@jbrowse/plugin-alignments 1.4.1 → 1.5.2

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

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d.types.compose("LinearAlignmentsDisplay",i.BaseDisplay,d.types.model({PileupDisplay:d.types.maybe(e.getDisplayType("LinearPileupDisplay").stateModel),SNPCoverageDisplay:d.types.maybe(e.getDisplayType("LinearSNPCoverageDisplay").stateModel),snpCovHeight:45,type:d.types.literal("LinearAlignmentsDisplay"),configuration:n.ConfigurationReference(t),height:250,showCoverage:!0,showPileup:!0})).volatile((function(){return{scrollTop:0}})).actions((function(e){return{toggleCoverage:function(){e.showCoverage=!e.showCoverage},togglePileup:function(){e.showPileup=!e.showPileup},setScrollTop:function(t){e.scrollTop=t},setSNPCoverageHeight:function(t){e.snpCovHeight=t}}})).views((function(e){var t=e.trackMenuItems;return{get pileupDisplayConfig(){var t=n.getConf(e,"pileupDisplay"),r=g.getContainingTrack(e);return J(J({},t),{},{type:"LinearPileupDisplay",name:"".concat(n.getConf(r,"name")," pileup"),displayId:"".concat(e.configuration.displayId,"_pileup_xyz")})},getFeatureByID:function(t,r){return e.PileupDisplay.getFeatureByID(t,r)},searchFeatureByID:function(t){return e.PileupDisplay.searchFeatureByID(t)},get features(){return e.PileupDisplay.features},get DisplayBlurb(){var t;return null===(t=e.PileupDisplay)||void 0===t?void 0:t.DisplayBlurb},get sortedBy(){return e.PileupDisplay.sortedBy},get sortedByPosition(){return e.PileupDisplay.sortedByPosition},get sortedByRefName(){return e.PileupDisplay.sortedByRefName},get snpCoverageDisplayConfig(){var t=n.getConf(e,"snpCoverageDisplay"),r=g.getContainingTrack(e);return J(J({},t),{},{type:"LinearSNPCoverageDisplay",name:"".concat(n.getConf(r,"name")," snp coverage"),displayId:"".concat(e.configuration.displayId,"_snpcoverage_xyz")})},trackMenuItems:function(){return[].concat(ie(t()),[{type:"subMenu",label:"Pileup settings",subMenu:e.PileupDisplay.trackMenuItems()},{type:"subMenu",label:"SNPCoverage 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this.setHeight(e.height+t)-r}}})).actions((function(e){return{afterAttach:function(){d.addDisposer(e,m.autorun((function(){e.SNPCoverageDisplay?h(e.snpCoverageDisplayConfig,d.getSnapshot(e.SNPCoverageDisplay.configuration))||(e.SNPCoverageDisplay.setHeight(e.snpCovHeight),e.SNPCoverageDisplay.setConfig(e.snpCoverageDisplayConfig)):e.setSNPCoverageDisplay(e.snpCoverageDisplayConfig),e.PileupDisplay?h(e.pileupDisplayConfig,d.getSnapshot(e.PileupDisplay.configuration))||e.PileupDisplay.setConfig(e.pileupDisplayConfig):e.setPileupDisplay(e.pileupDisplayConfig),e.PileupDisplay.filterBy&&!h(d.getSnapshot(e.PileupDisplay.filterBy),d.getSnapshot(e.SNPCoverageDisplay.filterBy))&&e.SNPCoverageDisplay.setFilterBy(d.getSnapshot(e.PileupDisplay.filterBy)),e.PileupDisplay.colorBy&&!h(d.getSnapshot(e.PileupDisplay.colorBy),e.SNPCoverageDisplay.colorBy?d.getSnapshot(e.SNPCoverageDisplay.colorBy):{})&&e.SNPCoverageDisplay.setColorBy(d.getSnapshot(e.PileupDisplay.colorBy))}))),d.addDisposer(e,m.autorun((function(){e.setSNPCoverageHeight(e.SNPCoverageDisplay.height)})))},renderSvg:function(t){return Q(ve.mark((function n(){var a;return ve.wrap((function(n){for(;;)switch(n.prev=n.next){case 0:return a=e.height-e.SNPCoverageDisplay.height,n.next=3,m.when((function(){return e.PileupDisplay.ready}));case 3:return n.t0=r,n.t1=r.Fragment,n.t2=r,n.next=8,e.SNPCoverageDisplay.renderSvg(t);case 8:return n.t3=n.sent,n.t4=n.t2.createElement.call(n.t2,"g",null,n.t3),n.t5=r,n.t6={transform:"translate(0 ".concat(e.SNPCoverageDisplay.height,")")},n.next=14,e.PileupDisplay.renderSvg(J(J({},t),{},{overrideHeight:a}));case 14:return n.t7=n.sent,n.t8=n.t5.createElement.call(n.t5,"g",n.t6,n.t7),n.abrupt("return",n.t0.createElement.call(n.t0,n.t1,null,n.t4,n.t8));case 17:case"end":return n.stop()}}),n)})))()}}}))};function De(e){var t=e.model,a=t.PileupDisplay,o=t.SNPCoverageDisplay,i=t.showPileup,l=t.showCoverage;return r.createElement("div",{"data-testid":"display-".concat(n.getConf(t,"displayId")),style:{position:"relative"}},r.createElement("div",{"data-testid":"Blockset-snpcoverage"},l?r.createElement(o.RenderingComponent,{model:o}):null),r.createElement(v.ResizeHandle,{onDrag:function(e){return o?(o.setHeight(o.height+e),e):0},style:{position:"absolute",top:l?o.height+2:0,height:3}}),r.createElement("div",{"data-testid":"Blockset-pileup",style:{position:"absolute",top:l?o.height+5:0,height:3}},i?r.createElement(a.RenderingComponent,{model:a}):null))}var Ae=y.observer(De);function Ie(e){var t=e.model,n=t.sortedBy;return n?r.createElement("div",{"data-testid":"blurb-".concat(t.sortedBy),style:{backgroundColor:"white"}},r.createElement(T,{color:"secondary",variant:"caption"},t.sortedBy?"Sorted by ".concat(n.type.toLowerCase()," at ").concat(n.refName,":").concat(n.pos):null)):null}var Le=y.observer(Ie);function qe(e,t,r,n){return Fe.apply(this,arguments)}function Fe(){return(Fe=Q(ve.mark((function e(t,r,n,a){var o,i,l,s;return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return o=g.getSession(t),i=o.rpcManager,l=t.adapterConfig,s=b.getRpcSessionId(t),e.next=5,i.call(b.getRpcSessionId(t),"PileupGetGlobalValueForTag",J({adapterConfig:l,tag:r.tag,sessionId:s,regions:n.contentBlocks},a));case 5:return e.abrupt("return",e.sent);case 7:case"end":return e.stop()}}),e)})))).apply(this,arguments)}function Oe(e,t,r,n,a){return je.apply(this,arguments)}function je(){return(je=Q(ve.mark((function e(t,r,n,a,o){var i,l,s;return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return i=g.getSession(t),l=i.rpcManager,s=b.getRpcSessionId(t),e.next=4,l.call(s,"PileupGetVisibleModifications",J({adapterConfig:r,tag:n.tag,sessionId:s,regions:a.contentBlocks},o));case 4:return e.abrupt("return",e.sent);case 6:case"end":return e.stop()}}),e)})))).apply(this,arguments)}var He=t.lazy((function(){return Promise.resolve().then((function(){return At}))})),Ve=t.lazy((function(){return 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d.types.compose("LinearPileupDisplay",u.BaseLinearDisplay,d.types.model({type:d.types.literal("LinearPileupDisplay"),configuration:n.ConfigurationReference(t),showSoftClipping:!1,featureHeight:d.types.maybe(d.types.number),noSpacing:d.types.maybe(d.types.boolean),fadeLikelihood:d.types.maybe(d.types.boolean),trackMaxHeight:d.types.maybe(d.types.number),mismatchAlpha:d.types.maybe(d.types.boolean),sortedBy:d.types.maybe(d.types.model({type:d.types.string,pos:d.types.number,tag:d.types.maybe(d.types.string),refName:d.types.string,assemblyName:d.types.string})),colorBy:d.types.maybe(d.types.model({type:d.types.string,tag:d.types.maybe(d.types.string),extra:d.types.frozen()})),filterBy:d.types.optional(d.types.model({flagInclude:d.types.optional(d.types.number,0),flagExclude:d.types.optional(d.types.number,1540),readName:d.types.maybe(d.types.string),tagFilter:d.types.maybe(d.types.model({tag:d.types.string,value:d.types.string}))}),{})})).volatile((function(){return{colorTagMap:m.observable.map({}),modificationTagMap:m.observable.map({}),ready:!1,currBpPerPx:0}})).actions((function(e){return{setReady:function(t){e.ready=t},setCurrBpPerPx:function(t){e.currBpPerPx=t},setMaxHeight:function(t){e.trackMaxHeight=t},setFeatureHeight:function(t){e.featureHeight=t},setNoSpacing:function(t){e.noSpacing=t},setColorScheme:function(t){e.colorTagMap=m.observable.map({}),e.colorBy=d.cast(t),e.ready=!1},updateModificationColorMap:function(t){var r=["red","blue","green","orange","purple"];t.forEach((function(t){if(!e.modificationTagMap.has(t)){var n=ie(e.modificationTagMap.keys()).length;e.modificationTagMap.set(t,r[n])}}))},updateColorTagMap:function(t){var r=["#BBCCEE","pink","#CCDDAA","#EEEEBB","#FFCCCC","lightblue","lightgreen","tan","#CCEEFF","lightsalmon"];t.forEach((function(t){if(!e.colorTagMap.has(t)){var n=ie(e.colorTagMap.keys()).length;e.colorTagMap.set(t,r[n])}}))}}})).actions((function(e){return{afterAttach:function(){d.addDisposer(e,m.autorun(Q(ve.mark((function t(){var r,a,o,i,l,s,c,u;return ve.wrap((function(t){for(;;)switch(t.prev=t.next){case 0:if(t.prev=0,r=g.getSession(e),a=r.rpcManager,o=e.sortedBy,i=e.colorBy,l=g.getContainingView(e),null==i||!i.tag){t.next=9;break}return t.next=7,qe(e,i,l.staticBlocks);case 7:e.updateColorTagMap(t.sent);case 9:if("modifications"!==(null==i?void 0:i.type)){t.next=14;break}return t.next=12,Oe(e,n.getConf(e.parentTrack,["adapter"]),i,l.staticBlocks);case 12:e.updateModificationColorMap(t.sent);case 14:if(!o){t.next=23;break}return u={start:s=o.pos,end:s+1,refName:o.refName,assemblyName:c=o.assemblyName},t.next=19,e.rendererType.renderInClient(a,J({assemblyName:c,regions:[u],adapterConfig:e.adapterConfig,rendererType:e.rendererType.name,sessionId:b.getRpcSessionId(e),timeout:1e6},e.renderProps()));case 19:e.setReady(!0),e.setCurrBpPerPx(l.bpPerPx),t.next=24;break;case 23:e.setReady(!0);case 24:t.next=30;break;case 26:t.prev=26,t.t0=t.catch(0),console.error(t.t0),e.setError(t.t0);case 30:case"end":return t.stop()}}),t,null,[[0,26]])}))),{delay:1e3}))},selectFeature:function(t){var r=g.getSession(e);if(g.isSessionModelWithWidgets(r)){var n=r.addWidget("AlignmentsFeatureWidget","alignmentFeature",{featureData:t.toJSON(),view:g.getContainingView(e)});r.showWidget(n)}r.setSelection(t)},clearSelected:function(){e.sortedBy=void 0},copyFeatureToClipboard:function(t){var r=t.toJSON();delete r.uniqueId;var n=g.getSession(e);S(JSON.stringify(r,null,4)),n.notify("Copied to clipboard","success")},toggleSoftClipping:function(){e.showSoftClipping=!e.showSoftClipping},toggleMismatchAlpha:function(){e.mismatchAlpha=!e.mismatchAlpha},setConfig:function(t){e.configuration=t},setSortedBy:function(t,r){var n=g.getContainingView(e).centerLineInfo;if(n){var a=n.refName,o=n.assemblyName,i=Math.round(n.offset)+1;i<0||(e.sortedBy={type:t,pos:i,refName:a,assemblyName:o,tag:r},e.ready=!1)}},setFilterBy:function(t){e.filterBy=d.cast(t)}}})).actions((function(e){var t=e.reload;return{reload:function(){e.clearSelected(),t()}}})).views((function(e){return{get maxHeight(){var t=n.getConf(e,["renderers",e.rendererTypeName])||{};return void 0!==e.trackMaxHeight?e.trackMaxHeight:t.maxHeight},get rendererConfig(){var t=n.getConf(e,["renderers",e.rendererTypeName])||{};return e.rendererType.configSchema.create(J(J({},t),{},{height:e.featureHeight,noSpacing:e.noSpacing,maxHeight:this.maxHeight,mismatchAlpha:e.mismatchAlpha}),d.getEnv(e))},get featureHeightSetting(){return e.featureHeight||n.readConfObject(this.rendererConfig,"height")},get mismatchAlphaSetting(){return void 0!==e.mismatchAlpha?e.mismatchAlpha:n.readConfObject(this.rendererConfig,"mismatchAlpha")}}})).views((function(e){var t=e.trackMenuItems,r=e.renderProps;return{get rendererTypeName(){var t=n.getConf(e,"defaultRendering"),r=Je.get(t);if(!r)throw new Error("unknown alignments view name ".concat(t));return r},contextMenuItems:function(){var t=e.contextMenuFeature;return t?[{label:"Open feature details",icon:x,onClick:function(){e.clearFeatureSelection(),t&&e.selectFeature(t)}},{label:"Copy info to clipboard",icon:w.ContentCopy,onClick:function(){t&&e.copyFeatureToClipboard(t)}}]:[]},get DisplayBlurb(){return Le},get filters(){var t=[];if(e.filterBy){var r=e.filterBy,n=r.flagInclude,a=r.flagExclude;if(t=["jexl:((get(feature,'flags')&".concat(n,")==").concat(n,") && !