@niagads/igv 0.1.0

package/dist/tracks/utils.js

@@ -0,0 +1,2 @@
+import{__awaiter as e,__asyncValues as r}from"tslib";import{ALWAYS_ON_TRACKS as i}from"../config/_constants.js";const d=(e,r)=>r.filter(r=>e.includes(r.id)),t=e=>{const r=e.track;return"id"in r?r.id:r.config.id},o=(e,r=i)=>{var d;return(null!==(d=null==e?void 0:e.trackViews)&&void 0!==d?d:[]).map(e=>t(e)).filter(e=>!r.includes(e))},n=(e,r)=>{var i;const d=(null!==(i=null==r?void 0:r.trackViews)&&void 0!==i?i:[]).filter(r=>t(r)===e);r.removeTrack(d[0].track)},a=(r,i)=>e(void 0,void 0,void 0,function*(){if("format"in r&&null!=r.format.match("^bed\\d{1,2}\\+\\d+$")){const{default:e}=yield import("../decoders/bedDecoder.js");r.decode=e}if(r.url.includes("$CHR")){const{default:e}=yield import("../readers/ShardedBedReader.js");r.reader=new e(r,i.genome)}r.type.includes("_service")&&(r.reader=yield c(r.type,{endpoint:r.url,track:r.id})),yield i.loadTrack(r)}),l=(i,d)=>e(void 0,void 0,void 0,function*(){var e,t,o;try{for(var n,l=!0,c=r(i.map(e=>a(e,d)));!(e=(n=yield c.next()).done);l=!0){n.value,l=!1}}catch(e){t={error:e}}finally{try{l||e||!(o=c.return)||(yield o.call(c))}finally{if(t)throw t.error}}}),c=(r,i)=>e(void 0,void 0,void 0,function*(){const{default:e}=yield import("../readers/GWASServiceReader.js"),{default:d}=yield import("../readers/VariantServiceReader.js");switch(r){case"gwas_service":return new e(i);case"variant_service":return new d(i);default:return null}});export{o as getLoadedTracks,d as getTrackConfig,t as getTrackID,a as loadTrack,l as loadTracks,n as removeTrackById,c as resolveServiceTrackReader};
+//# sourceMappingURL=utils.js.map

