3.6"
@@ -3391,55 +3391,55 @@
     tslib "^2.3.0"
     yargs-parser "21.1.1"
 
-"@nx/nx-darwin-arm64@20.1.2":
-  version "20.1.2"
-  resolved "https://registry.yarnpkg.com/@nx/nx-darwin-arm64/-/nx-darwin-arm64-20.1.2.tgz#880dc02d2256c3f6ec98e9ab51e7c88ceedf3610"
-  integrity sha512-PJ91TQhd28kitDBubKUOXMYvrtSDrG+rr8MsIe9cHo1CvU9smcGVBwuHBxniq0DXsyOX/5GL6ngq7hjN2nQ3XQ==
-
-"@nx/nx-darwin-x64@20.1.2":
-  version "20.1.2"
-  resolved "https://registry.yarnpkg.com/@nx/nx-darwin-x64/-/nx-darwin-x64-20.1.2.tgz#e9dc306affcb18a9900efbdbcadd514ecd5fbda5"
-  integrity sha512-1fopau7nxIhTF26vDTIzMxl15AtW4FvUSdy+r1mNRKrKyjjpqnlu00SQBW7JzGV0agDD1B/61yYei5Q2aMOt7Q==
-
-"@nx/nx-freebsd-x64@20.1.2":
-  version "20.1.2"
-  resolved "https://registry.yarnpkg.com/@nx/nx-freebsd-x64/-/nx-freebsd-x64-20.1.2.tgz#ca967f9da06f93e0039b92c0c072d0c9a93b7776"
-  integrity sha512-55YgIp3v4zz7xMzJO93dtglbOTER2XdS6jrCt8GbKaWGFl5drRrBoNGONtiGNU7C3hLx1VsorbynCkJT18PjKQ==
-
-"@nx/nx-linux-arm-gnueabihf@20.1.2":
-  version "20.1.2"
-  resolved "https://registry.yarnpkg.com/@nx/nx-linux-arm-gnueabihf/-/nx-linux-arm-gnueabihf-20.1.2.tgz#c9bad02ecbf0c47e1cf1e49bc348e962665074bd"
-  integrity sha512-sMhNA8uAV43UYVEXEa8TZ8Fjpom4CGq1umTptEGOF4TTtdNn2AUBreg+0bVODM8MMSzRWGI1VbkZzHESnAPwqw==
-
-"@nx/nx-linux-arm64-gnu@20.1.2":
-  version "20.1.2"
-  resolved "https://registry.yarnpkg.com/@nx/nx-linux-arm64-gnu/-/nx-linux-arm64-gnu-20.1.2.tgz#713e83f11a20bb1dc3832faf9b08c938b2cf4c31"
-  integrity sha512-bsevarNHglaYLmIvPNQOdHrBnBgaW3EOUM0flwaXdWuZbL1bWx8GoVwHp9yJpZOAOfIF/Nhq5iTpaZB2nYFrAA==
-
-"@nx/nx-linux-arm64-musl@20.1.2":
-  version "20.1.2"
-  resolved "https://registry.yarnpkg.com/@nx/nx-linux-arm64-musl/-/nx-linux-arm64-musl-20.1.2.tgz#5091e70d20603b7cd70b0bd6022b07c0a9779d79"
-  integrity sha512-GFZTptkhZPL/iZ3tYDmspIcPEaXyy/L/o59gyp33GoFAAyDhiXIF7J1Lz81Xn8VKrX6TvEY8/9qSh86pb7qzDQ==
-
-"@nx/nx-linux-x64-gnu@20.1.2":
-  version "20.1.2"
-  resolved "https://registry.yarnpkg.com/@nx/nx-linux-x64-gnu/-/nx-linux-x64-gnu-20.1.2.tgz#8c0089fd7e797950bbe6e6898c0762bbfa55716d"