(get(feature,'flags')&").concat(a,")")],e.filterBy.tagFilter){var o=e.filterBy.tagFilter,i=o.tag,l=o.value;t.push('jexl:"'.concat(l,"\" =='*' ? getTag(feature,\"").concat(i,'") != undefined : getTag(feature,"').concat(i,'") == "').concat(l,'"'))}e.filterBy.readName&&t.push("jexl:get(feature,'name') == \"".concat(e.filterBy.readName,'"'))}return new P({filters:t})},renderProps:function(){var t=g.getContainingView(e),n=e.ready,a=e.colorTagMap,o=e.modificationTagMap,i=e.sortedBy,l=e.colorBy,s=e.rpcDriverName;return J(J({},r()),{},{notReady:!n||i&&e.currBpPerPx!==t.bpPerPx,rpcDriverName:s,displayModel:e,sortedBy:i,colorBy:l,colorTagMap:JSON.parse(JSON.stringify(a)),modificationTagMap:JSON.parse(JSON.stringify(o)),filters:this.filters,showSoftClip:e.showSoftClipping,config:e.rendererConfig})},trackMenuItems:function(){return[].concat(ie(t()),[{label:"Show soft 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methylation",onClick:function(){g.getSession(e).setDialogComponent(Ue,{model:e})}},{label:"Insert size",onClick:function(){e.setColorScheme({type:"insertSize"})}},{label:"Stranded paired-end",onClick:function(){e.setColorScheme({type:"reverseTemplate"})}},{label:"Color by tag...",onClick:function(){g.getSession(e).setDialogComponent(He,{model:e})}}]},{label:"Filter by",icon:E,onClick:function(){g.getSession(e).setDialogComponent(Ve,{model:e})}},{label:"Set feature height",onClick:function(){g.getSession(e).setDialogComponent(Ge,{model:e})}},{label:"Set max height",onClick:function(){g.getSession(e).setDialogComponent(We,{model:e})}},{label:"Fade mismatches by quality",type:"checkbox",checked:e.mismatchAlphaSetting,onClick:function(){e.toggleMismatchAlpha()}}])}}}))},Qe=function(e){return e.toLocaleString("en-US")},Ze=r.forwardRef((function(e,t){var n=e.feature,a=n.get("start"),o=n.get("end"),i=[n.get("refName"),a===o?Qe(a):"".concat(Qe(a),"..").concat(Qe(o))].filter((function(e){return!!e})).join(":"),l=n.get("snpinfo"),s=l.total;return r.createElement("div",{ref:t},r.createElement("table",null,r.createElement("caption",null,i),r.createElement("thead",null,r.createElement("tr",null,r.createElement("th",null,"Base"),r.createElement("th",null,"Count"),r.createElement("th",null,"% of Total"),r.createElement("th",null,"Strands"),r.createElement("th",null,"Source"))),r.createElement("tbody",null,r.createElement("tr",null,r.createElement("td",null,"Total"),r.createElement("td",null,s),r.createElement("td",null)),Object.entries(l).map((function(e){var t=oe(e,2),n=t[0];return Object.entries(t[1]).map((function(e){var t=oe(e,2),a=t[0],o=t[1],i=o.strands;return r.createElement("tr",{key:a},r.createElement("td",null,a.toUpperCase()),r.createElement("td",null,o.total),r.createElement("td",null,"total"===a?"---":"".concat(Math.floor(o.total/s*100),"%")),r.createElement("td",null,i[-1]?"".concat(i[-1],"(-)"):"",i[1]?"".concat(i[1],"(+)"):""),r.createElement("td",null,n))}))})))))})),Ye=y.observer((function(e){return r.createElement(p.Tooltip,Object.assign({TooltipContents:Ze},e))})),$e=new Map([["snpcoverage","SNPCoverageRenderer"]]),Ke=function(e,t){return d.types.compose("LinearSNPCoverageDisplay",p.linearWiggleDisplayModelFactory(e,t),d.types.model({type:d.types.literal("LinearSNPCoverageDisplay"),drawInterbaseCounts:d.types.maybe(d.types.boolean),drawIndicators:d.types.maybe(d.types.boolean),filterBy:d.types.optional(d.types.model({flagInclude:d.types.optional(d.types.number,0),flagExclude:d.types.optional(d.types.number,1540),readName:d.types.maybe(d.types.string),tagFilter:d.types.maybe(d.types.model({tag:d.types.string,value:d.types.string}))}),{}),colorBy:d.types.maybe(d.types.model({type:d.types.string,tag:d.types.maybe(d.types.string)}))})).volatile((function(){return{modificationTagMap:m.observable.map({})}})).actions((function(e){return{setConfig:function(t){e.configuration=t},setFilterBy:function(t){e.filterBy=d.cast(t)},setColorBy:function(t){e.colorBy=d.cast(t)},updateModificationColorMap:function(t){var r=["red","blue","green","orange","purple"],n=0;t.forEach((function(t){if(!e.modificationTagMap.has(t)){var a=r[n++];e.modificationTagMap.set(t,a)}}))}}})).views((function(e){var t=e.renderProps;return{get rendererConfig(){var t=n.getConf(e,["renderers",e.rendererTypeName])||{};return e.rendererType.configSchema.create(J(J({},t),{},{drawInterbaseCounts:void 0===e.drawInterbaseCounts?t.drawInterbaseCounts:e.drawInterbaseCounts,drawIndicators:void 0===e.drawIndicators?t.drawIndicators:e.drawIndicators}),d.getEnv(e))},get drawInterbaseCountsSetting(){return void 0!==e.drawInterbaseCounts?e.drawInterbaseCounts:n.readConfObject(this.rendererConfig,"drawInterbaseCounts")},get drawIndicatorsSetting(){return void 0!==e.drawIndicators?e.drawIndicators:n.readConfObject(this.rendererConfig,"drawIndicators")},get modificationsReady(){var t;return"modifications"!==(null===(t=e.colorBy)||void 0===t?void 0:t.type)||Object.keys(JSON.parse(JSON.stringify(e.modificationTagMap))).length>0},renderProps:function(){return J(J({},t()),{},{notReady:!e.ready||!this.modificationsReady,filters:e.filters,modificationTagMap:JSON.parse(JSON.stringify(e.modificationTagMap)),colorBy:e.colorBy?d.getSnapshot(e.colorBy):void 0})}}})).actions((function(e){return{toggleDrawIndicators:function(){e.drawIndicators=!e.drawIndicatorsSetting},toggleDrawInterbaseCounts:function(){e.drawInterbaseCounts=!e.drawInterbaseCountsSetting},afterAttach:function(){d.addDisposer(e,m.autorun(Q(ve.mark((function t(){var r,a,o;return ve.wrap((function(t){for(;;)switch(t.prev=t.next){case 0:if(t.prev=0,r=e.colorBy,a=g.getContainingView(e),o=a.staticBlocks,"modifications"!==(null==r?void 0:r.type)){t.next=8;break}return t.next=6,Oe(e,n.getConf(e.parentTrack,"adapter"),r,o);case 6:e.updateModificationColorMap(t.sent);case 8:t.next=14;break;case 10:t.prev=10,t.t0=t.catch(0),console.error(t.t0),e.setError(t.t0);case 14:case"end":return t.stop()}}),t,null,[[0,10]])}))),{delay:1e3}))}}})).views((function(e){var t=e.trackMenuItems;return{get TooltipComponent(){return Ye},get adapterConfig(){return{type:"SNPCoverageAdapter",subadapter:n.getConf(e.parentTrack,"adapter")}},get rendererTypeName(){return $e.get("snpcoverage")},get needsScalebar(){return!0},contextMenuItems:function(){return[]},trackMenuItems:function(){return[].concat(ie(t()),[{label:"Draw insertion/clipping indicators",type:"checkbox",checked:e.drawIndicatorsSetting,onClick:function(){e.toggleDrawIndicators()}},{label:"Draw insertion/clipping counts",type:"checkbox",checked:e.drawInterbaseCountsSetting,onClick:function(){e.toggleDrawInterbaseCounts()}}])},get filters(){var t=[];if(e.filterBy){var r=e.filterBy,n=r.flagInclude,a=r.flagExclude,o=r.tagFilter,i=r.readName;if(t=["jexl:get(feature,'snpinfo') != undefined ? true : "+"((get(feature,'flags')&".concat(n,")==").concat(n,") && ")+"!((get(feature,'flags')&".concat(a,"))")],o){var l=o.tag,s=o.value;t.push("jexl:get(feature,'snpinfo') != undefined ? true : "+'"'.concat(s,"\" =='*' ? getTag(feature,\"").concat(l,'") != undefined : ')+'getTag(feature,"'.concat(l,'") == "').concat(s,'"'))}i&&t.push("jexl:get(feature,'snpinfo') != undefined ? true : "+"get(feature,'name') == \"".concat(i,'"'))}return new P({filters:t})}}}))};function et(e){var n=e.onMouseMove,a=e.blockKey,o=e.displayModel,i=e.width,l=e.height,s=e.bpPerPx,c=e.sortedBy,u=e.colorBy,p=o.selectedFeatureId,f=o.featureIdUnderMouse,d=o.contextMenuFeature,h=oe(e.regions,1)[0],m=t.useRef(null),y=oe(t.useState(!1),2),b=y[0],C=y[1],w=oe(t.useState(!1),2),S=w[0],x=w[1];function _(t,r){var n=e["onFeature".concat(t)],a=e["on".concat(t)];n&&f?n(r,f):a&&a(r,f)}t.useEffect((function(){var e,t,r=m.current;if(r){var n=r.getContext("2d");if(n){n.clearRect(0,0,r.width,r.height);var i=p?null===(e=o.getFeatureByID)||void 0===e?void 0:e.call(o,a,p):void 0;if(i){var l=oe(i,4),c=l[1],u=l[3],y=oe(g.bpSpanPx(l[0],l[2],h,s),2),v=y[0],b=y[1],C=Math.round(c),w=Math.round(u-c);n.shadowColor="#222266",n.shadowBlur=10,n.lineJoin="bevel",n.lineWidth=2,n.strokeStyle="#00b8ff",n.strokeRect(v-2,C-2,b-v+4,w+4),n.clearRect(v,C,b-v,w)}var S=f||(null==d?void 0:d.id()),x=S?null===(t=o.getFeatureByID)||void 0===t?void 0:t.call(o,a,S):void 0;if(x){var _=oe(x,4),k=_[1],E=_[3],P=oe(g.bpSpanPx(_[0],_[2],h,s),2),T=P[0],R=P[1],M=Math.round(k),N=Math.round(E-k);n.fillStyle="#0003",n.fillRect(T,M,R-T,N)}}}}),[s,h,a,p,o,f,d]);var k=Math.ceil(i);return r.createElement("div",{className:"PileupRendering","data-testid":"pileup-".concat(c||u?"".concat((null==c?void 0:c.type)||"").concat((null==u?void 0:u.type)||"").concat((null==u?void 0:u.tag)||""):"normal"),style:{position:"relative",width:k,height:l}},r.createElement(v.PrerenderedCanvas,Object.assign({},e,{style:{position:"absolute",left:0,top:0}})),r.createElement("canvas",{"data-testid":"pileup_overlay_canvas",width:k,height:l+100,style:{position:"absolute",left:0,top:0},className:"highlightOverlayCanvas",ref:m,onMouseDown:function(e){return function(e){C(!0),x(!1),_("MouseDown",e)}(e)},onMouseEnter:function(e){return function(e){_("MouseEnter",e)}(e)},onMouseOut:function(e){return function(e){_("MouseOut",e),_("MouseLeave",e)}(e)},onMouseOver:function(e){return function(e){_("MouseOver",e)}(e)},onMouseUp:function(e){return function(e){C(!1),_("MouseUp",e)}(e)},onMouseLeave:function(e){return function(e){_("MouseOut",e),_("MouseLeave",e)}(e)},onMouseMove:function(e){return function(e){b&&x(!0);var t=0,r=0;m.current&&(t=m.current.getBoundingClientRect().left,r=m.current.getBoundingClientRect().top),t=e.clientX-t;var l=o.getFeatureOverlapping(a,h.start+s*(h.reversed?i-t:t),r=e.clientY-r);n&&n(e,l)}(e)},onClick:function(e){return function(e){S||_("Click",e)}(e)},onContextMenu:function(e){return function(e){_("ContextMenu",e)}(e)},onFocus:function(){},onBlur:function(){}}))}var tt=y.observer(et),rt=n.ConfigurationSchema("PileupRenderer",{color:{type:"color",description:"the color of each feature in a pileup alignment",defaultValue:"#c8c8c8",contextVariable:["feature"]},orientationType:{type:"stringEnum",model:d.types.enumeration("orientationType",["fr","rf","ff"]),defaultValue:"fr",description:'read sequencer orienation. fr is normal "reads pointing at each other ---\x3e <--- while some other sequencers can use other options'},displayMode:{type:"stringEnum",model:d.types.enumeration("displayMode",["normal","compact","collapse"]),description:"Alternative display modes",defaultValue:"normal"},minSubfeatureWidth:{type:"number",description:"the minimum width in px for a pileup mismatch feature. use for increasing mismatch marker widths when zoomed out to e.g. 1px or 0.5px",defaultValue:0},maxHeight:{type:"integer",description:"the maximum height to be used in a pileup rendering",defaultValue:1200},maxClippingSize:{type:"integer",description:"the max clip size to be used in a pileup rendering",defaultValue:1e4},height:{type:"number",description:"the height of each feature in a pileup alignment",defaultValue:7,contextVariable:["feature"]},noSpacing:{type:"boolean",description:"remove spacing between features",defaultValue:!1},largeInsertionIndicatorScale:{type:"number",description:"scale at which to draw the large insertion indicators (bp/pixel)",defaultValue:10},mismatchAlpha:{type:"boolean",defaultValue:!1,description:"Fade low quality mismatches"}},{explicitlyTyped:!0});function nt(e,t){var r=e.get("tags");return r?r[t]:e.get(t)}function at(e,t,r){return nt(e,t)||nt(e,r)}var ot={fr:{F1R2:"LR",F2R1:"LR",F1F2:"LL",F2F1:"LL",R1R2:"RR",R2R1:"RR",R1F2:"RL",R2F1:"RL"},rf:{R1F2:"LR",R2F1:"LR",R1R2:"LL",R2R1:"LL",F1F2:"RR",F2F1:"RR",F1R2:"RL",F2R1:"RL"},ff:{F2F1:"LR",R1R2:"LR",F2R1:"LL",R1F2:"LL",R2F1:"RR",F1R2:"RR",R2R1:"RL",F1F2:"RL"}},it=function(e){ee(r,M.LayoutSession);var t=ne(r);function r(e){var n;return Z(this,r),(n=t.call(this,e)).showSoftClip=!1,n.config=e.config,n}return $(r,[{key:"cachedLayoutIsValid",value:function(e){return ae(te(r.prototype),"cachedLayoutIsValid",this).call(this,e)&&this.showSoftClip===e.showSoftClip&&h(this.sortedBy,e.sortedBy)}},{key:"layout",get:function(){return this.cachedLayout&&this.cachedLayoutIsValid(this.cachedLayout)||(this.cachedLayout={layout:this.makeLayout(),config:n.readConfObject(this.config),filters:this.filters,sortedBy:this.sortedBy,showSoftClip:this.showSoftClip}),this.cachedLayout.layout}}]),r}();function lt(e){return{A:e.palette.bases.A.main,C:e.palette.bases.C.main,G:e.palette.bases.G.main,T:e.palette.bases.T.main,deletion:"#808080"}}var st={color_fwd_strand_not_proper:"#ECC8C8",color_rev_strand_not_proper:"#BEBED8",color_fwd_strand:"#EC8B8B",color_rev_strand:"#8F8FD8",color_fwd_missing_mate:"#D11919",color_rev_missing_mate:"#1919D1",color_fwd_diff_chr:"#000",color_rev_diff_chr:"#969696",color_pair_lr:"#c8c8c8",color_pair_rr:"navy",color_pair_rl:"teal",color_pair_ll:"green",color_nostrand:"#999",color_interchrom:"orange",color_longinsert:"red",color_shortinsert:"pink"};function ct(e){return!