@jbrowse/plugin-alignments 1.7.0 → 1.7.1

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

@@ -1,2 +0,0 @@
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Pe=ke.get("strand"),Re=ke.get("xs"),Me="rgba(255,200,200,0.7)",Ne="rgba(200,200,255,0.7)";e.strokeStyle="+"===Re?Me:"-"===Re?Ne:1===Pe?Me:-1===Pe?Ne:"rgba(200,200,200,0.7)",e.lineWidth=Math.log(ke.get("score")+1),e.moveTo(Ee,w-2*b),e.bezierCurveTo(Ee,0,Te,0,Te,w-2*b),e.stroke()}s&&(e.lineWidth=1,e.strokeStyle="rgba(140,140,140,0.8)",h.values.forEach((function(t){e.beginPath(),e.moveTo(0,Math.round(R(t))),e.lineTo(v,Math.round(R(t))),e.stroke()})))}}}]),n}(),Qe=a.ConfigurationSchema("SNPCoverageRenderer",{},{baseConfiguration:Je,explicitlyTyped:!0});function Ze(e){e.addRendererType((function(){return new Xe({name:"SNPCoverageRenderer",ReactComponent:p.WiggleRendering,configSchema:Qe,pluginManager:e})}))}var $e=function(e){ee(r,d.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 oe(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 Ye(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"}}function Ke(e){return Object.fromEntries(Object.entries(Ye(e)).map((function(t){var r=ie(t,2);return[r[0],e.palette.getContrastText(r[1])]})))}var et={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 tt(e){return!["methylation","modifications"].includes(e||"")}var rt=function(e){ee(s,g);var t,n,o,i=ne(s);function s(){var e;return Z(this,s),(e=i.apply(this,arguments)).supportsSVG=!0,e}return Y(s,[{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,s=e.displayMode,c=0,l=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?c=g:l=g)}}var h=ie(r.bpSpanPx(t.get("start")-c,t.get("end")+l,o,a),2),m=h[0],y=h[1];if("compact"===s&&(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")-c,t.get("end")+l,i);return null===v?null:{feature:t,leftPx:m,rightPx:y,topPx:"collapse"===s?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,s=Math.max(i-o,r?Math.round(n):0);return J(J({},e),{},{start:Math.floor(Math.max(o-s,0)),end:Math.ceil(i+s)})}},{key:"colorByOrientation",value:function(e,t){return et[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"}[Ie[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:"colorByPerBaseLettering",value:function(e,t,n,a,o,i){for(var 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w=ie(r.bpSpanPx(f+g+v,f+g+v+1,a,o),1);e.fillRect(w[0],s,p+.5,c)}d+=m,g+=m}}}},{key:"colorByModifications",value:function(e,t,n,a,o,i){for(var s=t.feature,c=t.topPx,l=t.heightPx,u=i.modificationTagMap,p=void 0===u?{}:u,d=De(s,"MM","Mm")||"",g=De(s,"ML","Ml")||[],h=g?("string"==typeof g?g.split(",").map((function(e){return+e})):g).map((function(e){return e/255})):De(s,"MP","Mp").split("").map((function(e){return e.charCodeAt(0)-33})).map((function(e){return Math.min(1,e/50)})),m=s.get("CIGAR"),y=s.get("start"),v=s.get("end"),b=s.get("seq"),w=s.get("strand"),C=ve(m),S=xe(d,b,w),x=0,k=0;k<S.length;k++){var _,E=S[k],T=E.positions,P=f(p[E.type]||"black"),R=de(Se(C,T));try{for(R.s();!