-  integrity sha512-yqEW/iglKT4d9lgfnwSNhmDzPxCkRhtdmZqOYpGDM0eZFwYwJF+WRGjW8xIqMj8PA1yrGItzXZOmyFjJqHAF2w==
-
-"@nx/nx-linux-x64-musl@20.1.2":
-  version "20.1.2"
-  resolved "https://registry.yarnpkg.com/@nx/nx-linux-x64-musl/-/nx-linux-x64-musl-20.1.2.tgz#121d6c276b97017f62168c0a018e709ef679ca01"
-  integrity sha512-SP6PpWT4cQVrC4WJQdpfADrYJQzkbhgmcGleWbpr7II1HJgOsAcvoDwQGpPQX+3Wo+VBiNecvUAOzacMQkXPGw==
-
-"@nx/nx-win32-arm64-msvc@20.1.2":
-  version "20.1.2"
-  resolved "https://registry.yarnpkg.com/@nx/nx-win32-arm64-msvc/-/nx-win32-arm64-msvc-20.1.2.tgz#37a57b4c21e23bb377a5ddffa034939f2e465211"
-  integrity sha512-JZQx9gr39LY3D7uleiXlpxUsavuOrOQNBocwKHkAMnykaT/e1VCxTnm/hk+2b4foWwfURTqoRiFEba70iiCdYg==
-
-"@nx/nx-win32-x64-msvc@20.1.2":
-  version "20.1.2"
-  resolved "https://registry.yarnpkg.com/@nx/nx-win32-x64-msvc/-/nx-win32-x64-msvc-20.1.2.tgz#8b24ea16d06e5ebf97b9b9438bae5e3c2f57a0d3"
-  integrity sha512-6GmT8iswDiCvJaCtW9DpWeAQmLS/kfAuRLYBisfzlONuLPaDdjhgVIxZBqqUSFfclwcVz+NhIOGvdr0aGFZCtQ==
+"@nx/nx-darwin-arm64@20.1.3":
+  version "20.1.3"
+  resolved "https://registry.yarnpkg.com/@nx/nx-darwin-arm64/-/nx-darwin-arm64-20.1.3.tgz#4b81ee39c847d4d41304a34feaacbbc08e6de002"
+  integrity sha512-m0Rwawht7Jwq6u2QPmAtsv+khFsTUIZUfiO1kXGcKOX3nQdJ7i82zLRd5yGbrDTAyRbAsgWO3v8zWQyhC1oGjw==
+
+"@nx/nx-darwin-x64@20.1.3":
+  version "20.1.3"
+  resolved "https://registry.yarnpkg.com/@nx/nx-darwin-x64/-/nx-darwin-x64-20.1.3.tgz#e538453e27217d65dafbe678aef8e25196540167"
+  integrity sha512-WsQK1sxOJFzD0vOtFqSHpLzWuFO4vG7G1PUyJ1Y5mPo4vbRslqoAUTqF7n42bBRPY/lE2aT7BqAAj8hm4PgcnQ==
+
+"@nx/nx-freebsd-x64@20.1.3":
+  version "20.1.3"
+  resolved "https://registry.yarnpkg.com/@nx/nx-freebsd-x64/-/nx-freebsd-x64-20.1.3.tgz#5a2dbbbe01db1abaac76c4b3fd6eac1b183b64a7"
+  integrity sha512-HV57XMtCVPy/0LZtifcEHbOpVNKLTOBFUoUXkmGYBmAKfw7lccfF600/tunTCZ4aijsD6+opEeGHzlDUK0Ir1w==
+
+"@nx/nx-linux-arm-gnueabihf@20.1.3":
+  version "20.1.3"