["methylation","modifications"].includes(e||"")}var ut=function(e){ee(o,N);var t,r,a=ne(o);function o(){var e;return Z(this,o),(e=a.apply(this,arguments)).supportsSVG=!0,e}return $(o,[{key:"getCharWidthHeight",value:function(e){return{charWidth:e.measureText("A").width,charHeight:e.measureText("M").width}}},{key:"layoutFeature",value:function(e,t,r,a,o,i){var l=0,s=0,c=e.get("mismatches"),u=e.get("seq");if(i&&u)for(var p=0;p<c.length;p+=1){var f=c[p],d=f.cliplen,h=void 0===d?0:d;"softclip"===f.type&&(0===f.start?l=h:s=h)}var m=oe(g.bpSpanPx(e.get("start")-l,e.get("end")+s,o,a),2),y=m[0],v=m[1],b=n.readConfObject(r,"height",{feature:e}),C=n.readConfObject(r,"displayMode",{feature:e});if("compact"===C&&(b/=3),e.get("refName")!==o.refName)throw new Error("feature ".concat(e.id()," is not on the current region's reference sequence ").concat(o.refName));var w=t.addRect(e.id(),e.get("start")-l,e.get("end")+s,b);return null===w?null:{feature:e,leftPx:y,rightPx:v,topPx:"collapse"===C?0:w,heightPx:b}}},{key:"getExpandedRegion",value:function(e,t){var r=t.showSoftClip,a=n.readConfObject(t.config,"maxClippingSize"),o=e.start,i=e.end,l=Math.max(i-o,r?Math.round(a):0);return J(J({},e),{},{start:Math.floor(Math.max(o-l,0)),end:Math.ceil(i+l)})}},{key:"colorByOrientation",value:function(e,t){return st[this.getOrientation(e,t)||"color_nostrand"]}},{key:"getOrientation",value:function(e,t){var r=n.readConfObject(t,"orientationType");return{LR:"color_pair_lr",RR:"color_pair_rr",RL:"color_pair_rl",LL:"color_pair_ll"}[ot[r][e.get("pair_orientation")]]}},{key:"colorByInsertSize",value:function(e,t){return e.get("is_paired")&&e.get("seq_id")!==e.get("next_seq_id")?"#555":"hsl(".concat(Math.abs(e.get("template_length"))/10,",50%,50%)")}},{key:"colorByStranded",value:function(e,t){var r=e.get("flags"),n=e.get("strand");if(1&r){var a=64&r?-1:1;return 2&r?n*a==1?"color_rev_strand":"color_fwd_strand":e.get("multi_segment_next_segment_unmapped")?n*a==1?"color_rev_missing_mate":"color_fwd_missing_mate":e.get("seq_id")===e.get("next_seq_id")?n*a==1?"color_rev_strand_not_proper":"color_fwd_strand_not_proper":1===n?"color_fwd_diff_chr":"color_rev_diff_chr"}return 1===n?"color_fwd_strand":"color_rev_strand"}},{key:"colorByPerBaseQuality",value:function(e,t,r,n,a){for(var o=t.feature,i=t.topPx,l=t.heightPx,s=(o.get("qual")||"").split(" ").map((function(e){return+e})),c=Ce(o.get("CIGAR")),u=1/a,p=o.get("start"),f=0,d=0,h=0;h<s.length;f+=2,h++){var m=+c[f],y=c[f+1];if("S"===y||"I"===y)h+=m;else if("D"===y||"N"===y)d+=m;else if("M"===y||"X"===y||"="===y){for(var v=0;v<m;v++){var b=s[h+v];e.fillStyle="hsl(".concat(255===b?150:1.5*b,",55%,50%)");var C=oe(g.bpSpanPx(p+d+v,p+d+v+1,n,a),1);e.fillRect(C[0],i,u+.5,l)}d+=m}}}},{key:"colorByModifications",value:function(e,t,r,n,a,o){var i=t.feature,l=t.topPx,s=t.heightPx,c=o.modificationTagMap,u=void 0===c?{}:c,p=at(i,"MM","Mm")||"",f=at(i,"ML","Ml")||[],d=f?("string"==typeof f?f.split(",").map((function(e){return+e})):f).map((function(e){return e/255})):at(i,"MP","Mp").split("").map((function(e){return e.charCodeAt(0)-33})).map((function(e){return Math.min(1,e/50)})),h=i.get("CIGAR"),m=i.get("start"),y=i.get("end"),v=i.get("seq"),b=i.get("strand"),C=Ce(h),w=ke(p,v,b),S=0;w.forEach((function(t){var r,o=t.positions,i=B(u[t.type]||"black"),c=fe(_e(C,o));try{for(c.s();!(r=c.n()).done;){var p=r.value;if(p>=0&&m+p<y){var f=oe(g.bpSpanPx(m+p,m+p+1,n,a),2),h=f[0],v=f[1];e.fillStyle=i.alpha(d[S]+.1).hsl().string(),e.fillRect(h,l,v-h+.5,s)}S++}}catch(e){c.e(e)}finally{c.f()}}))}},{key:"colorByMethylation",value:function(e,t,r,n,a,o){var i=o.regionSequence,l=t.feature,s=t.topPx,c=t.heightPx,u=at(l,"MM","Mm")||"";if(!i)throw new Error("region sequence required for methylation");var p=l.get("CIGAR"),f=l.get("start"),d=l.get("end"),h=l.get("seq"),m=l.get("strand"),y=Ce(p),v=n.start,b=new Array(n.end-v).fill(0);ke(u,h,m).forEach((function(e){var t=e.positions;if("m"===e.type&&t){var r,n=fe(_e(y,t));try{for(n.s();!(r=n.n()).done;){var a=r.value+f-v;a>=0&&a<b.length&&(b[a]=1)}}catch(e){n.e(e)}finally{n.f()}}}));for(var C=f;C<d;C++){var w=C-v;if(w>=0&&w<b.length){var S=i[w].toLowerCase(),x=i[w+1].toLowerCase();if(a>2){if("c"===S&&"g"===x){var _=v+w,k=oe(g.bpSpanPx(_,_+2,n,a),2),E=k[0],P=k[1];e.fillStyle=b[w]||b[w+1]?"red":"blue",e.fillRect(E,s,P-E+.5,c)}}else if("c"===S&&"g"===x){var T=v+w,R=oe(g.bpSpanPx(T,T+1,n,a),2),M=R[0],N=R[1];e.fillStyle=b[w]?"red":"blue",e.fillRect(M,s,N-M+.5,c);var B=oe(g.bpSpanPx(T+1,T+2,n,a),2),D=B[0],A=B[1];e.fillStyle=b[w+1]?"red":"blue",e.fillRect(D,s,A-D+.5,c)}}}}},{key:"drawRect",value:function(e,t,r){var n=r.bpPerPx,a=t.heightPx,o=t.topPx,i=t.feature,l=oe(r.regions,1)[0],s=oe(g.bpSpanPx(i.get("start"),i.get("end"),l,n),2),c=s[0],u=s[1],p=l.reversed?-1:1,f=i.get("strand")*p;n<10?-1===f?(e.beginPath(),e.moveTo(c-5,o+a/2),e.lineTo(c,o+a),e.lineTo(u,o+a),e.lineTo(u,o),e.lineTo(c,o),e.closePath(),e.fill()):(e.beginPath(),e.moveTo(c,o),e.lineTo(c,o+a),e.lineTo(u,o+a),e.lineTo(u+5,o+a/2),e.lineTo(u,o),e.closePath(),e.fill()):e.fillRect(c,o,u-c,a)}},{key:"drawAlignmentRect",value:function(e,t,r){var a=r.config,o=r.bpPerPx,i=r.colorTagMap,l=void 0===i?{}:i,s=r.colorBy||{},c=s.tag,u=void 0===c?"":c,p=s.type,f=void 0===p?"":p,d=t.feature,g=r.regions[0];switch(f){case"insertSize":e.fillStyle=this.colorByInsertSize(d,a);break;case"strand":e.fillStyle=-1===d.get("strand")?"#8F8FD8":"#EC8B8B";break;case"mappingQuality":e.fillStyle="hsl(".concat(d.get("mq"),",50%,50%)");break;case"pairOrientation":e.fillStyle=this.colorByOrientation(d,a);break;case"stranded":e.fillStyle=st[this.colorByStranded(d,a)];break;case"xs":case"tag":var h=d.get("tags"),m=h?h[u]:d.get(u);if("XS"!==u&&"TS"!==u||(e.fillStyle=st[{"-":"color_rev_strand","+":"color_fwd_strand"}[m]||"color_nostrand"]),"ts"===u){var y={"-":-1===d.get("strand")?"color_fwd_strand":"color_rev_strand","+":-1===d.get("strand")?"color_rev_strand":"color_fwd_strand"};e.fillStyle=st[y[m]||"color_nostrand"]}else e.fillStyle=l[m]||"color_nostrand";break;case"insertSizeAndPairOrientation":break;case"normal":default:e.fillStyle=n.readConfObject(a,"color",{feature:d})}switch(this.drawRect(e,t,r),f){case"perBaseQuality":this.colorByPerBaseQuality(e,t,a,g,o);break;case"modifications":this.colorByModifications(e,t,a,g,o,r);break;case"methylation":this.colorByMethylation(e,t,a,g,o,r)}}},{key:"drawMismatches",value:function(e,t,r,a,o,i){var l=i.mismatchAlpha,s=i.drawSNPs,c=void 0===s||s,u=i.drawIndels,p=void 0===u||u,f=r.config,d=r.bpPerPx,h=r.regions,m=t.heightPx,y=t.topPx,v=t.feature,b=this.getCharWidthHeight(e),C=b.charWidth,w=b.charHeight,S=oe(h,1)[0],x=v.get("start"),_=n.readConfObject(f,"minSubfeatureWidth"),k=n.readConfObject(f,"largeInsertionIndicatorScale"),E=Math.min(1/d,2),P=Math.max(_,E),T=v.get("mismatches"),R=w-2;function M(e,t){var r=e;return l&&void 0!==t.qual&&(r=B(e).alpha(Math.min(1,t.qual/50)).hsl().string()),r}for(var N=0;N<T.length;N+=1){var D=T[N],A=oe(g.bpSpanPx(x+D.start,x+D.start+D.length,S,d),2),I=A[0],L=Math.max(_,Math.abs(I-A[1]));if("mismatch"===D.type&&c){var q=o[D.base]||"#888";e.fillStyle=M(q,D),e.fillRect(I,y,L,m),L>=C&&m>=R&&(e.fillStyle=M(a.palette.getContrastText(q),D),e.fillText(D.base,I+(L-C)/2+1,y+m))}else if("deletion"===D.type&&p){var F=o.deletion;e.fillStyle=F,e.fillRect(I,y,L,m),L>=C&&m>=R&&(e.fillStyle=a.palette.getContrastText(F),e.fillText(D.base,I+(L-C)/2+1,y+m))}else if("insertion"===D.type&&p){e.fillStyle="purple";var O=I-1;(+D.base||D.length)<10&&(e.fillRect(O,y,P,m),1/d>=C&&(e.fillRect(O-P,y,3*P,1),e.fillRect(O-P,y+m-1,3*P,1)),1/d>=C&&m>=R&&e.fillText("(".concat(D.base,")"),I+2,y+m))}else if("hardclip"===D.type||"softclip"===D.type){e.fillStyle="hardclip"===D.type?"red":"blue";var 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i=t.feature,l=t.topPx,s=t.heightPx,c=r.bpPerPx,u=oe(r.regions,1)[0],p=n.readConfObject(a,"minSubfeatureWidth"),f=i.get("mismatches"),d=i.get("seq"),h=this.getCharWidthHeight(e),m=h.charWidth,y=h.charHeight,v={A:o.palette.bases.A.main,C:o.palette.bases.C.main,G:o.palette.bases.G.main,T:o.palette.bases.T.main,deletion:"#808080"};d&&f.filter((function(e){return"softclip"===e.type})).forEach((function(t){for(var r=t.cliplen||0,n=0===t.start?i.get("start")-r:i.get("start")+t.start,a=0;a<r;a+=1){var f=d.charAt(a+t.start);if(!f)return;var h=oe(g.bpSpanPx(n+a,n+a+1,u,c),2),b=h[0],C=Math.max(p,Math.abs(b-h[1])),w=v[f]||"#000000";e.fillStyle=w,e.fillRect(b,l,C,s),C>=m&&s>=y-5&&(e.fillStyle=o.palette.getContrastText(w),e.fillText(f,b+(C-m)/2+1,l+s))}}))}},{key:"makeImageData",value:(r=Q(ve.mark((function e(t,r,a){var o,i,l,s,c,u,p,f,d=this;return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 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n.ConfigurationSchema("LinearPileupDisplay",{defaultRendering:{type:"stringEnum",model:d.types.enumeration("Rendering",["pileup","svg"]),defaultValue:"pileup"},renderers:n.ConfigurationSchema("RenderersConfiguration",{PileupRenderer:t,SvgFeatureRenderer:r}),renderer:"",maxDisplayedBpPerPx:{type:"number",description:"maximum bpPerPx that is displayed in the view",defaultValue:100},colorScheme:{type:"stringEnum",model:d.types.enumeration("colorScheme",["strand","normal","insertSize","insertSizeAndOrientation","mappingQuality","tag"]),description:"color scheme to use",defaultValue:"normal"}},{baseConfiguration:u.linearBasicDisplayConfigSchemaFactory(e),explicitlyTyped:!0})}(e);return new o({name:"LinearPileupDisplay",configSchema:t,stateModel:Xe(0,t),trackType:"AlignmentsTrack",viewType:"LinearGenomeView",ReactComponent:u.BaseLinearDisplayComponent})})),e.addDisplayType((function(){var t=function(e){var t=e.getRendererType("SNPCoverageRenderer").configSchema;return n.ConfigurationSchema("LinearSNPCoverageDisplay",{autoscale:{type:"stringEnum",defaultValue:"local",model:d.types.enumeration("Autoscale type",["local"]),description:"performs local autoscaling (no other options for SNP Coverage available)"},minScore:{type:"number",defaultValue:Number.MIN_VALUE,description:"minimum value for the y-scale"},maxScore:{type:"number",description:"maximum value for the y-scale",defaultValue:Number.MAX_VALUE},scaleType:{type:"stringEnum",model:d.types.enumeration("Scale type",["linear","log"]),description:"The type of scale to use",defaultValue:"linear"},inverted:{type:"boolean",description:"draw upside down",defaultValue:!1},maxDisplayedBpPerPx:{type:"number",description:"maximum bpPerPx that is displayed in the view",defaultValue:100},headroom:{type:"number",description:"round the upper value of the domain scale to the