package/dist/tracks/utils.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"utils.js","sources":["../../src/tracks/utils.tsx"],"sourcesContent":[null],"names":["getTrackConfig","trackIds","config","filter","c","includes","id","getTrackID","trackView","track","getLoadedTracks","browser","alwaysOnTracks","ALWAYS_ON_TRACKS","_a","trackViews","map","view","removeTrackById","trackId","removeTrack","loadTrack","__awaiter","format","match","default","decodeBedXY","import","decode","url","ShardedBedReader","reader","genome","type","resolveServiceTrackReader","endpoint","loadTracks","tracks","_f","_d","_e","__asyncValues","t","next","done","value","trackType","GWASServiceReader","VariantServiceReader"],"mappings":"gHAGO,MAAMA,EAAiB,CAACC,EAAoBC,IAC/CA,EAAOC,OAAQC,GAAMH,EAASI,SAASD,EAAEE,KAEhCC,EAAcC,IACvB,MAAMC,EAAQD,EAAUC,MACxB,MAAO,OAAQA,EAAQA,EAAMH,GAAKG,EAAMP,OAAOI,IAGtCI,EAAkB,CAACC,EAAcC,EAA2BC,WACrE,OAAoB,QAAnBC,EAAAH,aAAO,EAAPA,EAASI,kBAAU,IAAAD,EAAAA,EAAI,IACnBE,IAAKC,GAAcV,EAAWU,IAC9Bd,OAAQM,IAAmBG,EAAeP,SAASI,KAM/CS,EAAkB,CAACC,EAAiBR,WAC7C,MACMH,GADgC,QAAnBM,EAAAH,aAAO,EAAPA,EAASI,kBAAU,IAAAD,EAAAA,EAAI,IACbX,OAAQc,GAAcV,EAAWU,KAAUE,GACxER,EAAQS,YAAYZ,EAAU,GAAGC,QAIxBY,EAAY,CAAOZ,EAAwBE,IAAgBW,OAAA,OAAA,OAAA,EAAA,YACpE,GAAI,WAAYb,GAEsC,MAA9CA,EAAMc,OAAOC,MAAM,wBAAiC,CACpD,MAAQC,QAASC,SAAsBC,OAAO,6BAC9ClB,EAAMmB,OAASF,CACnB,CAEJ,GAAIjB,EAAMoB,IAAIxB,SAAS,QAAS,CAC5B,MAAQoB,QAASK,SAA2BH,OAAO,kCACnDlB,EAAMsB,OAAS,IAAID,EAAiBrB,EAAOE,EAAQqB,OACvD,CACIvB,EAAMwB,KAAK5B,SAAS,cACpBI,EAAMsB,aAAeG,EAA0BzB,EAAMwB,KAAM,CACvDE,SAAU1B,EAAMoB,IAChBpB,MAAOA,EAAMH,YAIfK,EAAQU,UAAUZ,EAC5B,GAEa2B,EAAa,CAAOC,EAA2B1B,IAAgBW,OAAA,OAAA,OAAA,EAAA,0BACxE,IAAsB,IAAwCgB,EAAxCC,GAAA,EAAAC,EAAAC,EAAAJ,EAAOrB,IAAK0B,GAAMrB,EAAUqB,EAAG/B,OAASG,GAAAwB,QAAAE,EAAAG,QAAAC,MAAAL,GAAA,EAAA,CAAxCD,EAAAO,MAAAN,GAAA,CAA0C,sGACpE,GAEaL,EAA4B,CAAOY,EAAmB5C,IAAeoB,OAAA,OAAA,OAAA,EAAA,YAE9E,MAAQG,QAASsB,SAA4BpB,OAAO,oCAC5CF,QAASuB,SAA+BrB,OAAO,sCAEvD,OAAQmB,GACJ,IAAK,eACD,OAAO,IAAIC,EAAkB7C,GACjC,IAAK,kBACD,OAAO,IAAI8C,EAAqB9C,GACpC,QACI,OAAO,KAEnB"}

package/dist/utils/browser.js

@@ -0,0 +1,2 @@
+import{__awaiter as i,__asyncValues as r}from"tslib";import{ALWAYS_ON_TRACKS as e}from"../config/_constants.js";import{getViewTrackIdentifier as o}from"./views.js";import{resolveServiceTrackReader as t}from"./track_config.js";const n=(i,r=e)=>{var t;return(null!==(t=null==i?void 0:i.trackViews)&&void 0!==t?t:[]).map(i=>o(i)).filter(i=>!r.includes(i))},d=(i,r)=>{var e;const t=(null!==(e=null==i?void 0:i.trackViews)&&void 0!==e?e:[]).filter(i=>o(i)===r);i.removeTrack(t[0].track)},l=(r,e)=>i(void 0,void 0,void 0,function*(){if("format"in e&&null!=e.format.match("^bed\\d{1,2}\\+\\d+$")){const{default:i}=yield import("../decoders/bedDecoder.js");e.decode=i}if(e.url.includes("$CHR")){const{default:i}=yield import("../readers/ShardedBedReader.js");e.reader=new i(e,r.genome)}e.type.includes("_service")&&(e.reader=yield t({endpoint:e.url,track:e.id},e.type)),yield r.loadTrack(e)}),c=(e,o)=>i(void 0,void 0,void 0,function*(){var i,t,n;try{for(var d,c=!0,a=r(o.map(i=>l(e,i)));!(i=(d=yield a.next()).done);c=!0){d.value,c=!1}}catch(i){t={error:i}}finally{try{c||i||!(n=a.return)||(yield n.call(a))}finally{if(t)throw t.error}}});function a(r,e,o){return i(this,void 0,void 0,function*(){const i=e.filter(i=>!o.includes(i.id));return i.length>0?(yield c(r,i),i.map(i=>i.id)):[]})}function s(r,e,o){return i(this,void 0,void 0,function*(){const i=o.filter(i=>!e.some(r=>r.id===i));for(const e of i)d(r,e);return i})}function f(r,e){return i(this,void 0,void 0,function*(){const i=n(r,r.config.alwaysOnTracks);yield a(r,e,i),yield s(r,e,i)})}export{n as getLoadedTracks,a as handleAddTracksToBrowser,s as handleRemoveTracksFromBrowser,f as handleUpdateBrowserTracks,l as loadTrack,c as loadTracks,d as removeTrackById};
+//# sourceMappingURL=browser.js.map