+  resolved "https://registry.yarnpkg.com/@nx/nx-linux-arm-gnueabihf/-/nx-linux-arm-gnueabihf-20.1.3.tgz#a242df34e82686024fa48bdc153c63ce20082d5f"
+  integrity sha512-RzP0vc4yhXktKxz7iiwVYFkgpyb5TN/lLGcKLMM4kjuyYJ0IUX58Kk5FDoqCy+HMKiMfGyTOT4fP+/UEsgW6qQ==
+
+"@nx/nx-linux-arm64-gnu@20.1.3":
+  version "20.1.3"
+  resolved "https://registry.yarnpkg.com/@nx/nx-linux-arm64-gnu/-/nx-linux-arm64-gnu-20.1.3.tgz#6a3459871a6f25ce5a5a8991708349f052139e71"
+  integrity sha512-WCaU5AiGx21C3t3v4+d7nrA1r5Xc5Wk7yVxZFWh+mKHdcqk1JebDIr1qj/7yoKHD2R9k2Vp5x5Kd0pzAGS8AyA==
+
+"@nx/nx-linux-arm64-musl@20.1.3":
+  version "20.1.3"
+  resolved "https://registry.yarnpkg.com/@nx/nx-linux-arm64-musl/-/nx-linux-arm64-musl-20.1.3.tgz#d829cc050fc08cdb055611bce6de2c9b50bff7aa"
+  integrity sha512-lKAvR9jNyx/qvk3UZGYNJAoK5mkZc+rDD4gA23tOGYPjNrWHJEgbWycCk5A9tQ4QX4CskCNmkgQx0lOMdLeXsw==
+
+"@nx/nx-linux-x64-gnu@20.1.3":
+  version "20.1.3"
+  resolved "https://registry.yarnpkg.com/@nx/nx-linux-x64-gnu/-/nx-linux-x64-gnu-20.1.3.tgz#85c14044c145a28618c9ba11262ee13ac59b602d"
+  integrity sha512-RKNm7RnTgCSl2HstDb/qMKO9r8o81EUe+UZB5fgjNR89PB757iHUX30kM0xbkiRZui1vIkMAvWcNsidxBnGGfg==
+
+"@nx/nx-linux-x64-musl@20.1.3":
+  version "20.1.3"
+  resolved "https://registry.yarnpkg.com/@nx/nx-linux-x64-musl/-/nx-linux-x64-musl-20.1.3.tgz#cbbfe982d633eef93c2c2f8818688e604e4ec179"
+  integrity sha512-aCXEWt1WQDPLzgp5I+NfqaP0y4ZKi2aauZMnSO6KE54MnZmvB+B4HQMZvqHM3dfU0jluvLRBmVIPLeTHiCccrw==
+
+"@nx/nx-win32-arm64-msvc@20.1.3":
+  version "20.1.3"
+  resolved "https://registry.yarnpkg.com/@nx/nx-win32-arm64-msvc/-/nx-win32-arm64-msvc-20.1.3.tgz#e06ce386354934bf3000d0989e734bf975de5864"
+  integrity sha512-625rRYFfoCTu73bjDZ+jOLU0lvEN2heiiUGlErc6GchfcWuIcZy16oyYQzZX69UQqryGkkZVTaoyMXhGS5p7Tg==
+
+"@nx/nx-win32-x64-msvc@20.1.3":
+  version "20.1.3"
+  resolved "https://registry.yarnpkg.com/@nx/nx-win32-x64-msvc/-/nx-win32-x64-msvc-20.1.3.tgz#a19e3916f2bc3400fafb292bf09eb17808bb2f63"
+  integrity sha512-XUbxSB6vUWoixNyCXkaXGkeUy/syqFOBXVh5Wbi6bqwTJ5o6EFUxCnzK/JsK55dfOz+I/jMXJzDWYEDAsikTSA==
 