nearest N",defaultValue:0},renderers:n.ConfigurationSchema("RenderersConfiguration",{SNPCoverageRenderer:t})},{baseConfiguration:u.baseLinearDisplayConfigSchema,explicitlyTyped:!0})}(e);return new o({name:"LinearSNPCoverageDisplay",configSchema:t,stateModel:Ke(e,t),trackType:"AlignmentsTrack",viewType:"LinearGenomeView",ReactComponent:p.LinearWiggleDisplayReactComponent})})),e.addDisplayType((function(){var t=function(e){var t=e.getDisplayType("LinearPileupDisplay").configSchema,r=e.getDisplayType("LinearSNPCoverageDisplay").configSchema;return n.ConfigurationSchema("LinearAlignmentsDisplay",{pileupDisplay:t,snpCoverageDisplay:r},{baseConfiguration:u.baseLinearDisplayConfigSchema,explicitlyTyped:!0})}(e);return new o({name:"LinearAlignmentsDisplay",configSchema:t,stateModel:Be(e,t),trackType:"AlignmentsTrack",viewType:"LinearGenomeView",ReactComponent:Ae})})),e.addWidgetType((function(){return new s({name:"AlignmentsFeatureWidget",heading:"Feature details",configSchema:de,stateModel:ge(e),ReactComponent:t.lazy((function(){return Promise.resolve().then((function(){return ir}))}))})})),e.addAdapterType((function(){return new a(J({name:"BamAdapter"},e.load(me)))})),e.addAdapterType((function(){return new a(J({name:"SNPCoverageAdapter"},e.load(bt)))})),e.addAdapterType((function(){return new a(J({name:"CramAdapter"},e.load(Re)))})),e.addAdapterType((function(){return new a(J({name:"HtsgetBamAdapter"},e.load(Ne)))})),e.addRendererType((function(){return new ut({name:"PileupRenderer",ReactComponent:tt,configSchema:rt,pluginManager:e})})),e.addRendererType((function(){return new wt({name:"SNPCoverageRenderer",ReactComponent:p.WiggleRendering,configSchema:St,pluginManager:e})})),e.addRpcMethod((function(){return new xt(e)})),e.addRpcMethod((function(){return new _t(e)}))}}]),f}(),Et=function(){function e(t,r,n){Z(this,e),this.record=t,this.adapter=r,this.ref=n}return $(e,[{key:"_get_name",value:function(){return this.record.get("name")}},{key:"_get_type",value:function(){return"match"}},{key:"_get_score",value:function(){return this.record.get("mq")}},{key:"_get_flags",value:function(){return this.record.flags}},{key:"_get_strand",value:function(){return this.record.isReverseComplemented()?-1:1}},{key:"_get_read_group_id",value:function(){return this.record.readGroupId}},{key:"_get_pair_orientation",value:function(){return this.record.isPaired()?this.record.getPairOrientation():void 0}},{key:"_get_next_seq_id",value:function(){return this.record._next_refid()}},{key:"_get_seq_id",value:function(){return this.record._refID}},{key:"_get_next_refName",value:function(){return this.adapter.refIdToName(this.record._next_refid())}},{key:"_get_next_segment_position",value:function(){return this.record.isPaired()?"".concat(this.adapter.refIdToName(this.record._next_refid()),":").concat(this.record._next_pos()+1):void 0}},{key:"_get_seq",value:function(){return this.record.getReadBases()}},{key:"_get_MD",value:function(){var e=this.record.get("MD"),t=this.get("seq");return!e&&t&&this.ref?xe(this.ref,this.record.getReadBases(),this.get("CIGAR")):e}},{key:"qualRaw",value:function(){return this.record.qualRaw()}},{key:"set",value:function(){}},{key:"tags",value:function(){var t=Object.getOwnPropertyNames(e.prototype);return ie(new Set(t.filter((function(e){return e.startsWith("_get_")&&"_get_mismatches"!==e&&"_get_skips_and_dels"!==e&&"_get_cram_read_features"!==e&&"_get_tags"!==e&&"_get_next_seq_id"!==e&&"_get_seq_id"!==e})).map((function(e){return e.replace("_get_","")})).concat(this.record._tags())))}},{key:"id",value:function(){return"".concat(this.adapter.id,"-").concat(this.record.id())}},{key:"get",value:function(e){var t="_get_".concat(e);return this[t]?this[t]():this.record.get(e)}},{key:"_get_refName",value:function(){return this.adapter.refIdToName(this.record.seq_id())}},{key:"parent",value:function(){}},{key:"children",value:function(){}},{key:"pairedFeature",value:function(){return!1}},{key:"toJSON",value:function(){var e=this;return J(J({},Object.fromEntries(this.tags().map((function(t){return[t,e.get(t)]})).filter((function(e){return void 0!==e[1]})))),{},{uniqueId:this.id()})}},{key:"_get_skips_and_dels",value:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{cigarAttributeName:"CIGAR"},t=e.cigarAttributeName,r=[],n=[],a=this.get(t);return a&&(n=Ce(a),r=r.concat(we(n,this.get("seq"),this.qualRaw()))),r}},{key:"_get_mismatches",value:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},t=e.cigarAttributeName,r=void 0===t?"CIGAR":t,n=e.mdAttributeName,a=void 0===n?"MD":n,o=[],i=[],l=this.get(r);l&&(i=Ce(l),o=o.concat(we(i,this.get("seq"),this.qualRaw())));var s=this.get(a);s&&(o=o.concat(Se(s,i,o,this.get("seq"),this.qualRaw())));var c={};return o.filter((function(e){var t="".concat(e.type,",").concat(e.start,",").concat(e.length),r=c[t];return c[t]=!0,!r}))}},{key:"_get_clipPos",value:function(){var e=this.get("CIGAR")||"";return-1===this.get("strand")?+(e.match(/(\d+)[SH]$/)||[])[1]||0:+(e.match(/^(\d+)([SH])/)||[])[1]||0}}]),e}(),Pt=function(e){ee(s,L.BaseFeatureDataAdapter);var t,r,a,o,i,l=ne(s);function s(){return Z(this,s),l.apply(this,arguments)}return $(s,[{key:"configure",value:(i=Q(ve.mark((function e(){var t,r,a,o,i,l,s;return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return this.configured||(t=n.readConfObject(this.config,"bamLocation"),r=n.readConfObject(this.config,["index","location"]),a=n.readConfObject(this.config,["index","indexType"]),o=n.readConfObject(this.config,"chunkSizeLimit"),i=n.readConfObject(this.config,"fetchSizeLimit"),l=new j.BamFile({bamFilehandle:H.openLocation(t),csiFilehandle:"CSI"===a?H.openLocation(r):void 0,baiFilehandle:"CSI"!==a?H.openLocation(r):void 0,chunkSizeLimit:o,fetchSizeLimit:i}),s=n.readConfObject(this.config,"sequenceAdapter"),this.configured=s&&this.getSubAdapter?this.getSubAdapter(s).then((function(e){return{bam:l,sequenceAdapter:e.dataAdapter}})):Promise.resolve({bam:l})),e.abrupt("return",this.configured);case 2:case"end":return e.stop()}}),e,this)}))),function(){return i.apply(this,arguments)})},{key:"getHeader",value:(o=Q(ve.mark((function e(t){return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.configure();case 2:return e.abrupt("return",e.sent.bam.getHeaderText(t));case 5:case"end":return e.stop()}}),e,this)}))),function(e){return o.apply(this,arguments)})},{key:"setup",value:(a=Q(ve.mark((function e(t){var r,n,a=this;return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return n=void 0===(r=(t||{}).statusCallback)?function(){}:r,this.setupP||(this.setupP=this.configure().then(function(){var e=Q(ve.mark((function e(r){var o,i,l;return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return o=r.bam,n("Downloading index"),e.next=4,o.getHeader(t);case 4:return i=[],l={},e.sent.filter((function(e){return"SQ"===e.tag})).forEach((function(e,t){e.data.forEach((function(e){if("SN"===e.tag){var r=e.value;l[r]=t,i[t]=r}}))})),n(""),a.samHeader={idToName:i,nameToId:l},e.abrupt("return",a.samHeader);case 11:case"end":return e.stop()}}),e)})));return function(t){return e.apply(this,arguments)}}()).catch((function(e){throw a.setupP=void 0,e}))),e.abrupt("return",this.setupP);case 3:case"end":return e.stop()}}),e,this)}))),function(e){return a.apply(this,arguments)})},{key:"getRefNames",value:(r=Q(ve.mark((function e(t){return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.setup(t);case 2:return e.abrupt("return",e.sent.idToName);case 5:case"end":return e.stop()}}),e,this)}))),function(e){return r.apply(this,arguments)})},{key:"seqFetch",value:(t=Q(ve.mark((function e(t,r,n){var a,o,i,l;return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.configure();case 2:if(a=e.sent.sequenceAdapter){e.next=7;break}return e.abrupt("return",void 0);case 7:if(t){e.next=9;break}return e.abrupt("return",void 0);case 9:return o=a.getFeatures({refName:t,start:r,end:n,assemblyName:""}),e.next=12,o.pipe(R.toArray()).toPromise();case 12:if(i=[],e.sent.sort((function(e,t){return e.get("start")-t.get("start")})).forEach((function(e){var t=e.get("start"),a=e.get("end"),o=Math.max(r-t,0),l=Math.min(n-t,a-t)-o,s=e.get("seq")||e.get("residues");i.push(s.substr(o,l))})),(l=i.join("")).length===n-r){e.next=18;break}throw new Error("sequence fetch failed: fetching ".concat(t,":").concat((r-1).toLocaleString(),"-").concat(n.toLocaleString()," returned ").concat(l.length.toLocaleString()," bases, but should have returned ").concat((n-r).toLocaleString()));case 18:return e.abrupt("return",l);case 19:case"end":return e.stop()}}),e,this)}))),function(e,r,n){return t.apply(this,arguments)})},{key:"getFeatures",value:function(e,t){var r=this,n=e.refName,a=e.start,o=e.end,i=e.originalRefName,l=t||{},s=l.signal,c=l.statusCallback,u=void 0===c?function(){}:c;return F.ObservableCreate(function(){var e=Q(ve.mark((function e(l){var c,p,f,d,h,m;return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,r.configure();case 2:return c=e.sent.bam,e.next=6,r.setup(t);case 6:return u("Downloading alignments"),e.next=9,c.getRecordsForRange(n,a,o,t);case 9:p=e.sent,g.checkAbortSignal(s),f=fe(p),e.prev=12,f.s();case 14:if((d=f.n()).done){e.next=24;break}if(m=void 0,(h=d.value).get("md")){e.next=21;break}return e.next=20,r.seqFetch(i||n,h.get("start"),h.get("end"));case 20:m=e.sent;case 21:l.next(new Et(h,r,m));case 22:e.next=14;break;case 24:e.next=29;break;case 26:e.prev=26,e.t0=e.catch(12),f.e(e.t0);case 29:return e.prev=29,f.f(),e.finish(29);case 32:u(""),l.complete();case 34:case"end":return e.stop()}}),e,null,[[12,26,29,32]])})));return function(t){return e.apply(this,arguments)}}(),s)}},{key:"freeResources",value:function(){}},{key:"refIdToName",value:function(e){var t;return null===(t=this.samHeader)||void 0===t?void 0:t.idToName[e]}}]),s}(),Tt={__proto__:null,default:Pt},Rt=function(){function e(t,r){Z(this,e),this.record=t,this._store=r}return $(e,[{key:"_get_name",value:function(){return this.record.readName}},{key:"_get_start",value:function(){return this.record.alignmentStart-1}},{key:"_get_end",value:function(){return this.record.alignmentStart+this.record.lengthOnRef-1}},{key:"_get_cram_read_features",value:function(){return this.record.readFeatures}},{key:"_get_type",value:function(){return"match"}},{key:"_get_score",value:function(){return this.record.mappingQuality}},{key:"_get_flags",value:function(){return this.record.flags}},{key:"_get_strand",value:function(){return this.record.isReverseComplemented()?-1:1}},{key:"_read_group_id",value:function(){var e=this._store.samHeader.readGroups;return e?e[this.record.readGroupId]:void 0}},{key:"_get_qual",value:function(){return(this.record.qualityScores||[]).join(" ")}},{key:"qualRaw",value:function(){return this.record.qualityScores}},{key:"_get_seq_id",value:function(){return this._store.refIdToName(this.record.sequenceId)}},{key:"_get_refName",value:function(){return this._get_seq_id()}},{key:"_get_is_paired",value:function(){return!!this.record.mate}},{key:"_get_pair_orientation",value:function(){return this.record.isPaired()?this.record.getPairOrientation():void 0}},{key:"_get_template_length",value:function(){return this.record.templateLength||this.record.templateSize}},{key:"_get_next_seq_id",value:function(){return this.record.mate?this._store.refIdToName(this.record.mate.sequenceId):void 0}},{key:"_get_next_pos",value:function(){return this.record.mate?this.record.mate.alignmentStart:void 0}},{key:"_get_next_segment_position",value:function(){return this.record.mate?"".concat(this._store.refIdToName(this.record.mate.sequenceId),":").concat(this.record.mate.alignmentStart):void 0}},{key:"_get_tags",value:function(){var e=this._read_group_id(),t=this.record.tags;return void 0!