@niagads/igv 0.1.1 → 0.1.2

package/dist/IGVBrowser.js

@@ -1,2 +1,2 @@
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 //# sourceMappingURL=IGVBrowser.js.map

package/dist/IGVBrowser.js.map

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package/dist/config/_constants.js

@@ -1,2 +1,2 @@
-const e=1e3,i=["ideogram","ruler","sequence","ENSEMBL_GENE"],r="/api/feature-lookup?id=$FEATURE$&flank=1000",a={name:"ADSP R4 Variants",url:"/service/track/variant",type:"variant_service",format:"webservice",visibilityWindow:1e5,supportsWholeGenome:!1,queryable:!0,description:"Variants from the Alzheimer''s Disease Sequencing Project (ADSP) 36K R4 whole genome sequencing effort - INDELs and SNVs that passed the ADSP biallelic quality control (QC) criteria. Variants are annotated by the ADSP Annotation Pipeline.",id:"ADSP_R4",order:1,infoURL:"/record",removable:!1};export{i as ALWAYS_ON_TRACKS,e as DEFAULT_FLANK,r as FEATURE_SEARCH_URL,a as VariantReferenceTrack};
+const e=1e3,i=["ideogram","ruler","sequence","ENSEMBL_GENE"],r="https://api.niagads.org",a=`${r}/genomics/legacy`,t=`${r}/genomics/service/igvbrowser/feature?id=$FEATURE$&flank=1000`,n="https://www.niagads.org/genomics/app",o={name:"ADSP R4 Variants",url:`${a}/service/track/variant`,type:"variant_service",format:"webservice",visibilityWindow:1e5,supportsWholeGenome:!1,queryable:!0,description:"Variants from the Alzheimer''s Disease Sequencing Project (ADSP) 36K R4 whole genome sequencing effort - INDELs and SNVs that passed the ADSP biallelic quality control (QC) criteria. Variants are annotated by the ADSP Annotation Pipeline.",id:"ADSP_R4",order:1,infoURL:"/record",removable:!1};export{i as ALWAYS_ON_TRACKS,r as API_ROOT,e as DEFAULT_FLANK,t as FEATURE_SEARCH_URL,n as GENOMICSDB_ROOT,a as LEGACY_API_ROOT,o as VariantReferenceTrack};
 //# sourceMappingURL=_constants.js.map

package/dist/config/_constants.js.map

@@ -1 +1 @@
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+{"version":3,"file":"_constants.js","sources":["../../src/config/_constants.ts"],"sourcesContent":[null],"names":["DEFAULT_FLANK","ALWAYS_ON_TRACKS","API_ROOT","LEGACY_API_ROOT","FEATURE_SEARCH_URL","GENOMICSDB_ROOT","VariantReferenceTrack","name","url","type","format","visibilityWindow","supportsWholeGenome","queryable","description","id","order","infoURL","removable"],"mappings":"AAAO,MAAMA,EAAgB,IAChBC,EAAmB,CAAC,WAAY,QAAS,WAAY,gBAGrDC,EAAW,0BACXC,EAAkB,GAAGD,oBACrBE,EAAqB,GAAGF,gEAExBG,EAAkB,uCAElBC,EAAwB,CACjCC,KAAM,mBACNC,IAAK,GAAGL,0BACRM,KAAM,kBACNC,OAAQ,aACRC,iBAAkB,IAClBC,qBAAqB,EACrBC,WAAW,EACXC,YACI,iPACJC,GAAI,UACJC,MAAO,EACPC,QAAS,UACTC,WAAW"}