package/dist/utils/browser.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"browser.js","sources":["../../src/utils/browser.tsx"],"sourcesContent":[null],"names":["getLoadedTracks","browser","alwaysOnTracks","ALWAYS_ON_TRACKS","_a","trackViews","map","view","getViewTrackIdentifier","filter","track","includes","removeTrackById","trackId","trackView","removeTrack","loadTrack","__awaiter","format","match","default","decodeBedXY","import","decode","url","ShardedBedReader","reader","genome","type","resolveServiceTrackReader","endpoint","id","loadTracks","tracks","_f","_d","_e","__asyncValues","t","next","done","value","handleAddTracksToBrowser","selectedTrackConfigs","loadedTrackIds","tracksToAdd","length","handleRemoveTracksFromBrowser","tracksToRemove","some","handleUpdateBrowserTracks","config"],"mappings":"kOAWO,MAAMA,EAAkB,CAACC,EAAcC,EAA2BC,WACrE,OAAoB,QAAnBC,EAAAH,aAAO,EAAPA,EAASI,kBAAU,IAAAD,EAAAA,EAAI,IACnBE,IAAKC,GAAcC,EAAuBD,IAC1CE,OAAQC,IAAmBR,EAAeS,SAASD,KAiB/CE,EAAkB,CAACX,EAAcY,WAC1C,MACMC,GADgC,QAAnBV,EAAAH,aAAO,EAAPA,EAASI,kBAAU,IAAAD,EAAAA,EAAI,IACbK,OAAQF,GAAcC,EAAuBD,KAAUM,GACpFZ,EAAQc,YAAYD,EAAU,GAAGJ,QASxBM,EAAY,CAAOf,EAAcS,IAA0BO,cAAA,OAAA,EAAA,YACpE,GAAI,WAAYP,GAEsC,MAA9CA,EAAMQ,OAAOC,MAAM,wBAAiC,CACpD,MAAQC,QAASC,SAAsBC,OAAO,6BAC9CZ,EAAMa,OAASF,CACnB,CAEJ,GAAIX,EAAMc,IAAIb,SAAS,QAAS,CAC5B,MAAQS,QAASK,SAA2BH,OAAO,kCACnDZ,EAAMgB,OAAS,IAAID,EAAiBf,EAAOT,EAAQ0B,OACvD,CACIjB,EAAMkB,KAAKjB,SAAS,cACpBD,EAAMgB,aAAeG,EACjB,CACIC,SAAUpB,EAAMc,IAChBd,MAAOA,EAAMqB,IAEjBrB,EAAMkB,aAIR3B,EAAQe,UAAUN,EAC5B,GAOasB,EAAa,CAAO/B,EAAcgC,IAA6BhB,cAAA,OAAA,EAAA,0BACxE,IAAsB,IAAwCiB,EAAxCC,GAAA,EAAAC,EAAAC,EAAAJ,EAAO3B,IAAKgC,GAAMtB,EAAUf,EAASqC,OAAGlC,GAAA8B,QAAAE,EAAAG,QAAAC,MAAAL,GAAA,EAAA,CAAxCD,EAAAO,MAAAN,GAAA,CAA0C,sGACpE,YAUsBO,EAClBzC,EACA0C,EACAC,2CAEA,MAAMC,EAAcF,EAAqBlC,OAAQC,IAA4BkC,EAAejC,SAASD,EAAMqB,KAC3G,OAAIc,EAAYC,OAAS,SACfd,EAAW/B,EAAS4C,GACnBA,EAAYvC,IAAKI,GAAUA,EAAMqB,KAErC,EACX,EAAC,UAUqBgB,EAClB9C,EACA0C,EACAC,2CAEA,MAAMI,EAAiBJ,EAAenC,OACjCsB,IAAgBY,EAAqBM,KAAMvC,GAAUA,EAAMqB,KAAOA,IAGvE,IAAK,MAAMlB,KAAWmC,EAClBpC,EAAgBX,EAASY,GAG7B,OAAOmC,CACX,EAAC,CAmBK,SAAgBE,EAA0BjD,EAAc0C,2CAC1D,MAAMC,EAAiB5C,EAAgBC,EAASA,EAAQkD,OAAOjD,sBACzDwC,EAAyBzC,EAAS0C,EAAsBC,SACxDG,EAA8B9C,EAAS0C,EAAsBC,EACvE,EAAC"}