==e?J(J({},t),{},{RG:e}):t}},{key:"_get_seq",value:function(){return this.record.getReadBases()}},{key:"_get_CIGAR",value:function(){var e="",t="",r="M",n=0,a=this.record._refRegion.seq,o=this.record._refRegion.start,i=this.record.alignmentStart,l=0;return void 0!==this.record.readFeatures?this.record.readFeatures.forEach((function(s){var c=s.code,u=s.refPos,p=s.sub,f=s.data;if(l=u-i,e+=a.substring(i-o,u-o),i=u,n&&"M"!==r&&(t+=n+r,n=0),l&&(r="M",n+=l),"b"===c){var d=f.split(","),g=String.fromCharCode.apply(String,ie(d));e+=g,i+=g.length,n+=g.length}else"B"===c||"X"===c?(e+=p,i++,n++):"D"===c||"N"===c?(i+=f,n&&(t+=n+r),t+=f+c,n=0):"I"===c||"S"===c?(e+=f,n&&(t+=n+r),t+=f.length+c,n=0):"i"===c?(e+=f,n&&(t+=n+r),t+="".concat(1,"I"),n=0):"P"===c?(n&&(t+=n+r),t+="".concat(f,"P")):"H"===c&&(n&&(t+=n+r),t+="".concat(f,"H"),n=0)})):l=this.record.readLength-e.length,e.length!==this.record.readLength&&(e+=a.substring(i-o,i-o+(l=this.record.readLength-e.length)),n&&"M"!==r&&(t+=n+r,n=0),r="M",n+=l),n&&(t+=n+r),t}},{key:"tags",value:function(){return Object.getOwnPropertyNames(e.prototype).filter((function(e){return e.startsWith("_get_")&&"_get_mismatches"!==e&&"_get_skips_and_dels"!==e&&"_get_cram_read_features"!==e})).map((function(e){return e.replace("_get_","")}))}},{key:"id",value:function(){return"".concat(this._store.id,"-").concat(this.record.uniqueId)}},{key:"get",value:function(e){var t="_get_".concat(e);if(this[t])return this[t]()}},{key:"parent",value:function(){}},{key:"children",value:function(){}},{key:"set",value:function(){}},{key:"pairedFeature",value:function(){return!1}},{key:"_get_clipPos",value:function(){var e=this.get("mismatches");if(e.length){var t=-1===this.get("strand")?e[e.length-1]:e[0],r=t.type;if("softclip"===r||"hardclip"===r)return t.cliplen}return 0}},{key:"toJSON",value:function(){var e=this,t={};return this.tags().forEach((function(r){var n=e.get(r);void 0!==n&&(t[r]=n)})),J(J({},t),{},{name:this.get("name"),type:this.get("type"),uniqueId:this.id()})}},{key:"_get_mismatches",value:function(){var e=this.get("cram_read_features"),t=this.qualRaw();if(!e)return[];var r=this.get("start"),n=[];return e.forEach((function(e){var a=e.code,o=e.data,i=e.refPos-1-r;if("X"===a)n.push({start:i,length:1,base:e.sub,qual:null==t?void 0:t[e.pos],altbase:e.ref,type:"mismatch"});else if("I"===a)n.push({start:i,type:"insertion",base:"".concat(o.length),length:0});else if("N"===a)n.push({type:"skip",length:o,start:i,base:"N"});else if("S"===a){var l=o.length;n.push({start:i,type:"softclip",base:"S".concat(l),cliplen:l,length:1})}else if("P"===a);else if("H"===a){var s=o;n.push({start:i,type:"hardclip",base:"H".concat(s),cliplen:s,length:1})}else"D"===a?n.push({type:"deletion",length:o,start:i,base:"*"}):"b"===a||"q"===a||"B"===a||"i"===a&&n.push({start:i,type:"insertion",base:o,length:1})})),n}},{key:"_get_skips_and_dels",value:function(){return this._get_mismatches()}}]),e}(),Mt={__proto__:null,default:function(e){ee(s,L.BaseFeatureDataAdapter);var t,r,a,o,i,l=ne(s);function s(){var e;return Z(this,s),(e=l.apply(this,arguments)).samHeader={},e.seqIdToOriginalRefName=[],e}return $(s,[{key:"configure",value:(i=Q(ve.mark((function e(){var t,r,a,o;return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:if(t=n.readConfObject(this.config,"cramLocation"),r=n.readConfObject(this.config,"craiLocation"),t){e.next=4;break}throw new Error("missing cramLocation argument");case 4:if(r){e.next=6;break}throw new Error("missing craiLocation argument");case 6:if(this.cram=new V.IndexedCramFile({cramFilehandle:H.openLocation(t),index:new V.CraiIndex({filehandle:H.openLocation(r)}),seqFetch:this.seqFetch.bind(this),checkSequenceMD5:!1,fetchSizeLimit:this.config.fetchSizeLimit||6e8}),a=n.readConfObject(this.config,["sequenceAdapter","type"]),this.getSubAdapter){e.next=10;break}throw new Error("Error getting subadapter");case 10:return e.next=12,this.getSubAdapter(n.readConfObject(this.config,"sequenceAdapter"));case 12:if(!((o=e.sent.dataAdapter)instanceof L.BaseFeatureDataAdapter)){e.next=18;break}this.sequenceAdapter=o,e.next=19;break;case 18:throw new Error("CRAM feature adapters cannot use sequence adapters of type '".concat(a,"'"));case 19:return e.abrupt("return",{sequenceAdapter:this.sequenceAdapter});case 20:case"end":return e.stop()}}),e,this)}))),function(){return i.apply(this,arguments)})},{key:"getHeader",value:(o=Q(ve.mark((function e(t){return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.configure();case 2:return e.abrupt("return",this.cram.cram.getHeaderText(t));case 3:case"end":return e.stop()}}),e,this)}))),function(e){return o.apply(this,arguments)})},{key:"seqFetch",value:(a=Q(ve.mark((function e(t,r,n){var a,o,i,l,s;return ve.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:if(r-=1,a=this.sequenceAdapter){e.next=4;break}return e.abrupt("return",void 0);case 4:if(o=this.refIdToOriginalName(t)||this.refIdToName(t)){e.next=7;break}return e.abrupt("return",void 0);case 7:return i=a.getFeatures({refName:o,start:r,end:n,assemblyName:""},{}),e.next=10,i.pipe(R.toArray()).toPromise();case 10:if(l=[],e.sent.sort((function(e,t){return e.get("start")-t.get("start")})).forEach((function(e){var 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e.abrupt("return",{bins:e.sent,skipmap:f});case 20:case"end":return e.stop()}}),e,this)}))),function(e,r,n){return t.apply(this,arguments)})}]),u}(),Oe=qe.capabilities,je={__proto__:null,default:qe,capabilities:Oe},He=function(e){e.addAdapterType((function(){return new n({name:"SNPCoverageAdapter",adapterMetadata:{category:null,displayName:null,hiddenFromGUI:!0,description:null},getAdapterClass:function(){return Promise.resolve().then((function(){return je})).then((function(e){return e.default}))},configSchema:Re(e),adapterCapabilities:Oe})}))},Ve=a.ConfigurationSchema("SNPCoverageRenderer",{clipColor:{type:"color",description:"the color of the clipping marker",defaultValue:"red"},indicatorThreshold:{type:"number",description:"the proportion of reads containing a insertion/clip indicator",defaultValue:.3},drawArcs:{type:"boolean",description:"Draw sashimi-style arcs for intron features",defaultValue:!0},drawInterbaseCounts:{type:"boolean",description:'draw count "upsidedown histogram" 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l=t.get("strand"),s=t.get("xs"),c="rgb(255,200,200)",u="rgb(200,200,255)";e.strokeStyle="+"===s?c:"-"===s?u:1===l?c:-1===l?u:"rgb(200,200,200)",e.lineWidth=Math.log(t.get("score")+1),e.moveTo(a,b-2*v),e.bezierCurveTo(a,0,o,0,o,b-2*v),e.stroke()})),l&&(e.lineWidth=1,e.strokeStyle="rgba(140,140,140,0.8)",g.forEach((function(t){e.beginPath(),e.moveTo(0,Math.round(M(t))),e.lineTo(y,Math.round(M(t))),e.stroke()})))}}]),n}(),Ge=a.ConfigurationSchema("SNPCoverageRenderer",{},{baseConfiguration:Ve,explicitlyTyped:!0});function We(e){e.addRendererType((function(){return new ze({name:"SNPCoverageRenderer",ReactComponent:p.WiggleRendering,configSchema:Ge,pluginManager:e})}))}var Ue=function(e){ee(r,f.LayoutSession);var t=ne(r);function r(e){var n;return Z(this,r),(n=t.call(this,e)).showSoftClip=!1,n.config=e.config,n}return Y(r,[{key:"cachedLayoutIsValid",value:function(e){return ae(te(r.prototype),"cachedLayoutIsValid",this).call(this,e)&&this.showSoftClip===e.showSoftClip&&v(this.sortedBy,e.sortedBy)}},{key:"layout",get:function(){return this.cachedLayout&&this.cachedLayoutIsValid(this.cachedLayout)||(this.cachedLayout={layout:this.makeLayout(),config:a.readConfObject(this.config),filters:this.filters,sortedBy:this.sortedBy,showSoftClip:this.showSoftClip}),this.cachedLayout.layout}}]),r}();function Je(e){return{A:e.palette.bases.A.main,C:e.palette.bases.C.main,G:e.palette.bases.G.main,T:e.palette.bases.T.main,deletion:"#808080"}}var Xe={color_fwd_strand_not_proper:"#ECC8C8",color_rev_strand_not_proper:"#BEBED8",color_fwd_strand:"#EC8B8B",color_rev_strand:"#8F8FD8",color_fwd_missing_mate:"#D11919",color_rev_missing_mate:"#1919D1",color_fwd_diff_chr:"#000",color_rev_diff_chr:"#969696",color_pair_lr:"#c8c8c8",color_pair_rr:"navy",color_pair_rl:"teal",color_pair_ll:"green",color_nostrand:"#c8c8c8",color_interchrom:"orange",color_longinsert:"red",color_shortinsert:"pink"};function Qe(e){return!["methylation","modifications"].includes(e||"")}var Ze=function(e){ee(i,d);var t,n,o=ne(i);function i(){var e;return Z(this,i),(e=o.apply(this,arguments)).supportsSVG=!0,e}return Y(i,[{key:"getCharWidthHeight",value:function(e){return{charWidth:e.measureText("A").width,charHeight:e.measureText("M").width}}},{key:"layoutFeature",value:function(e){var t=e.feature,n=e.layout,a=e.bpPerPx,o=e.region,i=e.heightPx,l=e.displayMode,s=0,c=0;if(e.showSoftClip){var u=t.get("mismatches");if(t.get("seq"))for(var p=0;p<u.length;p+=1){var f=u[p],d=f.cliplen,g=void 0===d?0:d;"softclip"===f.type&&(0===f.start?s=g:c=g)}}var h=oe(r.bpSpanPx(t.get("start")-s,t.get("end")+c,o,a),2),m=h[0],y=h[1];if("compact"===l&&(i/=3),t.get("refName")!==o.refName)throw new Error("feature ".concat(t.id()," is not on the current region's reference sequence ").concat(o.refName));var v=n.addRect(t.id(),t.get("start")-s,t.get("end")+c,i);return null===v?null:{feature:t,leftPx:m,rightPx:y,topPx:"collapse"===l?0:v,heightPx:i}}},{key:"getExpandedRegion",value:function(e,t){var r=t.showSoftClip,n=a.readConfObject(t.config,"maxClippingSize"),o=e.start,i=e.end,l=Math.max(i-o,r?Math.round(n):0);return J(J({},e),{},{start:Math.floor(Math.max(o-l,0)),end:Math.ceil(i+l)})}},{key:"colorByOrientation",value:function(e,t){return Xe[this.getOrientation(e,t)||"color_nostrand"]}},{key:"getOrientation",value:function(e,t){var r=a.readConfObject(t,"orientationType");return{LR:"color_pair_lr",RR:"color_pair_rr",RL:"color_pair_rl",LL:"color_pair_ll"}[De[r][e.get("pair_orientation")]]}},{key:"colorByInsertSize",value:function(e,t){return e.get("is_paired")&&e.get("seq_id")!==e.get("next_seq_id")?"#555":"hsl(".concat(Math.abs(e.get("template_length"))/10,",50%,50%)")}},{key:"colorByStranded",value:function(e,t){var r=e.get("flags"),n=e.get("strand");if(1&r){var a=64&r?-1:1;return 2&r?n*a==1?"color_rev_strand":"color_fwd_strand":e.get("multi_segment_next_segment_unmapped")?n*a==1?"color_rev_missing_mate":"color_fwd_missing_mate":e.get("seq_id")===e.get("next_seq_id")?n*a==1?"color_rev_strand_not_proper":"color_fwd_strand_not_proper":1===n?"color_fwd_diff_chr":"color_rev_diff_chr"}return 1===n?"color_fwd_strand":"color_rev_strand"}},{key:"colorByPerBaseQuality",value:function(e,t,n,a,o){for(var i=t.feature,l=t.topPx,s=t.heightPx,c=(i.get("qual")||"").split(" 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n,i=t.positions,l=g(p[t.type]||"black"),u=fe(Ce(w,i));try{for(u.s();!(n=u.n()).done;){var f=n.value;if(f>=0&&y+f<v){var d=oe(r.bpSpanPx(y+f,y+f+1,a,o),2),m=d[0],b=d[1];e.fillStyle=l.alpha(h[x]+.1).hsl().string(),e.fillRect(m,s,b-m+.5,c)}x++}}catch(e){u.e(e)}finally{u.f()}}))}},{key:"colorByMethylation",value:function(e,t,n,a,o,i){var l=i.regionSequence,s=t.feature,c=t.topPx,u=t.heightPx,p=Ae(s,"MM","Mm")||"";if(!l)throw new Error("region sequence required for methylation");var f=s.get("CIGAR"),d=s.get("start"),g=s.get("end"),h=s.get("seq"),m=s.get("strand"),y=me(f),v=a.start,b=new Array(a.end-v).fill(0);we(p,h,m).forEach((function(e){var t=e.positions;if("m"===e.type&&t){var r,n=fe(Ce(y,t));try{for(n.s();!