@jbrowse/plugin-variants 1.6.4 → 1.6.7

package/dist/plugin-variants.cjs.production.min.js

@@ -1,2 +1,2 @@
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r=this;if(!t||t===[])return["remark","no alternative alleles"];var n=new Set,a=new Set;if(t.forEach((function(t){var i=J(r._getSOAndDescFromAltDefs(e,t),2),o=i[0],c=i[1];if(!o){var u=J(r._getSOAndDescByExamination(e,t),2);o=u[0],c=u[1]}o&&c&&(n.add(o),a.add(c))})),a.size>1){var i=new Set(Y(a).map((function(e){var t=e.split("->");return t[1]?t[0]:e}))),o=Y(i).map((function(e){var t=Y(a).map((function(t){var r=t.split("-> ");return r[1]&&r[0]===e?r[1]:""})).filter((function(e){return!!e}));return t.length?e+"-> "+t.join(","):Y(a).join(",")}));a=new Set(o)}return n.size?[Y(n).join(","),Y(a).join(",")]:[void 0,void 0]}},{key:"_getSOAndDescFromAltDefs",value:function(t,r){if("string"==typeof r&&!r.startsWith("<"))return[void 0,void 0];var n=e._altTypeToSO[r];if(!n&&this.parser.getMetadata("ALT",r)&&(n="sequence_variant"),n)return[n,r];var a=r.split(":");return a.length>1?this._getSOAndDescFromAltDefs(t,"<".concat(a.slice(0,a.length-1).join(":"),">")):[void 0,void 0]}},{key:"_getSOAndDescByExamination",value:function(e,t){return m.parseBreakend(t)?["breakend",t]:1===e.length&&1===t.length?["SNV",this._makeDescriptionString("SNV",e,t)]:"<INS>"===t?["insertion",t]:"<DEL>"===t||"<INV>"===t?["deletion",t]:"<TRA>"===t?["translocation",t]:t.includes("<")?["sv",t]:e.length===t.length?e.split("").reverse().join("")===t?["inversion",this._makeDescriptionString("inversion",e,t)]:["substitution",this._makeDescriptionString("substitution",e,t)]:e.length<=t.length?["insertion",this._makeDescriptionString("insertion",e,t)]:e.length>t.length?["deletion",this._makeDescriptionString("deletion",e,t)]:["indel",this._makeDescriptionString("indel",e,t)]}},{key:"_makeDescriptionString",value:function(e,t,r){return"".concat(e," ").concat(t," -> ").concat(r)}},{key:"toJSON",value:function(){return _(_(_({uniqueId:this._id},this.variant),this.data),{},{samples:this.variant.SAMPLES})}}]),e}();fe._altTypeToSO={DEL:"deletion",INS:"insertion",DUP:"duplication",INV:"inversion",INVDUP:"inverted duplication",CNV:"copy_number_variation",TRA:"translocation","DUP:TANDEM":"tandem_duplication",NON_REF:"sequence_variant","*":"sequence_variant"};var pe=function(e){B(f,s);var r=W(f);function f(){var e;return A(this,f),(e=r.apply(this,arguments)).name="VariantsPlugin",e}return I(f,[{key:"install",value:function(e){e.addAdapterType((function(){return new a({name:"VcfTabixAdapter",configSchema:se,getAdapterClass:function(){return Promise.resolve().then((function(){return de})).then((function(e){return e.default}))}})})),e.addToExtensionPoint("Core-guessAdapterForLocation",(function(e){return function(t,r,n){var a=p.getFileName(t),i=r&&p.getFileName(r),o={type:"VcfTabixAdapter",vcfGzLocation:t,index:{location:r||p.makeIndex(t,".tbi"),indexType:p.makeIndexType(i,"CSI","TBI")}};return/\.vcf\.b?gz$/i.test(a)&&!n||"VcfTabixAdapter"===n?o:e(t,r,n)}})),e.addToExtensionPoint("Core-guessTrackTypeForLocation",(function(e){return function(t){return"VcfTabixAdapter"===t?"VariantTrack":e(t)}})),e.addAdapterType((function(){return new a({name:"VcfAdapter",configSchema:le,getAdapterClass:function(){return Promise.resolve().then((function(){return ge})).then((function(e){return e.default}))}})})),e.addToExtensionPoint("Core-guessAdapterForLocation",(function(e){return function(t,r,n){var a=p.getFileName(t);return/\.vcf$/i.test(a)||"VcfAdapter"===n?