package/dist/utils/selector_actions.js

@@ -0,0 +1,2 @@
+import{__awaiter as i}from"tslib";import{getLoadedTracks as o,loadTracks as n,removeTrackById as t}from"./browser.js";function r(n,t){return i(this,void 0,void 0,function*(){const i=o(n,n.config.alwaysOnTracks);yield e(n,t,i),yield s(n,t,i)})}function e(o,t,r){return i(this,void 0,void 0,function*(){const i=t.filter(i=>!r.includes(i.id));return i.length>0?(yield n(o,i),i.map(i=>i.id)):[]})}function s(o,n,r){return i(this,void 0,void 0,function*(){const i=r.filter(i=>!n.some(o=>o.id===i));for(const n of i)t(o,n);return i})}export{e as handleAddTracksToBrowser,s as handleRemoveTracksFromBrowser,r as handleUpdateBrowserTracks};
+//# sourceMappingURL=selector_actions.js.map

package/dist/utils/selector_actions.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"selector_actions.js","sources":["../../src/utils/selector_actions.tsx"],"sourcesContent":[null],"names":["handleUpdateBrowserTracks","browser","selectedTrackConfigs","loadedTrackIds","getLoadedTracks","config","alwaysOnTracks","handleAddTracksToBrowser","handleRemoveTracksFromBrowser","tracksToAdd","filter","track","includes","id","length","loadTracks","map","tracksToRemove","some","trackId","removeTrackById"],"mappings":"sHAmEM,SAAgBA,EAA0BC,EAAcC,2CAC1D,MAAMC,EAAiBC,EAAgBH,EAASA,EAAQI,OAAOC,sBACzDC,EAAyBN,EAASC,EAAsBC,SACxDK,EAA8BP,EAASC,EAAsBC,EACvE,EAAC,UAUqBI,EAClBN,EACAC,EACAC,2CAEA,MAAMM,EAAcP,EAAqBQ,OAAQC,IAA4BR,EAAeS,SAASD,EAAME,KAC3G,OAAIJ,EAAYK,OAAS,SACfC,EAAWd,EAASQ,GACnBA,EAAYO,IAAKL,GAAUA,EAAME,KAErC,EACX,EAAC,UAUqBL,EAClBP,EACAC,EACAC,2CAEA,MAAMc,EAAiBd,EAAeO,OACjCG,IAAgBX,EAAqBgB,KAAMP,GAAUA,EAAME,KAAOA,IAGvE,IAAK,MAAMM,KAAWF,EAClBG,EAAgBnB,EAASkB,GAG7B,OAAOF,CACX,EAAC"}

package/dist/utils/track_config.js

@@ -0,0 +1,2 @@
+import{__awaiter as e}from"tslib";const r=(e,r)=>e.filter(e=>r.includes(e.id)),i=(r,i)=>e(void 0,void 0,void 0,function*(){switch(i){case"gwas_service":const{default:e}=yield import("../readers/GWASServiceReader.js");return new e(r);case"variant_service":const{default:i}=yield import("../readers/VariantServiceReader.js");return new i(r);default:return null}});function t(e,i){if("string"==typeof i[0]){if(!e)throw new Error("resolveTrackConfigs: config must be provided when tracks is a string[]");return r(e,i)}return i}function n(e){return"string"==typeof e[0]?e:e.map(e=>e.id)}export{r as findTrackConfigs,i as resolveServiceTrackReader,t as resolveTrackConfigs,n as resolveTrackIds};
+//# sourceMappingURL=track_config.js.map