(r=n.n()).done;){var a=r.value+d-v;a>=0&&a<b.length&&(b[a]=1)}}catch(e){n.e(e)}finally{n.f()}}}));for(var C=d;C<g;C++){var w=C-v;if(w>=0&&w<b.length){var S=l[w].toLowerCase(),x=l[w+1].toLowerCase();if(o>2){if("c"===S&&"g"===x){var k=v+w,_=oe(r.bpSpanPx(k,k+2,a,o),2),E=_[0],P=_[1];e.fillStyle=b[w]||b[w+1]?"red":"blue",e.fillRect(E,c,P-E+.5,u)}}else if("c"===S&&"g"===x){var T=v+w,M=oe(r.bpSpanPx(T,T+1,a,o),2),R=M[0],N=M[1];e.fillStyle=b[w]?"red":"blue",e.fillRect(R,c,N-R+.5,u);var A=oe(r.bpSpanPx(T+1,T+2,a,o),2),D=A[0],B=A[1];e.fillStyle=b[w+1]?"red":"blue",e.fillRect(D,c,B-D+.5,u)}}}}},{key:"drawRect",value:function(e,t,n){var a=n.bpPerPx,o=t.heightPx,i=t.topPx,l=t.feature,s=oe(n.regions,1)[0],c=oe(r.bpSpanPx(l.get("start"),l.get("end"),s,a),2),u=c[0],p=c[1],f=s.reversed?-1:1,d=l.get("strand")*f;a<10?-1===d?(e.beginPath(),e.moveTo(u-5,i+o/2),e.lineTo(u,i+o),e.lineTo(p,i+o),e.lineTo(p,i),e.lineTo(u,i),e.closePath(),e.fill()):(e.beginPath(),e.moveTo(u,i),e.lineTo(u,i+o),e.lineTo(p,i+o),e.lineTo(p+5,i+o/2),e.lineTo(p,i),e.closePath(),e.fill()):e.fillRect(u,i,p-u,o)}},{key:"drawAlignmentRect",value:function(e,t,r){var n=r.defaultColor,o=r.config,i=r.bpPerPx,l=r.colorTagMap,s=void 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M=_[T],R=S+M.start,N=M.base,A=oe(r.bpSpanPx(R,R+M.length,w,y),2),D=A[0],B=Math.max(l,Math.abs(D-A[1]));if("mismatch"===M.type&&p){var I=o[M.base]||"#888";e.fillStyle=P(I,M),e.fillRect(D,b,B,v),B>=h&&v>=E&&(e.fillStyle=P(a.palette.getContrastText(I),M),e.fillText(N,D+(B-h)/2+1,b+v))}else if("deletion"===M.type&&d){var L=o.deletion;e.fillStyle=L,e.fillRect(D,b,B,v),B>=h&&v>=E&&(e.fillStyle=a.palette.getContrastText(L),e.fillText(N,D+(B-h)/2+1,b+v))}else if("insertion"===M.type&&d){e.fillStyle="purple";var F=D-1;(+M.base||M.length)<10&&(e.fillRect(F,b,k,v),1/y>=h&&(e.fillRect(F-k,b,3*k,1),e.fillRect(F-k,b+v-1,3*k,1)),1/y>=h&&v>=E&&e.fillText("(".concat(M.base,")"),D+2,b+v))}else if("hardclip"===M.type||"softclip"===M.type){e.fillStyle="hardclip"===M.type?"red":"blue";var q=D-1;e.fillRect(q,b+1,k,v-2),e.fillRect(q-k,b,3*k,1),e.fillRect(q-k,b+v-1,3*k,1),B>=h&&v>=E&&e.fillText("(".concat(M.base,")"),D+2,b+v)}else"skip"===M.type&&(D+B>0&&e.clearRect(D,b,B-(y>10?1.5:0),v),e.fillStyle="#333",e.fillRect(D,b+v/2,B,2))}if(d)for(var O=0;O<_.length;O+=1){var j=_[O],H=S+j.start,V=oe(r.bpSpanPx(H,H+j.length,w,y),1)[0],z=+j.base||j.length,G="".concat(z);if("insertion"===j.type&&z>=10)if(y>s)e.fillStyle="purple",e.fillRect(V-1,b,2,v);else if(v>m){var W=e.measureText(G);e.fillStyle="purple",e.fillRect(V-W.width/2-5,b,W.width+10,v),e.fillStyle="white",e.fillText(G,V-W.width/2,b+v)}else e.fillStyle="purple",e.fillRect(V-2,b,4,v)}}},{key:"drawSoftClipping",value:function(e,t,n,o,i){var l=t.feature,s=t.topPx,c=t.heightPx,u=n.bpPerPx,p=oe(n.regions,1)[0],f=a.readConfObject(o,"minSubfeatureWidth"),d=l.get("mismatches"),g=l.get("seq"),h=this.getCharWidthHeight(e),m=h.charWidth,y=h.charHeight,v={A:i.palette.bases.A.main,C:i.palette.bases.C.main,G:i.palette.bases.G.main,T:i.palette.bases.T.main,deletion:"#808080"};g&&d.filter((function(e){return"softclip"===e.type})).forEach((function(t){for(var n=t.cliplen||0,a=0===t.start?l.get("start")-n:l.get("start")+t.start,o=0;o<n;o+=1){var d=g.charAt(o+t.start);if(!d)return;var h=oe(r.bpSpanPx(a+o,a+o+1,p,u),2),b=h[0],C=Math.max(f,Math.abs(b-h[1])),w=v[d]||"#000000";e.fillStyle=w,e.fillRect(b,s,C,c),C>=m&&c>=y-5&&(e.fillStyle=i.palette.getContrastText(w),e.fillText(d,b+(C-m)/2+1,s+c))}}))}},{key:"makeImageData",value:(n=Q(ge.mark((function e(t,r,n){var o,i,l,s,c,p,f,d,g,h,m,y,v,b,C=this;return ge.wrap((function(e){for(;;)switch(e.prev=e.next){case 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t=this,n=e.layout,o=e.features,i=e.sortedBy,l=e.config,s=e.bpPerPx,c=e.showSoftClip,u=oe(e.regions,1)[0];if(!n)throw new Error("layout required");if(!n.addRect)throw new Error("invalid layout object");var p=null!=i&&i.type&&u.start===i.pos?function(e,t){var r=Array.from(e.values()),n=[],a=[],o=t.pos,i=t.type;r.forEach((function(e){var t=e,r=t.get("start"),i=t.get("end");y.doesIntersect2(o-1,o,r,i)?n.push(e):a.push(e)}));var l=!!r.length&&r[0].get("tags");switch(i){case"Start location":n.sort((function(e,t){return e.get("start")-t.get("start")}));break;case"tag":var s=t.tag,c=function(e,t){return l?e.get("tags")[t]:e.get(t)},u=n[0]&&"string"==typeof c(n[0],s);n.sort(u?function(e,t){return c(t,s).localeCompare(c(e,s))}:function(e,t){return(c(t,s)||0)-(c(e,s)||0)});break;case"Base pair":var p=[];n.forEach((function(e){e.get("mismatches").forEach((function(t){var r=e.get("start")+t.start+1;o>=r&&o<r+("insertion"===t.type||"softclip"===t.type?0:t.length)&&p.push([e.id(),t])}))}));var f=new Map(p);n.sort((function(e,t){var r=f.get(e.id()),n=f.get(t.id()),a=n&&n.base.toUpperCase(),o=r&&r.base.toUpperCase();return a===o&&"*"===a?r.length-n.length:(a?a.charCodeAt(0):0)-(o?o.charCodeAt(0):0)}));break;case"Read strand":n.sort((function(e,t){return e.get("strand")<=t.get("strand")?1:-1}))}return new Map(n.concat(a).map((function(e){return[e.id(),e]})))}(o,i):o,f=a.readConfObject(l,"height"),d=a.readConfObject(l,"displayMode");return r.iterMap(p.values(),(function(e){return t.layoutFeature({feature:e,layout:n,bpPerPx:s,region:u,showSoftClip:c,heightPx:f,displayMode:d})}),p.size)}},{key:"render",value:(t=Q(ge.mark((function e(t){var r,n,a,o,l,s,u,p,f,d,g,y,v,b,C,w,S,x,k,_=this;return ge.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return r=t.sessionId,n=t.bpPerPx,a=t.regions,o=t.adapterConfig.sequenceAdapter,e.next=4,this.getFeatures(t);case 4:if(l=e.sent,s=this.createLayoutInWorker(t),u=this.layoutFeats(J(J({},t),{},{features:l,layout:s})),p=oe(a,1),g=(f=p[0]).end,y=f.start,v=f.originalRefName,b=f.refName,!o){e.next=18;break}return e.next=12,m.getAdapter(this.pluginManager,r,o);case 12:return w=e.sent.dataAdapter,e.next=16,w.getFeatures(J(J({},f),{},{refName:v||b,end:f.end+1})).pipe(c.toArray()).toPromise();case 16:d=null===(C=e.sent[0])||void 0===C?void 0:C.get("seq");case 18:return S=(g-y)/n,x=Math.max(s.getTotalHeight(),1),e.next=22,h.renderToAbstractCanvas(S,x,t,(function(e){return _.makeImageData(e,u,J(J({},t),{},{layout:s,features:l,regionSequence:d}))}));case 22:return k=e.sent,e.next=25,ae(te(i.prototype),"render",this).call(this,J(J(J({},t),k),{},{features:l,layout:s,height:x,width:S}));case 25:return e.abrupt("return",J(J(J({},e.sent),k),{},{features:l,layout:s,height:x,width:S,maxHeightReached:s.maxHeightReached}));case 27:case"end":return e.stop()}}),e,this)}))),function(e){return t.apply(this,arguments)})},{key:"createSession",value:function(e){return new Ue(e)}}]),i}();function $e(e){var t=e.onMouseMove,n=e.blockKey,a=e.displayModel,o=e.width,i=e.height,l=e.bpPerPx,s=e.sortedBy,c=e.colorBy,p=a.selectedFeatureId,f=a.featureIdUnderMouse,d=a.contextMenuFeature,g=oe(e.regions,1)[0],h=C.useRef(null),m=oe(C.useState(!1),2),y=m[0],v=m[1],b=oe(C.useState(!1),2),S=b[0],x=b[1];function k(t,r){var n=e["onFeature".concat(t)],a=e["on".concat(t)];n&&f?n(r,f):a&&a(r,f)}C.useEffect((function(){var e,t,o=h.current;if(o){var i=o.getContext("2d");if(i){i.clearRect(0,0,o.width,o.height);var s=p?null===(e=a.getFeatureByID)||void 0===e?void 0:e.call(a,n,p):void 0;if(s){var c=oe(s,4),u=c[1],m=c[3],y=oe(r.bpSpanPx(c[0],c[2],g,l),2),v=y[0],b=y[1],C=Math.round(u),w=Math.round(m-u);i.shadowColor="#222266",i.shadowBlur=10,i.lineJoin="bevel",i.lineWidth=2,i.strokeStyle="#00b8ff",i.strokeRect(v-2,C-2,b-v+4,w+4),i.clearRect(v,C,b-v,w)}var S=f||(null==d?void 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function(e){k("MouseOut",e),k("MouseLeave",e)}(e)},onMouseOver:function(e){return function(e){k("MouseOver",e)}(e)},onMouseUp:function(e){return function(e){v(!1),k("MouseUp",e)}(e)},onMouseLeave:function(e){return function(e){k("MouseOut",e),k("MouseLeave",e)}(e)},onMouseMove:function(e){return function(e){y&&x(!0);var r=0,i=0;h.current&&(r=h.current.getBoundingClientRect().left,i=h.current.getBoundingClientRect().top),r=e.clientX-r;var s=a.getFeatureOverlapping(n,g.start+l*(g.reversed?o-r:r),i=e.clientY-i);t&&t(e,s)}(e)},onClick:function(e){return function(e){S||k("Click",e)}(e)},onContextMenu:function(e){return function(e){k("ContextMenu",e)}(e)},onFocus:function(){},onBlur:function(){}}))}var Ye=b.observer($e),Ke=a.ConfigurationSchema("PileupRenderer",{color:{type:"color",description:"the color of each feature in a pileup 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o.types.compose("LinearAlignmentsDisplay",k.BaseDisplay,o.types.model({PileupDisplay:o.types.maybe(e.getDisplayType("LinearPileupDisplay").stateModel),SNPCoverageDisplay:o.types.maybe(e.getDisplayType("LinearSNPCoverageDisplay").stateModel),snpCovHeight:45,type:o.types.literal("LinearAlignmentsDisplay"),configuration:a.ConfigurationReference(t),height:250,showCoverage:!0,showPileup:!0})).volatile((function(){return{scrollTop:0}})).actions((function(e){return{toggleCoverage:function(){e.showCoverage=!e.showCoverage},togglePileup:function(){e.showPileup=!e.showPileup},setScrollTop:function(t){e.scrollTop=t},setSNPCoverageHeight:function(t){e.snpCovHeight=t}}})).views((function(e){var t=e.trackMenuItems;return{get pileupDisplayConfig(){var t=a.getConf(e,"pileupDisplay"),n=r.getContainingTrack(e);return J(J({},t),{},{type:"LinearPileupDisplay",name:"".concat(a.getConf(n,"name")," pileup"),displayId:"".concat(e.configuration.displayId,"_pileup_xyz")})},getFeatureByID:function(t,r){return e.PileupDisplay.getFeatureByID(t,r)},searchFeatureByID:function(t){return e.PileupDisplay.searchFeatureByID(t)},get features(){return e.PileupDisplay.features},get DisplayBlurb(){var t;return null===(t=e.PileupDisplay)||void 0===t?void 0:t.DisplayBlurb},get sortedBy(){return e.PileupDisplay.sortedBy},get sortedByPosition(){return e.PileupDisplay.sortedByPosition},get sortedByRefName(){return e.PileupDisplay.sortedByRefName},get snpCoverageDisplayConfig(){var t=a.getConf(e,"snpCoverageDisplay"),n=r.getContainingTrack(e);return J(J({},t),{},{type:"LinearSNPCoverageDisplay",name:"".concat(a.getConf(n,"name")," snp coverage"),displayId:"".concat(e.configuration.displayId,"_snpcoverage_xyz")})},trackMenuItems:function(){return[].concat(ie(t()),[{type:"subMenu",label:"Pileup settings",subMenu:e.PileupDisplay.trackMenuItems()},{type:"subMenu",label:"SNPCoverage 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Q(ge.mark((function r(){var n;return ge.wrap((function(r){for(;;)switch(r.prev=r.next){case 0:return n=e.height-e.SNPCoverageDisplay.height,r.next=3,_.when((function(){return e.PileupDisplay.ready}));case 3:return r.t0=w,r.t1=w.Fragment,r.t2=w,r.next=8,e.SNPCoverageDisplay.renderSvg(t);case 8:return r.t3=r.sent,r.t4=r.t2.createElement.call(r.t2,"g",null,r.t3),r.t5=w,r.t6={transform:"translate(0 ".concat(e.SNPCoverageDisplay.height,")")},r.next=14,e.PileupDisplay.renderSvg(J(J({},t),{},{overrideHeight:n}));case 14:return r.t7=r.sent,r.t8=r.t5.createElement.call(r.t5,"g",r.t6,r.t7),r.abrupt("return",r.t0.createElement.call(r.t0,r.t1,null,r.t4,r.t8));case 17:case"end":return r.stop()}}),r)})))()}}}))};function rt(e){var t=e.model,r=t.PileupDisplay,n=t.SNPCoverageDisplay,o=t.showPileup,i=t.showCoverage;return w.createElement("div",{"data-testid":"display-".concat(a.getConf(t,"displayId")),style:{position:"relative"}},w.createElement("div",{"data-testid":"Blockset-snpcoverage"},i?w.createElement(n.RenderingComponent,{model:n}):null),w.createElement(u.ResizeHandle,{onDrag:function(e){return n?