 "@oclif/core@4.0.19":
   version "4.0.19"
@@ -5083,16 +5083,16 @@
     "@types/node" "*"
 
 "@types/node@*", "@types/node@^22.0.0", "@types/node@^22.5.5":
-  version "22.9.1"
-  resolved "https://registry.yarnpkg.com/@types/node/-/node-22.9.1.tgz#bdf91c36e0e7ecfb7257b2d75bf1b206b308ca71"
-  integrity sha512-p8Yy/8sw1caA8CdRIQBG5tiLHmxtQKObCijiAa9Ez+d4+PRffM4054xbju0msf+cvhJpnFEeNjxmVT/0ipktrg==
+  version "22.9.3"
+  resolved "https://registry.yarnpkg.com/@types/node/-/node-22.9.3.tgz#08f3d64b3bc6d74b162d36f60213e8a6704ef2b4"
+  integrity sha512-F3u1fs/fce3FFk+DAxbxc78DF8x0cY09RRL8GnXLmkJ1jvx3TtPdWoTT5/NiYfI5ASqXBmfqJi9dZ3gxMx4lzw==
   dependencies:
     undici-types "~6.19.8"
 
 "@types/node@^20.0.0", "@types/node@^20.9.0":
-  version "20.17.6"
-  resolved "https://registry.yarnpkg.com/@types/node/-/node-20.17.6.tgz#6e4073230c180d3579e8c60141f99efdf5df0081"
-  integrity sha512-VEI7OdvK2wP7XHnsuXbAJnEpEkF6NjSN45QJlL4VGqZSXsnicpesdTWsg9RISeSdYd3yeRj/y3k5KGjUXYnFwQ==
+  version "20.17.7"
+  resolved "https://registry.yarnpkg.com/@types/node/-/node-20.17.7.tgz#790151a28c5a172773d95d53a0c23d3c59a883c4"
+  integrity sha512-sZXXnpBFMKbao30dUAvzKbdwA2JM1fwUtVEq/kxKuPI5mMwZiRElCpTXb0Biq/LMEVpXDZL5G5V0RPnxKeyaYg==
   dependencies:
     undici-types "~6.19.2"
 
@@ -12646,9 +12646,9 @@ nwsapi@^2.2.12, nwsapi@^2.2.2:
   integrity sha512-cTGB9ptp9dY9A5VbMSe7fQBcl/tt22Vcqdq8+eN93rblOuE0aCFu4aZ2vMwct/2t+lFnosm8RkQW1I0Omb1UtQ==
 
 "nx@>=17.1.2 < 21":
-  version "20.1.2"
-  resolved "https://registry.yarnpkg.com/nx/-/nx-20.1.2.tgz#acb5e7f01c0eb89ff21a645e383b09c75c68180c"
-  integrity sha512-CvjmuQmI0RWLYZxRSIgQZmzsQv6dPp9oI0YZE3L1dagBPfTf5Cun65I0GLt7bdkDnVx2PGYkDbIoJSv2/V+83Q==
+  version "20.1.3"
+  resolved "https://registry.yarnpkg.com/nx/-/nx-20.1.3.tgz#e3f302cdfdbe8ab25985f64a77cc27dc0c285fc5"
+  integrity sha512-mipsacEpn0gLd/4NSlOgyHW6Ozl++8ZIfuv42RtZEnS3BaGnnW+L2dkt85h4zffq+zBILoudd/VDFzaLY7Yrfw==
   dependencies:
     "@napi-rs/wasm-runtime" "0.2.4"
     "@yarnpkg/lockfile" "^1.1.0"
@@ -12683,16 +12683,16 @@ nwsapi@^2.2.12, nwsapi@^2.2.2:
     yargs "^17.6.2"
     yargs-parser "21.1.1"
   optionalDependencies:
-    "@nx/nx-darwin-arm64" "20.1.2"
-    "@nx/nx-darwin-x64" "20.1.2"
-    "@nx/nx-freebsd-x64" "20.1.2"
-    "@nx/nx-linux-arm-gnueabihf" "20.1.2"
-    "@nx/nx-linux-arm64-gnu" "20.1.2"
-    "@nx/nx-linux-arm64-musl" "20.1.2"
-    "@nx/nx-linux-x64-gnu" "20.1.2"
-    "@nx/nx-linux-x64-musl" "20.1.2"
-    "@nx/nx-win32-arm64-msvc" "20.1.2"
-    "@nx/nx-win32-x64-msvc" "20.1.2"
+    "@nx/nx-darwin-arm64" "20.1.3"
+    "@nx/nx-darwin-x64" "20.1.3"
+    "@nx/nx-freebsd-x64" "20.1.3"
+    "@nx/nx-linux-arm-gnueabihf" "20.1.3"
+    "@nx/nx-linux-arm64-gnu" "20.1.3"
+    "@nx/nx-linux-arm64-musl" "20.1.3"
+    "@nx/nx-linux-x64-gnu" "20.1.3"
+    "@nx/nx-linux-x64-musl" "20.1.3"
+    "@nx/nx-win32-arm64-msvc" "20.1.3"
+    "@nx/nx-win32-x64-msvc" "20.1.3"
 