package/dist/utils/track_config.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"track_config.js","sources":["../../src/utils/track_config.tsx"],"sourcesContent":[null],"names":["findTrackConfigs","config","trackIds","filter","c","includes","id","resolveServiceTrackReader","trackType","__awaiter","default","GWASServiceReader","import","VariantServiceReader","resolveTrackConfigs","tracks","Error","resolveTrackIds","map","t"],"mappings":"kCAQO,MAAMA,EAAmB,CAACC,EAA2BC,IACxDD,EAAOE,OAAQC,GAAMF,EAASG,SAASD,EAAEE,KAShCC,EAA4B,CAAON,EAAaO,IAAqBC,cAAA,OAAA,EAAA,YAG9E,OAAQD,GACJ,IAAK,eACD,MAAQE,QAASC,SAA4BC,OAAO,mCACpD,OAAO,IAAID,EAAkBV,GACjC,IAAK,kBACD,MAAQS,QAASG,SAA+BD,OAAO,sCACvD,OAAO,IAAIC,EAAqBZ,GACpC,QACI,OAAO,KAEnB,GAUM,SAAUa,EACZb,EACAc,GAEA,GAAyB,iBAAdA,EAAO,GAAiB,CAC/B,IAAKd,EACD,MAAM,IAAIe,MAAM,0EAEpB,OAAOhB,EAAiBC,EAAQc,EACpC,CACA,OAAOA,CACX,CASM,SAAUE,EAAgBF,GAC5B,MAAyB,iBAAdA,EAAO,GACPA,EAEHA,EAA6BG,IAAKC,GAAMA,EAAEb,GACtD"}

package/dist/utils/views.js

@@ -0,0 +1,2 @@
+const i=i=>{const n=i.track;return"id"in n?n.id:n.config.id};export{i as getViewTrackIdentifier};
+//# sourceMappingURL=views.js.map

package/dist/utils/views.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"views.js","sources":["../../src/utils/views.tsx"],"sourcesContent":[null],"names":["getViewTrackIdentifier","trackView","track","id","config"],"mappings":"AAAO,MAAMA,EAA0BC,IACnC,MAAMC,EAAQD,EAAUC,MACxB,MAAO,OAAQA,EAAQA,EAAMC,GAAKD,EAAME,OAAOD"}

package/package.json

@@ -0,0 +1,48 @@
+{
+    "name": "@niagads/igv",
+    "version": "0.1.0",
+    "description": "NIAGADS IGV Browser Component",
+    "repository": {
+        "type": "git",
+        "url": "https://github.com/NIAGADS/niagads-viz-monorepo.git"
+    },
+    "license": "GPL-3.0-only",
+    "scripts": {
+        "build": "rollup -c"
+    },
+    "dependencies": {
+        "@niagads/common": "^0.1.0",
+        "@niagads/table": "^0.1.0",
+        "@niagads/ui": "^0.1.0",
+        "igv": "github:NIAGADS/igv.js#NIAGADS-01102025",
+        "jquery": "^3.7.1"
+    },
+    "devDependencies": {
+        "@rollup/plugin-commonjs": "^28.0.2",
+        "@rollup/plugin-node-resolve": "^16.0.0",
+        "@rollup/plugin-terser": "^0.4.4",
+        "@rollup/plugin-typescript": "^12.1.2",
+        "@types/jquery": "^3.5.32",
+        "@types/lodash.find": "^4.6.9",
+        "@types/lodash.noop": "^3.0.9",
+        "postcss-import": "^16.1.1",
+        "rollup": "^4.28.1",
+        "rollup-plugin-delete": "^2.1.0",
+        "rollup-plugin-dts": "^6.1.1",
+        "rollup-plugin-peer-deps-external": "^2.2.4",
+        "rollup-plugin-postcss": "^4.0.2"
+    },
+    "files": [
+        "dist"
+    ],
+    "publishConfig": {
+        "access": "public"
+    },
+    "exports": {
+        ".": {
+            "default": "./dist/index.js",
+            "types": "./dist/index.d.ts"
+        }
+    },
+    "gitHead": "5962101eb3af53695309d0340fe9b9c8e0bcaef4"
+}