(n.setHeight(n.height+e),e):0},style:{position:"absolute",top:i?n.height+2:0,height:3}}),w.createElement("div",{"data-testid":"Blockset-pileup",style:{position:"absolute",top:i?n.height+5:0,height:3}},o?w.createElement(r.RenderingComponent,{model:r}):null))}var nt=b.observer(rt);function at(e){e.addDisplayType((function(){var t=function(e){var t=e.getDisplayType("LinearPileupDisplay").configSchema,r=e.getDisplayType("LinearSNPCoverageDisplay").configSchema;return a.ConfigurationSchema("LinearAlignmentsDisplay",{pileupDisplay:t,snpCoverageDisplay:r},{baseConfiguration:x.baseLinearDisplayConfigSchema,explicitlyTyped:!0})}(e);return new 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t;return"modifications"!==(null===(t=e.colorBy)||void 0===t?void 0:t.type)||Object.keys(JSON.parse(JSON.stringify(e.modificationTagMap))).length>0},renderProps:function(){return J(J({},t()),{},{notReady:!e.ready||!this.modificationsReady,filters:e.filters,modificationTagMap:JSON.parse(JSON.stringify(e.modificationTagMap)),colorBy:e.colorBy?o.getSnapshot(e.colorBy):void 0})}}})).actions((function(e){return{toggleDrawIndicators:function(){e.drawIndicators=!e.drawIndicatorsSetting},toggleDrawInterbaseCounts:function(){e.drawInterbaseCounts=!e.drawInterbaseCountsSetting},toggleDrawArcs:function(){e.drawArcs=!e.drawArcsSetting},afterAttach:function(){o.addDisposer(e,_.autorun(Q(ge.mark((function t(){var n,o,i;return ge.wrap((function(t){for(;;)switch(t.prev=t.next){case 0:if(t.prev=0,n=e.colorBy,o=r.getContainingView(e),i=o.staticBlocks,"modifications"!==(null==n?void 0:n.type)){t.next=8;break}return t.next=6,ut(e,a.getConf(e.parentTrack,"adapter"),n,i);case 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r=e.filterBy,n=r.flagInclude,a=r.flagExclude,o=r.tagFilter,i=r.readName;if(t=["jexl:get(feature,'snpinfo') != undefined ? true : "+"((get(feature,'flags')&".concat(n,")==").concat(n,") && ")+"!((get(feature,'flags')&".concat(a,"))")],o){var l=o.tag,s=o.value;t.push("jexl:get(feature,'snpinfo') != undefined ? true : "+'"'.concat(s,"\" =='*' ? getTag(feature,\"").concat(l,'") != undefined : ')+'getTag(feature,"'.concat(l,'") == "').concat(s,'"'))}i&&t.push("jexl:get(feature,'snpinfo') != undefined ? true : "+"get(feature,'name') == \"".concat(i,'"'))}return new E({filters:t})}}}))};function gt(e){e.addDisplayType((function(){var t=function(e){var t=e.getRendererType("SNPCoverageRenderer").configSchema;return a.ConfigurationSchema("LinearSNPCoverageDisplay",{autoscale:{type:"stringEnum",defaultValue:"local",model:o.types.enumeration("Autoscale type",["local"]),description:"performs local autoscaling (no other options for SNP Coverage 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S({name:"LinearSNPCoverageDisplay",configSchema:t,stateModel:dt(e,t),trackType:"AlignmentsTrack",viewType:"LinearGenomeView",ReactComponent:p.LinearWiggleDisplayReactComponent})}))}function ht(e){var t=e.model,r=t.sortedBy;return r?w.createElement("div",{"data-testid":"blurb-".concat(t.sortedBy),style:{backgroundColor:"white"}},w.createElement(I,{color:"secondary",variant:"caption"},t.sortedBy?"Sorted by ".concat(r.type.toLowerCase()," at ").concat(r.refName,":").concat(r.pos):null)):null}var mt=b.observer(ht),yt=["uniqueId"],vt=C.lazy((function(){return Promise.resolve().then((function(){return Vt}))})),bt=C.lazy((function(){return Promise.resolve().then((function(){return Jt}))})),Ct=C.lazy((function(){return Promise.resolve().then((function(){return Zt}))})),wt=C.lazy((function(){return Promise.resolve().then((function(){return Kt}))})),St=C.lazy((function(){return Promise.resolve().then((function(){return rr}))})),xt=C.lazy((function(){return Promise.resolve().then((function(){return ir}))})),kt=new Map([["pileup","PileupRenderer"],["svg","SvgFeatureRenderer"]]),_t=function(e){return o.types.compose("LinearPileupDisplay",x.BaseLinearDisplay,o.types.model({type:o.types.literal("LinearPileupDisplay"),configuration:a.ConfigurationReference(e),showSoftClipping:!1,featureHeight:o.types.maybe(o.types.number),noSpacing:o.types.maybe(o.types.boolean),fadeLikelihood:o.types.maybe(o.types.boolean),trackMaxHeight:o.types.maybe(o.types.number),mismatchAlpha:o.types.maybe(o.types.boolean),sortedBy:o.types.maybe(o.types.model({type:o.types.string,pos:o.types.number,tag:o.types.maybe(o.types.string),refName:o.types.string,assemblyName:o.types.string})),colorBy:o.types.maybe(o.types.model({type:o.types.string,tag:o.types.maybe(o.types.string),extra:o.types.frozen()})),filterBy:o.types.optional(o.types.model({flagInclude:o.types.optional(o.types.number,0),flagExclude:o.types.optional(o.types.number,1540),readName:o.types.maybe(o.types.string),tagFilter:o.types.maybe(o.types.model({tag:o.types.string,value:o.types.string}))}),{})})).volatile((function(){return{colorTagMap:_.observable.map({}),modificationTagMap:_.observable.map({}),ready:!1,currBpPerPx:0}})).actions((function(e){return{setReady:function(t){e.ready=t},setCurrBpPerPx:function(t){e.currBpPerPx=t},setMaxHeight:function(t){e.trackMaxHeight=t},setFeatureHeight:function(t){e.featureHeight=t},setNoSpacing:function(t){e.noSpacing=t},setColorScheme:function(t){e.colorTagMap=_.observable.map({}),e.colorBy=o.cast(t),e.ready=!1},updateModificationColorMap:function(t){var r=["red","blue","green","orange","purple"];t.forEach((function(t){if(!e.modificationTagMap.has(t)){var n=ie(e.modificationTagMap.keys()).length;e.modificationTagMap.set(t,r[n])}}))},updateColorTagMap:function(t){var r=["#BBCCEE","pink","#CCDDAA","#EEEEBB","#FFCCCC","lightblue","lightgreen","tan","#CCEEFF","lightsalmon"];t.forEach((function(t){if(!e.colorTagMap.has(t)){var n=ie(e.colorTagMap.keys()).length;e.colorTagMap.set(t,r[n])}}))}}})).actions((function(e){return{afterAttach:function(){o.addDisposer(e,_.autorun(Q(ge.mark((function t(){var n,o,i,l,s,c,u,p;return ge.wrap((function(t){for(;;)switch(t.prev=t.next){case 0:if(t.prev=0,n=r.getSession(e),o=n.rpcManager,i=e.sortedBy,l=e.colorBy,s=r.getContainingView(e),null==l||!l.tag){t.next=9;break}return t.next=7,st(e,l,s.staticBlocks);case 7:e.updateColorTagMap(t.sent);case 9:if("modifications"!==(null==l?void 0:l.type)){t.next=14;break}return t.next=12,ut(e,a.getConf(e.parentTrack,["adapter"]),l,s.staticBlocks);case 12:e.updateModificationColorMap(t.sent);case 14:if(!i){t.next=23;break}return p={start:c=i.pos,end:c+1,refName:i.refName,assemblyName:u=i.assemblyName},t.next=19,e.rendererType.renderInClient(o,J({assemblyName:u,regions:[p],adapterConfig:e.adapterConfig,rendererType:e.rendererType.name,sessionId:P.getRpcSessionId(e),timeout:1e6},e.renderProps()));case 19:e.setReady(!0),e.setCurrBpPerPx(s.bpPerPx),t.next=24;break;case 23:e.setReady(!0);case 24:t.next=30;break;case 26:t.prev=26,t.t0=t.catch(0),console.error(t.t0),e.setError(t.t0);case 30:case"end":return t.stop()}}),t,null,[[0,26]])}))),{delay:1e3}))},selectFeature:function(t){var n=r.getSession(e);if(r.isSessionModelWithWidgets(n)){var a=n.addWidget("AlignmentsFeatureWidget","alignmentFeature",{featureData:t.toJSON(),view:r.getContainingView(e)});n.showWidget(a)}n.setSelection(t)},clearSelected:function(){e.sortedBy=void 0},copyFeatureToClipboard:function(t){var n=function(e,t){if(null==e)return{};var 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maxHeight(){var t=a.getConf(e,["renderers",e.rendererTypeName])||{};return void 0!==e.trackMaxHeight?e.trackMaxHeight:t.maxHeight},get rendererConfig(){var t=a.getConf(e,["renderers",e.rendererTypeName])||{};return e.rendererType.configSchema.create(J(J({},t),{},{height:e.featureHeight,noSpacing:e.noSpacing,maxHeight:this.maxHeight,mismatchAlpha:e.mismatchAlpha}),o.getEnv(e))},get featureHeightSetting(){return e.featureHeight||a.readConfObject(this.rendererConfig,"height")},get mismatchAlphaSetting(){return void 0!==e.mismatchAlpha?e.mismatchAlpha:a.readConfObject(this.rendererConfig,"mismatchAlpha")}}})).views((function(e){var t=e.trackMenuItems,n=e.renderProps;return{get rendererTypeName(){var t=a.getConf(e,"defaultRendering"),r=kt.get(t);if(!r)throw new Error("unknown alignments view name ".concat(t));return r},contextMenuItems:function(){var t=e.contextMenuFeature;return t?[{label:"Open feature 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J(J({},n()),{},{notReady:!a||l&&e.currBpPerPx!==t.bpPerPx,rpcDriverName:c,displayModel:e,sortedBy:l,colorBy:s,colorTagMap:JSON.parse(JSON.stringify(o)),modificationTagMap:JSON.parse(JSON.stringify(i)),filters:this.filters,showSoftClip:e.showSoftClipping,config:e.rendererConfig})},trackMenuItems:function(){return[].concat(ie(t()),[{label:"Show soft clipping",icon:T,type:"checkbox",checked:e.showSoftClipping,onClick:function(){e.toggleSoftClipping(),e.showSoftClipping&&e.clearSelected()}},{label:"Sort by",icon:A,disabled:e.showSoftClipping,subMenu:[].concat(ie(["Start location","Read strand","Base pair"].map((function(t){return{label:t,onClick:function(){return e.setSortedBy(t)}}}))),[{label:"Sort by tag...",onClick:function(){r.getSession(e).queueDialog((function(t){return[Ct,{model:e,handleClose:t}]}))}},{label:"Clear sort",onClick:function(){return e.clearSelected()}}])},{label:"Color scheme",icon:D,subMenu:[{label:"Normal",onClick:function(){e.setColorScheme({type:"normal"})}},{label:"Mapping quality",onClick:function(){e.setColorScheme({type:"mappingQuality"})}},{label:"Strand",onClick:function(){e.setColorScheme({type:"strand"})}},{label:"Pair orientation",onClick:function(){e.setColorScheme({type:"pairOrientation"})}},{label:"Per-base quality",onClick:function(){e.setColorScheme({type:"perBaseQuality"})}},{label:"Modifications or methylation",onClick:function(){r.getSession(e).queueDialog((function(t){return[xt,{model:e,handleClose:t}]}))}},{label:"Insert size",onClick:function(){e.setColorScheme({type:"insertSize"})}},{label:"Stranded paired-end",onClick:function(){e.setColorScheme({type:"reverseTemplate"})}},{label:"Color by tag...",onClick:function(){r.getSession(e).queueDialog((function(t){return[vt,{model:e,handleClose:t}]}))}}]},{label:"Filter by",icon:B,onClick:function(){r.getSession(e).queueDialog((function(t){return[bt,{model:e,handleClose:t}]}))}},{label:"Set feature height",onClick:function(){r.getSession(e).queueDialog((function(t){return[wt,{model:e,handleClose:t}]}))}},{label:"Set max height",onClick:function(){r.getSession(e).queueDialog((function(t){return[St,{model:e,handleClose:t}]}))}},{label:"Fade mismatches by quality",type:"checkbox",checked:e.mismatchAlphaSetting,onClick:function(){e.toggleMismatchAlpha()}}])}}}))};function Et(e){e.addDisplayType((function(){var t=function(e){var t=e.getRendererType("PileupRenderer").configSchema,r=e.getRendererType("SvgFeatureRenderer").configSchema;return a.ConfigurationSchema("LinearPileupDisplay",{defaultRendering:{type:"stringEnum",model:o.types.enumeration("Rendering",["pileup","svg"]),defaultValue:"pileup"},renderers:a.ConfigurationSchema("RenderersConfiguration",{PileupRenderer:t,SvgFeatureRenderer:r}),renderer:"",maxDisplayedBpPerPx:{type:"number",description:"maximum bpPerPx that is displayed in the view",defaultValue:100},colorScheme:{type:"stringEnum",model:o.types.enumeration("colorScheme",["strand","normal","insertSize","insertSizeAndOrientation","mappingQuality","tag"]),description:"color scheme to use",defaultValue:"normal"}},{baseConfiguration:x.linearBasicDisplayConfigSchemaFactory(e),explicitlyTyped:!0})}(e);return new S({name:"LinearPileupDisplay",configSchema:t,stateModel:_t(t),trackType:"AlignmentsTrack",viewType:"LinearGenomeView",ReactComponent:x.BaseLinearDisplayComponent})}))}function Pt(e){e.addTrackType((function(){var t=function(e){return a.ConfigurationSchema("AlignmentsTrack",{},{baseConfiguration:k.createBaseTrackConfig(e)})}(e),r=new L({name:"AlignmentsTrack",configSchema:t,stateModel:k.createBaseTrackModel(e,"AlignmentsTrack",t)}),n=e.getDisplayType("LinearAlignmentsDisplay");return r.addDisplayType(n),r}))}var Tt=a.ConfigurationSchema("AlignmentsFeatureWidget",{});function Mt(e){return o.types.model("AlignmentsFeatureWidget",{id:F.ElementId,type:o.types.literal("AlignmentsFeatureWidget"),featureData:o.types.frozen(),view:o.types.safeReference(e.pluggableMstType("view","stateModel"))}).actions((function(e){return{setFeatureData:function(t){e.featureData=t},clearFeatureData:function(){e.featureData=void 0}}}))}function Rt(e){e.addWidgetType((function(){return new q({name:"AlignmentsFeatureWidget",heading:"Feature details",configSchema:Tt,stateModel:Mt(e),ReactComponent:C.lazy((function(){return Promise.resolve().then((function(){return gr}))}))})}))}var Nt=function(e){ee(o,O);var t,n,a=ne(o);function o(){var e;return Z(this,o),(e=a.apply(this,arguments)).name="PileupGetGlobalValueForTag",e}return Y(o,[{key:"serializeArguments",value:(n=Q(ge.mark((function e(t,n){var a,i,l,s;return ge.