package/dist/config/_igvGenomes.js

@@ -1,2 +1,2 @@
-const e=[{id:"GRCh38_refseq",name:"Human (GRCh38/hg38)",fastaURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",indexURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",cytobandURL:"https://s3.amazonaws.com/igv.org.genomes/hg38/annotations/cytoBandIdeo.txt.gz",aliasURL:"https://s3.amazonaws.com/igv.org.genomes/hg38/hg38_alias.tab",tracks:[{name:"Genes (RefSeq)",id:"REFSEQ_GENE",track:"REFSEQ_GENE",description:"Gene models from NCBI Gene (RefSeq)",format:"refgene",url:"https://s3.amazonaws.com/igv.org.genomes/hg38/ncbiRefSeq.sorted.txt.gz",indexURL:"https://s3.amazonaws.com/igv.org.genomes/hg38/ncbiRefSeq.sorted.txt.gz.tbi",visibilityWindow:-1,supportsWholeGenome:!1,removable:!1,order:1e6}],chromosomeOrder:"chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY"},{id:"GRCh38",name:"Human 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150)":o.includes("processed_transcript")?"purple":o.includes("processed_pseudogene")?"#028401":o.includes("unprocessed_pseudogene")?"#888501":o.includes("lncRNA")?"#ff726e":"snRNA"===o?"#ffce6e":"grey"}}],chromosomeOrder:"chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY"},{id:"GRCh37",name:"Human (GRCh37/hg19)",fastaURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta",indexURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta.fai",cytobandURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/cytoBand.txt",aliasURL:"https://s3.amazonaws.com/igv.org.genomes/hg19/hg19_alias.tab",tracks:[{name:"Genes (RefSeq)",id:"REFSEQ_GENE",track:"REFSEQ_GENE",description:"Gene models from NCBI Gene 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(ce11)",fastaURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/ce11/ce11.fa",indexURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/ce11/ce11.fa.fai",cytobandURL:"https://s3.amazonaws.com/igv.org.genomes/ce11/cytoBandIdeo.txt.gz",tracks:[{name:"Refseq Genes",format:"refgene",url:"https://s3.amazonaws.com/igv.org.genomes/ce11/refGene.sorted.txt.gz",indexed:!1,order:1e6,removable:!1,searchable:!0}]},{id:"dm6",name:"D. melanogaster (dm6)",fastaURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/dm6/dm6.fa",indexURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/dm6/dm6.fa.fai",cytobandURL:"https://s3.amazonaws.com/igv.org.genomes/dm6/cytoBandIdeo.txt.gz",tracks:[{name:"Refseq Genes",format:"refgene",url:"https://s3.amazonaws.com/igv.org.genomes/dm6/ncbiRefSeq.txt.gz",indexed:!1,order:1e6,removable:!1,searable:!0}]}];export{e as _genomes};
+import{GENOMICSDB_ROOT as e}from"./_constants.js";const s=[{id:"GRCh38_refseq",name:"Human (GRCh38/hg38)",fastaURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",indexURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",cytobandURL:"https://s3.amazonaws.com/igv.org.genomes/hg38/annotations/cytoBandIdeo.txt.gz",aliasURL:"https://s3.amazonaws.com/igv.org.genomes/hg38/hg38_alias.tab",tracks:[{name:"Genes (RefSeq)",id:"REFSEQ_GENE",track:"REFSEQ_GENE",description:"Gene models from NCBI Gene (RefSeq)",format:"refgene",url:"https://s3.amazonaws.com/igv.org.genomes/hg38/ncbiRefSeq.sorted.txt.gz",indexURL:"https://s3.amazonaws.com/igv.org.genomes/hg38/ncbiRefSeq.sorted.txt.gz.tbi",visibilityWindow:-1,supportsWholeGenome:!1,removable:!1,order:1e6}],chromosomeOrder:"chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY"},{id:"GRCh38",name:"Human (GRCh38/hg38)",fastaURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa",indexURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg38/hg38.fa.fai",cytobandURL:"https://s3.amazonaws.com/igv.org.genomes/hg38/annotations/cytoBandIdeo.txt.gz",aliasURL:"https://s3.amazonaws.com/igv.org.genomes/hg38/hg38_alias.tab",tracks:[{name:"Genes",id:"ENSEMBL_GENE",description:"Gene models from ENSEMBL",format:"gff3",filterTypes:["chromosome"],url:"https://wanglab-genomicsdb.s3.us-east-1.amazonaws.com/public/website-data/GRCh38/tracks/gene/hs.GRCh38.108.gff3.gz",indexURL:"https://wanglab-genomicsdb.s3.us-east-1.amazonaws.com/public/website-data/GRCh38/tracks/gene/hs.GRCh38.108.gff3.gz.tbi",visibilityWindow:-1,supportsWholeGenome:!1,removable:!1,order:1e6,colorBy:"biotype",infoURL:`${e}/record/gene/$$`,color:e=>{const s=e.geneObject?e.geneObject.getAttributeValue("biotype"):e.getAttributeValue("biotype");return void 0===s?"grey":s.includes("antisense")?"#891100":s.includes("protein_coding")?"#000096":s.includes("retained_intron")?"rgb(0, 150, 150)":s.includes("processed_transcript")?"purple":s.includes("processed_pseudogene")?"#028401":s.includes("unprocessed_pseudogene")?"#888501":s.includes("lncRNA")?"#ff726e":"snRNA"===s?"#ffce6e":"grey"}}],chromosomeOrder:"chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY"},{id:"GRCh37",name:"Human (GRCh37/hg19)",fastaURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta",indexURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/hg19.fasta.fai",cytobandURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/hg19/cytoBand.txt",aliasURL:"https://s3.amazonaws.com/igv.org.genomes/hg19/hg19_alias.tab",tracks:[{name:"Genes (RefSeq)",id:"REFSEQ_GENE",track:"REFSEQ_GENE",description:"Gene models from NCBI Gene (RefSeq)",format:"refgene",url:"https://s3.amazonaws.com/igv.org.genomes/hg19/ncbiRefSeq.sorted.txt.gz",indexURL:"https://s3.amazonaws.com/igv.org.genomes/hg19/ncbiRefSeq.sorted.txt.gz.tbi",visibilityWindow:-1,supportsWholeGenome:!1,removable:!1,order:1e6,infoURL:"https://www.ncbi.nlm.nih.gov/gene/?term=$$"}],chromosomeOrder:"chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22, chrX, chrY"},{id:"mm10",name:"Mouse (GRCm38/mm10)",fastaURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/mm10/mm10.fa",indexURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/mm10/mm10.fa.fai",cytobandURL:"https://s3.amazonaws.com/igv.broadinstitute.org/annotations/mm10/cytoBandIdeo.txt.gz",order:1e6,tracks:[{name:"Refseq 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(ce11)",fastaURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/ce11/ce11.fa",indexURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/ce11/ce11.fa.fai",cytobandURL:"https://s3.amazonaws.com/igv.org.genomes/ce11/cytoBandIdeo.txt.gz",tracks:[{name:"Refseq Genes",format:"refgene",url:"https://s3.amazonaws.com/igv.org.genomes/ce11/refGene.sorted.txt.gz",indexed:!1,order:1e6,removable:!1,searchable:!0}]},{id:"dm6",name:"D. melanogaster (dm6)",fastaURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/dm6/dm6.fa",indexURL:"https://s3.amazonaws.com/igv.broadinstitute.org/genomes/seq/dm6/dm6.fa.fai",cytobandURL:"https://s3.amazonaws.com/igv.org.genomes/dm6/cytoBandIdeo.txt.gz",tracks:[{name:"Refseq Genes",format:"refgene",url:"https://s3.amazonaws.com/igv.org.genomes/dm6/ncbiRefSeq.txt.gz",indexed:!1,order:1e6,removable:!1,searable:!0}]}];export{s as _genomes};
 //# sourceMappingURL=_igvGenomes.js.map