 object-assign@^4, object-assign@^4.0.1, object-assign@^4.1.1:
   version "4.1.1"
@@ -14860,9 +14860,9 @@ sort-object-keys@^1.1.3:
   integrity sha512-855pvK+VkU7PaKYPc+Jjnmt4EzejQHyhhF33q31qG8x7maDzkeFhAAThdCYay11CISO+qAMwjOBP+fPZe0IPyg==
 
 sort-package-json@^2.10.1:
-  version "2.11.0"
-  resolved "https://registry.yarnpkg.com/sort-package-json/-/sort-package-json-2.11.0.tgz#51d02a1dd739ce42f4274612d1a2e32a8742c1d4"
-  integrity sha512-pBs3n/wcsbnMSiO5EYV4AVnZVtyQslfZ/0v6VbrRRVApqyNf0Uqo4MOXJsBmIplGY1hYZ4bq5qjO9xTgY+K8xw==
+  version "2.12.0"
+  resolved "https://registry.yarnpkg.com/sort-package-json/-/sort-package-json-2.12.0.tgz#4196a1ba82ba63c4a512add1d00ab39026bf8ab7"
+  integrity sha512-/HrPQAeeLaa+vbAH/znjuhwUluuiM/zL5XX9kop8UpDgjtyWKt43hGDk2vd/TBdDpzIyzIHVUgmYofzYrAQjew==
   dependencies:
     detect-indent "^7.0.1"
     detect-newline "^4.0.0"
@@ -15773,16 +15773,16 @@ typed-array-byte-offset@^1.0.2:
     reflect.getprototypeof "^1.0.6"
 
 typed-array-length@^1.0.6:
-  version "1.0.6"
-  resolved "https://registry.yarnpkg.com/typed-array-length/-/typed-array-length-1.0.6.tgz#57155207c76e64a3457482dfdc1c9d1d3c4c73a3"
-  integrity sha512-/OxDN6OtAk5KBpGb28T+HZc2M+ADtvRxXrKKbUwtsLgdoxgX13hyy7ek6bFRl5+aBs2yZzB0c4CnQfAtVypW/g==
+  version "1.0.7"
+  resolved "https://registry.yarnpkg.com/typed-array-length/-/typed-array-length-1.0.7.tgz#ee4deff984b64be1e118b0de8c9c877d5ce73d3d"
+  integrity sha512-3KS2b+kL7fsuk/eJZ7EQdnEmQoaho/r6KUef7hxvltNA5DR8NAUM+8wJMbJyZ4G9/7i3v5zPBIMN5aybAh2/Jg==
   dependencies:
     call-bind "^1.0.7"
     for-each "^0.3.3"
     gopd "^1.0.1"
-    has-proto "^1.0.3"
     is-typed-array "^1.1.13"
     possible-typed-array-names "^1.0.0"
+    reflect.getprototypeof "^1.0.6"
 
 typedarray@^0.0.6:
   version "0.0.6"