{type:"VcfAdapter",vcfLocation:t}:e(t,r,n)}})),e.addRendererType((function(){return e.jbrequire(oe)})),e.addTrackType((function(){var t=n.ConfigurationSchema("VariantTrack",{},{baseConfiguration:o.createBaseTrackConfig(e)});return new c({name:"VariantTrack",configSchema:t,stateModel:o.createBaseTrackModel(e,"VariantTrack",t)})})),e.addDisplayType((function(){return e.jbrequire(X)})),e.addDisplayType((function(){var t=function(e){var t=l.linearBasicDisplayConfigSchemaFactory(e);return n.ConfigurationSchema("LinearVariantDisplay",{},{baseConfiguration:t,explicitlyTyped:!0})}(e);return new i({name:"LinearVariantDisplay",configSchema:t,stateModel:te(t),trackType:"VariantTrack",viewType:"LinearGenomeView",ReactComponent:l.BaseLinearDisplayComponent})})),e.addWidgetType((function(){return new u({name:"VariantFeatureWidget",heading:"Feature details",configSchema:ce,stateModel:ue(e),ReactComponent:t.lazy((function(){return Promise.resolve().then((function(){return Oe}))}))})}))}}]),f}(),de={__proto__:null,default:function(e){B(u,k.BaseFeatureDataAdapter);var t,r,a,i,o,c=W(u);function u(){return A(this,u),c.apply(this,arguments)}return I(u,[{key:"configurePre",value:(o=N(ee.mark((function e(){var t,r,a,i,o,c;return ee.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return t=n.readConfObject(this.config,"vcfGzLocation"),r=n.readConfObject(this.config,["index","location"]),a=n.readConfObject(this.config,["index","indexType"]),i=x.openLocation(t,this.pluginManager),c=new C.TabixIndexedFile({filehandle:i,csiFilehandle:(o="CSI"===a)?x.openLocation(r,this.pluginManager):void 0,tbiFilehandle:o?void 0:x.openLocation(r,this.pluginManager),chunkCacheSize:50*Math.pow(2,20),chunkSizeLimit:1e9}),e.next=8,c.getHeader();case 8:return e.abrupt("return",{filehandle:i,vcf:c,parser:new b({header:e.sent})});case 10:case"end":return e.stop()}}),e,this)}))),function(){return o.apply(this,arguments)})},{key:"configure",value:(i=N(ee.mark((function e(){var t=this;return ee.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return this.configured||(this.configured=this.configurePre().catch((function(e){throw t.configured=void 0,e}))),e.abrupt("return",this.configured);case 2:case"end":return 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e.stop()}}),e,this)}))),function(){return t.apply(this,arguments)})},{key:"getFeatures",value:function(e){var t=this,r=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{};return T.ObservableCreate(function(){var n=N(ee.mark((function n(a){var i,o,c,u,s,l;return ee.wrap((function(n){for(;;)switch(n.prev=n.next){case 0:return i=e.refName,o=e.start,c=e.end,n.next=3,t.configure();case 3:return s=(u=n.sent).vcf,l=u.parser,n.next=8,s.getLines(i,o,c,_({lineCallback:function(e,r){a.next(new fe({variant:l.parseLine(e),parser:l,id:"".concat(t.id,"-vcf-").concat(r)}))}},r));case 8:a.complete();case 9:case"end":return n.stop()}}),n)})));return function(e){return n.apply(this,arguments)}}(),r.signal)}},{key:"getFeaturesInMultipleRegions",value:function(e){var t=this,r=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{},n=U(z(u.prototype),"getFeaturesInMultipleRegions",this);return