package/dist/config/_igvGenomes.js.map

@@ -1 +1 @@
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package/dist/utils/browser.js

@@ -1,2 +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};
+import{__awaiter as i,__asyncValues as r}from"tslib";import{GENOMICSDB_ROOT as o,ALWAYS_ON_TRACKS as e}from"../config/_constants.js";import{getViewTrackIdentifier as n}from"./views.js";import{resolveServiceTrackReader as t}from"./track_config.js";const d=(i,r=e)=>{var o;return(null!==(o=null==i?void 0:i.trackViews)&&void 0!==o?o:[]).map(i=>n(i)).filter(i=>!r.includes(i))},c=(i,r)=>{var o;const e=(null!==(o=null==i?void 0:i.trackViews)&&void 0!==o?o:[]).filter(i=>n(i)===r);i.removeTrack(e[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)),e.infoURL&&"/record"===e.infoURL&&(e.infoURL=`${o}/record`),yield r.loadTrack(e)}),a=(o,e)=>i(void 0,void 0,void 0,function*(){var i,n,t;try{for(var d,c=!0,a=r(e.map(i=>l(o,i)));!(i=(d=yield a.next()).done);c=!0){d.value,c=!1}}catch(i){n={error:i}}finally{try{c||i||!(t=a.return)||(yield t.call(a))}finally{if(n)throw n.error}}});function f(r,o,e){return i(this,void 0,void 0,function*(){const i=o.filter(i=>!e.includes(i.id));return i.length>0?(yield a(r,i),i.map(i=>i.id)):[]})}function s(r,o,e){return i(this,void 0,void 0,function*(){const i=e.filter(i=>!o.some(r=>r.id===i));for(const o of i)c(r,o);return i})}function u(r,o){return i(this,void 0,void 0,function*(){const i=d(r,r.config.alwaysOnTracks);yield f(r,o,i),yield s(r,o,i)})}export{d as getLoadedTracks,f as handleAddTracksToBrowser,s as handleRemoveTracksFromBrowser,u as handleUpdateBrowserTracks,l as loadTrack,a as loadTracks,c as removeTrackById};
 //# sourceMappingURL=browser.js.map