(_=R.n()).done;){var M=_.value;if(M>=0&&y+M<v){var N=ie(r.bpSpanPx(y+M,y+M+1,a,o),2),A=N[0],B=N[1];e.fillStyle=P.alpha(h[x]+.1).hsl().string(),e.fillRect(A,c,B-A+.5,l)}x++}}catch(e){R.e(e)}finally{R.f()}}}},{key:"colorByMethylation",value:function(e,t,n,a,o,i){var s=i.regionSequence,c=t.feature,l=t.topPx,u=t.heightPx,p=De(c,"MM","Mm")||"";if(!s)throw new Error("region sequence required for methylation");for(var f=c.get("CIGAR"),d=c.get("start"),g=c.get("end"),h=c.get("seq"),m=c.get("strand"),y=ve(f),v=a.start,b=new Array(a.end-v).fill(0),w=xe(p,h,m),C=0;C<w.length;C++){var S=w[C],x=S.positions;if("m"===S.type&&x){var k,_=de(Se(y,x));try{for(_.s();!(k=_.n()).done;){var E=k.value+d-v;E>=0&&E<b.length&&(b[E]=1)}}catch(e){_.e(e)}finally{_.f()}}}for(var T=d;T<g;T++){var P=T-v;if(P>=0&&P<b.length){var R=s[P].toLowerCase(),M=s[P+1].toLowerCase();if(o>2){if("c"===R&&"g"===M){var N=v+P,A=ie(r.bpSpanPx(N,N+2,a,o),2),B=A[0],D=A[1];e.fillStyle=b[P]||b[P+1]?"red":"blue",e.fillRect(B,l,D-B+.5,u)}}else if("c"===R&&"g"===M){var I=v+P,F=ie(r.bpSpanPx(I,I+1,a,o),2),L=F[0],O=F[1];e.fillStyle=b[P]?"red":"blue",e.fillRect(L,l,O-L+.5,u);var q=ie(r.bpSpanPx(I+1,I+2,a,o),2),j=q[0],H=q[1];e.fillStyle=b[P+1]?"red":"blue",e.fillRect(j,l,H-j+.5,u)}}}}},{key:"drawRect",value:function(e,t,n){var a=n.bpPerPx,o=t.heightPx,i=t.topPx,s=t.feature,c=ie(n.regions,1)[0],l=ie(r.bpSpanPx(s.get("start"),s.get("end"),c,a),2),u=l[0],p=l[1],f=c.reversed?-1:1,d=s.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,s=r.colorTagMap,c=void 0===s?{}:s,l=r.colorForBase,u=r.contrastForBase,p=r.charWidth,f=r.charHeight,d=r.colorBy||{},g=d.tag,h=void 0===g?"":g,m=d.type,y=void 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x=v.get("flags");e.fillStyle=16&x?"#c8dcc8":"#c8c8c8";break;case"normal":default:e.fillStyle=n?"#c8c8c8":a.readConfObject(o,"color",{feature:v})}switch(this.drawRect(e,t,r),y){case"perBaseQuality":this.colorByPerBaseQuality(e,t,o,b,i);break;case"perBaseLettering":this.colorByPerBaseLettering(e,t,o,b,i,{colorForBase:l,contrastForBase:u,charWidth:p,charHeight:f});break;case"modifications":this.colorByModifications(e,t,o,b,i,r);break;case"methylation":this.colorByMethylation(e,t,o,b,i,r)}}},{key:"drawMismatches",value:function(e,t,n,a){var o=a.minSubfeatureWidth,i=a.largeInsertionIndicatorScale,s=a.mismatchAlpha,c=a.drawSNPs,l=void 0===c||c,u=a.drawIndels,p=void 0===u||u,d=a.charWidth,g=a.charHeight,h=a.colorForBase,m=a.contrastForBase,y=n.bpPerPx,v=t.heightPx,b=t.topPx,w=t.feature,C=ie(n.regions,1)[0],S=w.get("start"),x=Math.min(1/y,2),k=Math.max(o,x),_=w.get("mismatches"),E=g-2;function T(e,t){var r=e;return s&&void 0!==t.qual&&(r=f(e).alpha(Math.min(1,t.qual/50)).hsl().string()),r}for(var P=C.reversed?1/y+1:-1,R=0;R<_.length;R+=1){var M=_[R],N=S+M.start,A=M.base,B=ie(r.bpSpanPx(N,N+M.length,C,y),2),D=B[0],I=B[1],F=Math.max(o,Math.abs(D-I));if("mismatch"===M.type&&l)e.fillStyle=T(h[M.base]||"#888",M),e.fillRect(D,b,F,v),F>=d&&v>=E&&(e.fillStyle=T(m[M.base],M),e.fillText(A,D+(F-d)/2+1,b+v));else if("deletion"===M.type&&p){e.fillStyle=h.deletion,e.fillRect(D,b,F,v);var L="".concat(M.length),O=r.measureText(L,10);F>=O&&v>=E&&(e.fillStyle=m.deletion,e.fillText(L,(D+I)/2-O/2,b+v))}else if("insertion"===M.type&&p){e.fillStyle="purple";var