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:if(l=null==(i=this.pluginManager.rootModel)||null===(a=i.session)||void 0===a?void 0:a.assemblyManager){e.next=4;break}throw new Error("no assembly manager available");case 4:return e.next=6,r.renameRegionsIfNeeded(l,t);case 6:return s=e.sent,e.abrupt("return",ae(te(o.prototype),"serializeArguments",this).call(this,s,n));case 8:case"end":return e.stop()}}),e,this)}))),function(e,t){return n.apply(this,arguments)})},{key:"execute",value:(t=Q(ge.mark((function e(t,r){var n,a,o,i,l,s,u,p;return ge.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.deserializeArguments(t,r);case 2:return a=(n=e.sent).adapterConfig,o=n.sessionId,i=n.regions,l=n.tag,e.next=6,m.getAdapter(this.pluginManager,o,a);case 6:return s=e.sent.dataAdapter.getFeaturesInMultipleRegions(i),e.next=10,s.pipe(c.toArray()).toPromise();case 10:return u=e.sent,p=new Set,u.forEach((function(e){var t=e.get("tags"),r=t?t[l]:e.get(l);void 0!==r&&p.add("".concat(r))})),e.abrupt("return",ie(p));case 14:case"end":return e.stop()}}),e,this)}))),function(e,r){return t.apply(this,arguments)})}]),o}(),At=function(e){ee(o,O);var t,n,a=ne(o);function o(){var e;return Z(this,o),(e=a.apply(this,arguments)).name="PileupGetVisibleModifications",e}return Y(o,[{key:"serializeArguments",value:(n=Q(ge.mark((function e(t,n){var a,i,l,s;return ge.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:if(l=null==(i=this.pluginManager.rootModel)||null===(a=i.session)||void 0===a?void 0:a.assemblyManager){e.next=4;break}throw new Error("no assembly manager available");case 4:return e.next=6,r.renameRegionsIfNeeded(l,t);case 6:return s=e.sent,e.abrupt("return",ae(te(o.prototype),"serializeArguments",this).call(this,s,n));case 8:case"end":return 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t(e)})),e.addToExtensionPoint("Core-guessAdapterForLocation",(function(e){return function(t,r,n){var a=P.getFileName(t);return/\.cram$/i.test(a)||"CramAdapter"===n?{type:"CramAdapter",cramLocation:t,craiLocation:r||P.makeIndex(t,".crai")}:e(t,r,n)}})),e.addToExtensionPoint("Core-guessAdapterForLocation",(function(e){return function(t,r,n){var a=P.getFileName(t),o=r&&P.getFileName(r);return/\.bam$/i.test(a)||"BamAdapter"===n?{type:"BamAdapter",bamLocation:t,index:{location:r||P.makeIndex(t,".bai"),indexType:P.makeIndexType(o,"CSI","BAI")}}:e(t,r,n)}})),e.addToExtensionPoint("Core-guessTrackTypeForLocation",(function(e){return function(t){return"BamAdapter"===t||"CramAdapter"===t?"AlignmentsTrack":e(t)}})),e.addRpcMethod((function(){return new Nt(e)})),e.addRpcMethod((function(){return new At(e)}))}}]),n}(),Bt=function(){function e(t,r){Z(this,e),this.record=t,this._store=r}return Y(e,[{key:"_get_name",value:function(){return this.record.readName}},{key:"_get_start",value:function(){return this.record.alignmentStart-1}},{key:"_get_end",value:function(){return this.record.alignmentStart+this.record.lengthOnRef-1}},{key:"_get_cram_read_features",value:function(){return this.record.readFeatures}},{key:"_get_type",value:function(){return"match"}},{key:"_get_score",value:function(){return this.record.mappingQuality}},{key:"_get_flags",value:function(){return this.record.flags}},{key:"_get_strand",value:function(){return this.record.isReverseComplemented()?-1:1}},{key:"_read_group_id",value:function(){var e=this._store.samHeader.readGroups;return e?e[this.record.readGroupId]:void 0}},{key:"_get_qual",value:function(){return(this.record.qualityScores||[]).join(" ")}},{key:"qualRaw",value:function(){return this.record.qualityScores}},{key:"_get_seq_id",value:function(){return this._store.refIdToName(this.record.sequenceId)}},{key:"_get_refName",value:function(){return this._get_seq_id()}},{key:"_get_is_paired",value:function(){return!!this.record.mate}},{key:"_get_pair_orientation",value:function(){return this.record.isPaired()?this.record.getPairOrientation():void 0}},{key:"_get_template_length",value:function(){return this.record.templateLength||this.record.templateSize}},{key:"_get_next_seq_id",value:function(){return this.record.mate?this._store.refIdToName(this.record.mate.sequenceId):void 0}},{key:"_get_next_pos",value:function(){return this.record.mate?this.record.mate.alignmentStart:void 0}},{key:"_get_next_segment_position",value:function(){return this.record.mate?"".concat(this._store.refIdToName(this.record.mate.sequenceId),":").concat(this.record.mate.alignmentStart):void 0}},{key:"_get_tags",value:function(){var e=this._read_group_id(),t=this.record.tags;return void 0!==e?J(J({},t),{},{RG:e}):t}},{key:"_get_seq",value:function(){return this.record.getReadBases()}},{key:"_get_CIGAR",value:function(){var e="",t="",r="M",n=0,a=this.record._refRegion.seq,o=this.record._refRegion.start,i=this.record.alignmentStart,l=0;return void 0!==this.record.readFeatures?this.record.readFeatures.forEach((function(s){var c=s.code,u=s.refPos,p=s.sub,f=s.data;if(l=u-i,e+=a.substring(i-o,u-o),i=u,n&&"M"!==r&&(t+=n+r,n=0),l&&(r="M",n+=l),"b"===c){var d=f.split(","),g=String.fromCharCode.apply(String,ie(d));e+=g,i+=g.length,n+=g.length}else"B"===c||"X"===c?(e+=p,i++,n++):"D"===c||"N"===c?(i+=f,n&&(t+=n+r),t+=f+c,n=0):"I"===c||"S"===c?(e+=f,n&&(t+=n+r),t+=f.length+c,n=0):"i"===c?(e+=f,n&&(t+=n+r),t+="".concat(1,"I"),n=0):"P"===c?(n&&(t+=n+r),t+="".concat(f,"P")):"H"===c&&(n&&(t+=n+r),t+="".concat(f,"H"),n=0)})):l=this.record.readLength-e.length,e.length!==this.record.readLength&&(e+=a.substring(i-o,i-o+(l=this.record.readLength-e.length)),n&&"M"!==r&&(t+=n+r,n=0),r="M",n+=l),n&&(t+=n+r),t}},{key:"tags",value:function(){return Object.getOwnPropertyNames(e.prototype).filter((function(e){return 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e=this.get("cram_read_features"),t=this.qualRaw();if(!e)return[];var r=this.get("start"),n=[];return e.forEach((function(e){var a=e.code,o=e.data,i=e.refPos-1-r;if("X"===a)n.push({start:i,length:1,base:e.sub,qual:null==t?void 0:t[e.pos],altbase:e.ref,type:"mismatch"});else if("I"===a)n.push({start:i,type:"insertion",base:"".concat(o.length),length:0});else if("N"===a)n.push({type:"skip",length:o,start:i,base:"N"});else if("S"===a){var l=o.length;n.push({start:i,type:"softclip",base:"S".concat(l),cliplen:l,length:1})}else if("P"===a);else if("H"===a){var s=o;n.push({start:i,type:"hardclip",base:"H".concat(s),cliplen:s,length:1})}else"D"===a?n.push({type:"deletion",length:o,start:i,base:"*"}):"b"===a||"q"===a||"B"===a||"i"===a&&n.push({start:i,type:"insertion",base:o,length:1})})),n}},{key:"_get_skips_and_dels",value:function(){return this._get_mismatches()}}]),e}(),It={__proto__:null,default:function(e){ee(f,i.BaseFeatureDataAdapter);var t,n,o,l,u,p=ne(f);function f(){var e;return 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12:if(!((o=e.sent.dataAdapter)instanceof i.BaseFeatureDataAdapter)){e.next=18;break}this.sequenceAdapter=o,e.next=19;break;case 18:throw new Error("CRAM feature adapters cannot use sequence adapters of type '".concat(n,"'"));case 19:return e.abrupt("return",{sequenceAdapter:this.sequenceAdapter});case 20:case"end":return e.stop()}}),e,this)}))),function(){return u.apply(this,arguments)})},{key:"getHeader",value:(l=Q(ge.mark((function e(t){return ge.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.configure();case 2:return e.abrupt("return",this.cram.cram.getHeaderText(t));case 3:case"end":return e.stop()}}),e,this)}))),function(e){return l.apply(this,arguments)})},{key:"seqFetch",value:(o=Q(ge.mark((function e(t,r,n){var a,o,i,l,s;return ge.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:if(r-=1,a=this.sequenceAdapter){e.next=4;break}return e.abrupt("return",void 0);case 4:if(o=this.refIdToOriginalName(t)||this.refIdToName(t)){e.next=7;break}return e.abrupt("return",void 0);case 7:return i=a.getFeatures({refName:o,start:r,end:n,assemblyName:""},{}),e.next=10,i.pipe(c.toArray()).toPromise();case 10:if(l=[],e.sent.sort((function(e,t){return e.get("start")-t.get("start")})).forEach((function(e){var t=e.get("start"),a=e.get("end"),o=Math.max(r-t,0),i=Math.min(n-t,a-t)-o,s=e.get("seq")||e.get("residues");l.push(s.substr(o,i))})),(s=l.join("")).length===n-r){e.next=16;break}throw new Error("sequence fetch failed: fetching ".concat(o,":").concat((r-1).toLocaleString(),"-").concat(n.toLocaleString()," returned ").concat(s.length.toLocaleString()," bases, but should have returned ").concat((n-r).toLocaleString()));case 16:return e.abrupt("return",s);case 17:case"end":return e.stop()}}),e,this)}))),function(e,t,r){return o.apply(this,arguments)})},{key:"setup",value:(n=Q(ge.mark((function e(t){var r,n,a=this;return ge.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return n=void 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0===i?function(){}:i,c=e.refName,u=e.start,p=e.end,f=e.originalRefName;return s.ObservableCreate(function(){var e=Q(ge.mark((function e(a){var i,s;return ge.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,n.setup(t);case 2:if(!n.sequenceAdapter||n.seqIdToRefName){e.next=6;break}return e.next=5,n.sequenceAdapter.getRefNames(t);case 5:n.seqIdToRefName=e.sent;case 6:if(void 0===(i=n.refNameToId(c))){e.next=15;break}return f&&(n.seqIdToOriginalRefName[i]=f),l("Downloading alignments"),e.next=12,n.cram.getRecordsForRange(i,u,p,t);case 12:s=e.sent,r.checkAbortSignal(o),s.forEach((function(e){a.next(n.cramRecordToFeature(e))}));case 15:l(""),a.complete();case 17:case"end":return e.stop()}}),e)})));return function(t){return e.apply(this,arguments)}}(),o)}},{key:"freeResources",value:function(){}},{key:"cramRecordToFeature",value:function(e){return new Bt(e,this)}}]),f}()},Lt=function(){function e(t,r,n){Z(this,e),this.record=t,this.adapter=r,this.ref=n}return Y(e,[{key:"_get_name",value:function(){return this.record.get("name")}},{key:"_get_type",value:function(){return"match"}},{key:"_get_score",value:function(){return this.record.get("mq")}},{key:"_get_flags",value:function(){return this.record.flags}},{key:"_get_strand",value:function(){return this.record.isReverseComplemented()?-1:1}},{key:"_get_read_group_id",value:function(){return this.record.readGroupId}},{key:"_get_pair_orientation",value:function(){return this.record.isPaired()?this.record.getPairOrientation():void 0}},{key:"_get_next_seq_id",value:function(){return this.record._next_refid()}},{key:"_get_seq_id",value:function(){return this.record._refID}},{key:"_get_next_refName",value:function(){return this.adapter.refIdToName(this.record._next_refid())}},{key:"_get_next_segment_position",value:function(){return this.record.isPaired()?"".concat(this.adapter.refIdToName(this.record._next_refid()),":").concat(this.record._next_pos()+1):void 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