package/dist/utils/browser.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
     "name": "@niagads/igv",
-    "version": "0.1.1",
+    "version": "0.1.2",
     "description": "NIAGADS IGV Browser Component",
     "repository": {
         "type": "git",
@@ -11,9 +11,9 @@
         "build": "rollup -c"
     },
     "dependencies": {
-        "@niagads/common": "^0.1.1",
-        "@niagads/table": "^0.1.1",
-        "@niagads/ui": "^0.1.1",
+        "@niagads/common": "^0.1.2",
+        "@niagads/table": "^0.1.2",
+        "@niagads/ui": "^0.1.2",
         "igv": "github:NIAGADS/igv.js#NIAGADS-01102025",
         "jquery": "^3.7.1",
         "tslib": "^2"
@@ -45,5 +45,5 @@
             "types": "./dist/index.d.ts"
         }
     },
-    "gitHead": "63f41fcc1d7c86715a1d03f6f3ca606e8573a461"
+    "gitHead": "441719054629d0a9dba672e3d77adf2b579c8020"
 }

package/dist/TrackSelectorTable.js

@@ -1,2 +0,0 @@
-import{__awaiter as t}from"tslib";import e,{useState as i,useEffect as o}from"react";import n from"@niagads/table";import{loadTracks as r,getTrackConfig as l,removeTrackById as s}from"./tracks/utils.js";function a(e,i,o){return t(this,void 0,void 0,function*(){if("add"===i){let t=[];e.forEach(e=>{o.data.filter(t=>t.row_id===e).length>0?o.toggleRowSelected(e,!0):t.push(e)}),t.length>0&&alert(`Invalid track identifier(s): ${t.toString()} specified in URL string or session file.\nNOTE: track identifiers are CASE SENSITIVE.`)}else e.forEach(t=>{o.toggleRowSelected(t,!1)})})}function c(e,i,o,n){return t(this,void 0,void 0,function*(){const t=[],s=e.filter(t=>!i.includes(t));return s.length>0&&(yield r(l(s,o),n),t.push(...s)),t})}function d(e,i,o,n){return t(this,void 0,void 0,function*(){const t=[];return i.filter(t=>!e.includes(t)).forEach(e=>{o.filter(t=>t.id===e).forEach(e=>{s(e.id,n),t.push(e.id)})}),t})}const f=({table:t,handleRowSelect:r,onTableLoad:l})=>{const[s,a]=i({}),[c,d]=i(!0);return t.options||(t.options={}),Object.assign(t.options,{onTableLoad:l,rowSelect:{onRowSelect:t=>{a(t)},enableMultiRowSelect:!0,rowId:"id"}}),o(()=>{0===Object.keys(s).length?d(!0):(d(!1),r(Object.keys(s)))},[s]),e.createElement("main",null,e.createElement(n,{id:t.id,data:t.data,columns:t.columns,options:t.options}))};export{f as default,c as handleLoadTracks,d as handleUnloadTracks,a as toggleTrackSelection};
-//# sourceMappingURL=TrackSelectorTable.js.map

package/dist/TrackSelectorTable.js.map

@@ -1 +0,0 @@
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package/dist/tracks/utils.js

@@ -1,2 +0,0 @@
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-//# sourceMappingURL=utils.js.map

package/dist/tracks/utils.js.map

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package/dist/utils/selector_actions.js

@@ -1,2 +0,0 @@
-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

@@ -1 +0,0 @@
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