T.ObservableCreate(function(){var a=N(ee.mark((function a(i){var o,c,u,s;return ee.wrap((function(a){for(;;)switch(a.prev=a.next){case 0:return a.next=2,t.configure();case 2:return o=a.sent.vcf,a.next=6,d.bytesForRegions(e,o.index);case 6:return c=a.sent,a.next=9,t.configure();case 9:return u=a.sent.filehandle,a.next=13,u.stat();case 13:(s=Math.round(c/a.sent.size*100))>100&&(s=100),s>60&&console.warn("getFeaturesInMultipleRegions fetching ".concat(s,"% of VCF file, but whole-file streaming not yet implemented")),n.call(t,e,r).subscribe(i);case 18:case"end":return a.stop()}}),a)})));return function(e){return a.apply(this,arguments)}}())}},{key:"freeResources",value:function(){}}]),u}()},he=function(e){var t=e.split("\n"),r=[],n=[];return t.forEach((function(e){e.startsWith("#")?r.push(e):e&&n.push(e)})),{header:r.join("\n"),lines:n}};function ve(e){return 31===e[0]&&139===e[1]&&8===e[2]}var ye=function(e){B(u,k.BaseFeatureDataAdapter);var t,r,a,i,o,c=W(u);function u(){return A(this,u),c.apply(this,arguments)}return I(u,[{key:"getHeader",value:(o=N(ee.mark((function e(){return ee.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.setup();case 2:return e.abrupt("return",e.sent.header);case 5:case"end":return e.stop()}}),e,this)}))),function(){return o.apply(this,arguments)})},{key:"getMetadata",value:(i=N(ee.mark((function e(){var t;return ee.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.setup();case 2:return t=new b({header:e.sent.header}),e.abrupt("return",t.getMetadata());case 6:case"end":return e.stop()}}),e,this)}))),function(){return i.apply(this,arguments)})},{key:"setupP",value:(a=N(ee.mark((function e(){var t,r,a,i,o,c;return ee.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,x.openLocation(n.readConfObject(this.config,"vcfLocation"),this.pluginManager).readFile();case 2:if(!ve(t=e.sent)){e.next=9;break}return e.next=6,S.unzip(t);case 6:e.t0=e.sent,e.next=10;break;case 9:e.t0=t;case 10:if(!((r=e.t0).length>536870888)){e.next=13;break}throw new Error("Data exceeds maximum string length (512MB)");case 13:return a=(new TextDecoder).decode(r),i=he(a),o=i.header,c=i.lines.map((function(e,t){var r,n=J(e.split("\t"),8),a=n[3],i=+n[1]-1;return{line:e,refName:n[0],start:i,end:+((null===(r=n[7].match(/END=(\d+)/))||void 0===r?void 0:r[1].trim())||i+a.length),id:t}})).reduce((function(e,t){var r=t.refName;return e[r]||(e[r]=new O),e[r].insert([t.start,t.end],t),e}),{}),e.abrupt("return",{header:o,intervalTree:c});case 17:case"end":return e.stop()}}),e,this)}))),function(){return a.apply(this,arguments)})},{key:"setup",value:(r=N(ee.mark((function e(){var t=this;return ee.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return this.vcfFeatures||(this.vcfFeatures=this.setupP().catch((function(e){throw t.vcfFeatures=void 0,e}))),e.abrupt("return",this.vcfFeatures);case 2:case"end":return e.stop()}}),e,this)}))),function(){return r.apply(this,arguments)})},{key:"getRefNames",value:(t=N(ee.mark((function e(){return ee.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=3,this.setup();case 3:return e.abrupt("return",Object.keys(e.sent.intervalTree));case 6:case"end":return e.stop()}}),e,this)}))),function(){return t.apply(this,arguments)})},{key:"getFeatures",value:function(e){var t=this,r=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{};return T.ObservableCreate(function(){var r=N(ee.mark((function r(n){var a,i,o,c,u,s,l;return ee.wrap((function(r){for(;;)switch(r.prev=r.next){case 0:return r.prev=0,i=e.start,o=e.end,c=e.refName,r.next=4,t.setup();case 4:s=(u=r.sent).intervalTree,l=new b({header:u.header}),null===(a=s[c])||void 0===a||a.search([i,o]).forEach((function(e){return n.next(new fe({variant:l.parseLine(e.line),parser:l,id:"".concat(t.id,"-").concat(e.id)}))})),n.complete(),r.next=15;break;case 12:r.prev=12,r.t0=r.catch(0),n.error(r.t0);case 15:case"end":return r.stop()}}),r,null,[[0,12]])})));return function(e){return r.apply(this,arguments)}}(),r.signal)}},{key:"freeResources",value:function(){}}]),u}();ye.capabilities=["getFeatures","getRefNames"];var ge={__proto__:null,default:ye},me=L.makeStyles((function(e){return{closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]},block:{display:"block"}}}));function be(e){var n=e.model,a=e.handleClose,i=e.feature,o=e.viewType,c=me(),u=J(t.useState(!0),2),s=u[0],l=u[1],f=J(t.useState(!0),2),p=f[0],v=f[1];return r.createElement(E.Dialog,{open:!0,onClose:a},r.createElement(E.DialogTitle,null,"Breakpoint split view options",a?r.createElement(E.IconButton,{className:c.closeButton,onClick:function(){a()}},r.createElement(P,null)):null),r.createElement(E.Divider,null),r.createElement(E.DialogContent,null,r.createElement(E.FormControlLabel,{className:c.block,control:r.createElement(E.Checkbox,{checked:s,onChange:function(){return l((function(e){return!e}))}}),label:"Copy tracks into the new view"}),r.createElement(E.FormControlLabel,{className:c.block,control:r.createElement(E.Checkbox,{checked:p,onChange:function(){return v((function(e){return!e}))}}),label:"Mirror tracks vertically in vertically stacked view"})),r.createElement(E.DialogActions,null,r.createElement(E.Button,{onClick:function(){var e=n.view,t=d.getSession(n),r=o.snapshotFromBreakendFeature(i,e);r.views[0].offsetPx-=e.width/2+100,r.views[1].offsetPx-=e.width/2+100,r.featureData=i;var c=h.getSnapshot(e.tracks);r.views[0].tracks=c,r.views[1].tracks=p?c.slice().reverse():c,t.addView("BreakpointSplitView",r),a()},variant:"contained",color:"primary",autoFocus:!0},"OK"),r.createElement(E.Button,{onClick:function(){a()},color:"secondary",variant:"contained",autoFocus:!0},"Cancel")))}var we=y.observer(be),ke=["samples"];function xe(e){var n=J(t.useState({}),2),a=n[0],i=n[1],o=J(t.useState(!1),2),c=o[0],u=o[1],s=e.feature.samples,l=Object.entries(void 0===s?{}:s);if(!l.length)return null;var f,p=["sample"].concat(Y(Object.keys(l[0][1]))).map((function(e){return{field:e}})),d=[],h=Object.keys(a);try{d=l.map((function(e){return _(_({},Object.fromEntries(Object.entries(e[1]).map((function(e){return[e[0],String(e[1])]})))),{},{sample:e[0],id:e[0]})})).filter((function(e){return!h.length||h.every((function(t){var r=a[t];return!r||e[t].match(new RegExp(r,"i"))}))}))}catch(e){f=e}return r.createElement(F.BaseCard,Object.assign({},e,{title:"Samples"}),f?r.createElement(E.Typography,{color:"error"},"".concat(f)):null,r.createElement(E.FormControlLabel,{control:r.createElement(E.Checkbox,{checked:c,onChange:function(){return u((function(e){return!e}))}}),label:"Show sample filters"}),c?r.createElement(r.Fragment,null,r.createElement(E.Typography,null,"These filters can use a plain text search or regex style query, e.g. in the genotype field, entering 1 will query for all genotypes that include the first alternate allele e.g. 0|1 or 1|1, entering [1-9]\\d* will find any non-zero allele e.g. 0|2 or 2/33"),p.map((function(e){var t=e.field;return r.createElement(E.TextField,{key:"filter-".concat(t),placeholder:"Filter ".concat(t),value:a[t]||"",onChange:function(e){return i(_(_({},a),{},q({},t,e.target.value)))}})}))):null,r.createElement("div",{style:{height:600,width:"100%",overflow:"auto"}},r.createElement(D.DataGrid,{rows:d,columns:p,rowHeight:20,headerHeight:25,disableSelectionOnClick:!0,disableColumnMenu:!0})))}function Te(e){var n,a=e.model,i=e.locStrings,o=e.feature,c=d.getSession(a),u=h.getEnv(c).pluginManager,s=J(t.useState(!1),2),l=s[0],f=s[1];try{n=u.getViewType("BreakpointSplitView")}catch(e){}var p=new j(o);return r.createElement(F.BaseCard,Object.assign({},e,{title:"Breakends"}),r.createElement(E.Typography,null,"Link to linear view of breakend endpoints"),r.createElement("ul",null,i.map((function(e){return r.createElement("li",{key:"".concat(JSON.stringify(e))},r.createElement(E.Link,{href:"#",onClick:function(t){t.preventDefault();var r,n=a.view;n?null===(r=n.navToLocString)||void 0===r||r.call(n,e):c.notify("No view associated with this feature detail panel anymore","warning")}},"LGV - ".concat(e)))}))),n?r.createElement("div",null,r.createElement(E.Typography,null,"Launch split views with breakend source and target"),r.createElement("ul",null,i.map((function(e){return r.createElement("li",{key:"".concat(JSON.stringify(e))},r.createElement(E.Link,{href:"#",onClick:function(e){e.preventDefault(),f(!0)}},"".concat(o.refName,":").concat(o.start," // ").concat(e," (split view)")))}))),l?r.createElement(we,{model:a,feature:p,viewType:n,handleClose:function(){f(!1)}}):null):null)}function Ce(e){var t=e.model,n=t.descriptions,a=JSON.parse(JSON.stringify(t.featureData)),i=function(e,t){if(null==e)return{};var r,n,a=function(e,t){if(null==e)return{};var r,n,a={},i=Object.keys(e);for(n=0;n<i.length;n++)t.indexOf(r=i[n])>=0||(a[r]=e[r]);return a}(e,t);if(Object.getOwnPropertySymbols){var i=Object.getOwnPropertySymbols(e);for(n=0;n<i.length;n++)t.indexOf(r=i[n])>=0||Object.prototype.propertyIsEnumerable.call(e,r)&&(a[r]=e[r])}return a}(a,ke);return r.createElement(E.Paper,{"data-testid":"variant-side-drawer"},r.createElement(F.FeatureDetails,Object.assign({feature:i,descriptions:_(_({},{CHROM:"chromosome: An identifier from the reference genome",POS:"position: The reference position, with the 1st base having position 1",ID:"identifier: Semi-colon separated list of unique identifiers where available",REF:"reference base(s): Each base must be one of A,C,G,T,N (case insensitive).",ALT:"alternate base(s): Comma-separated list of alternate non-reference alleles",QUAL:"quality: Phred-scaled quality score for the assertion made in ALT",FILTER:"filter status: PASS if this position has passed all filters, otherwise a semicolon-separated list of codes for filters that fail"}),n)},e)),r.createElement(E.Divider,null),"breakend"===a.type?r.createElement(Te,{feature:a,locStrings:a.ALT.map((function(e){var t;return(null===(t=m.parseBreakend(e))||void 0===t?void 0:t.MatePosition)||""})),model:t}):null,"translocation"===a.type?r.createElement(Te,{feature:a,model:t,locStrings:["".concat(a.INFO.CHR2[0],":").concat(a.INFO.END)]}):null,r.createElement(xe,Object.assign({feature:a},e)))}var Oe={__proto__:null,default:y.observer(Ce)};exports.VcfFeature=fe,exports.default=pe;
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Z.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=3,this.setup();case 3:return e.abrupt("return",Object.keys(e.sent.intervalTree));case 6:case"end":return e.stop()}}),e,this)}))),function(){return t.apply(this,arguments)})},{key:"getFeatures",value:function(e){var t=this,r=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{};return T.ObservableCreate(function(){var r=V(Z.mark((function r(n){var a,i,o,c,u,s,l;return Z.wrap((function(r){for(;;)switch(r.prev=r.next){case 0:return r.prev=0,i=e.start,o=e.end,c=e.refName,r.next=4,t.setup();case 4:s=(u=r.sent).intervalTree,l=new b({header:u.header}),null===(a=s[c])||void 0===a||a.search([i,o]).forEach((function(e){return n.next(new le({variant:l.parseLine(e.line),parser:l,id:"".concat(t.id,"-").concat(e.id)}))})),n.complete(),r.next=15;break;case 12:r.prev=12,r.t0=r.catch(0),n.error(r.t0);case 15:case"end":return r.stop()}}),r,null,[[0,12]])})));return function(e){return r.apply(this,arguments)}}(),r.signal)}},{key:"freeResources",value:function(){}}]),u}();ve.capabilities=["getFeatures","getRefNames"];var ye={__proto__:null,default:ve},ge=E.makeStyles((function(e){return{closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]},block:{display:"block"}}}));function me(e){var n=e.model,a=e.handleClose,i=e.feature,o=e.viewType,c=ge(),u=U(t.useState(!0),2),s=u[0],l=u[1],f=U(t.useState(!0),2),p=f[0],v=f[1];return r.createElement(E.Dialog,{open:!0,onClose:a},r.createElement(E.DialogTitle,null,"Breakpoint split view options",a?r.createElement(E.IconButton,{className:c.closeButton,onClick:function(){return a()}},r.createElement(F,null)):null),r.createElement(E.Divider,null),r.createElement(E.DialogContent,null,r.createElement(E.FormControlLabel,{className:c.block,control:r.createElement(E.Checkbox,{checked:s,onChange:function(){return l((function(e){return!e}))}}),label:"Copy tracks into the new 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r.createElement("li",{key:"".concat(JSON.stringify(e))},r.createElement(E.Link,{href:"#",onClick:function(t){t.preventDefault();var r=a.view;try{if(!r)throw new Error("No view associated with this feature detail panel anymore");var n;null===(n=r.navToLocString)||void 0===n||n.call(r,e)}catch(e){console.error(e),c.notify("".concat(e))}}},"LGV - ".concat(e)))}))),n?r.createElement("div",null,r.createElement(E.Typography,null,"Launch split views with breakend source and target"),r.createElement("ul",null,i.map((function(e){return r.createElement("li",{key:"".concat(JSON.stringify(e))},r.createElement(E.Link,{href:"#",onClick:function(e){e.preventDefault(),f(!0)}},"".concat(o.refName,":").concat(o.start," // ").concat(e," (split view)")))}))),l?r.createElement(be,{model:a,feature:p,viewType:n,handleClose:function(){f(!1)}}):null):null)}function Te(e){var t=e.model,n=t.descriptions,a=JSON.parse(JSON.stringify(t.featureData)),i=function(e,t){if(null==e)return{};var 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