q=D+P,j=+M.base||M.length,H=Math.max(o,Math.min(1.2,1/y));j<10&&(e.fillRect(q,b,H,v),1/y>=d&&v>=E&&(e.fillRect(q-H,b,3*H,1),e.fillRect(q-H,b+v-1,3*H,1),e.fillText("(".concat(M.base,")"),q+3,b+v)))}else if("hardclip"===M.type||"softclip"===M.type){e.fillStyle="hardclip"===M.type?"red":"blue";var z=D+P;e.fillRect(z,b,k,v),1/y>=d&&v>=E&&(e.fillRect(z-k,b,3*k,1),e.fillRect(z-k,b+v-1,3*k,1),e.fillText("(".concat(M.base,")"),z+3,b+v))}else if("skip"===M.type&&D+F>0){var V=F-(y>10?1.5:0);e.clearRect(D,b,V,v),e.fillStyle="#333",e.fillRect(Math.max(0,D),b+v/2-1,V+(D<0?D:0),2)}}if(p)for(var G=0;G<_.length;G+=1){var W=_[G],U=S+W.start,J=ie(r.bpSpanPx(U,U+W.length,C,y),1)[0],X=+W.base||W.length,Q="".concat(X);if("insertion"===W.type&&X>=10)if(y>i)e.fillStyle="purple",e.fillRect(J-1,b,2,v);else if(v>g){var Z=e.measureText(Q);e.fillStyle="purple",e.fillRect(J-Z.width/2-5,b,Z.width+10,v),e.fillStyle="white",e.fillText(Q,J-Z.width/2,b+v)}else e.fillStyle="purple",e.fillRect(J-2,b,4,v)}}},{key:"drawSoftClipping",value:function(e,t,n,o,i){var s=t.feature,c=t.topPx,l=t.heightPx,u=n.bpPerPx,p=ie(n.regions,1)[0],f=a.readConfObject(o,"minSubfeatureWidth"),d=s.get("mismatches"),g=s.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=s.get("start"),o=0===t.start?a-n:a+t.start,d=0;d<n;d+=1){var h=g.charAt(d+t.start);if(!h)return;var b=ie(r.bpSpanPx(o+d,o+d+1,p,u),2),w=b[0],C=Math.max(f,Math.abs(w-b[1])),S=v[h]||"#000000";e.fillStyle=S,e.fillRect(w,c,C,l),C>=m&&l>=y-5&&(e.fillStyle=i.palette.getContrastText(S),e.fillText(h,w+(C-m)/2+1,c+l))}}))}},{key:"makeImageData",value:(o=Q(he.mark((function e(t,r,n){var o,i,s,c,l,p,f,d,g,h,m,y,v,b,w,C=this;return he.wrap((function(e){for(;;)switch(e.prev=e.next){case 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o.apply(this,arguments)})},{key:"layoutFeats",value:function(e){var t=this,n=e.layout,o=e.features,i=e.sortedBy,s=e.config,c=e.bpPerPx,l=e.showSoftClip,u=ie(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 s=!!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 c=t.tag,l=function(e,t){return s?e.get("tags")[t]:e.get(t)},u=n[0]&&"string"==typeof l(n[0],c);n.sort(u?function(e,t){return l(t,c).localeCompare(l(e,c))}:function(e,t){return(l(t,c)||0)-(l(e,c)||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(s,"height"),d=a.readConfObject(s,"displayMode");return r.iterMap(p.values(),(function(e){return t.layoutFeature({feature:e,layout:n,bpPerPx:c,region:u,showSoftClip:l,heightPx:f,displayMode:d})}),p.size)}},{key:"fetchSequence",value:(n=Q(he.mark((function e(t){var r,n,a,o,i;return he.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:if(r=t.sessionId,n=t.regions,a=t.adapterConfig.sequenceAdapter){e.next=4;break}return e.abrupt("return",void 0);case 4:return e.next=6,m.getAdapter(this.pluginManager,r,a);case 6:return o=e.sent.dataAdapter,i=ie(n,1),e.abrupt("return",Fe(i[0],o));case 10:case"end":return e.stop()}}),e,this)}))),function(e){return n.apply(this,arguments)})},{key:"render",value:(t=Q(he.mark((function e(t){var r,n,a,o,i,c,l,u,p,f,d,g,m=this;return he.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.getFeatures(t);case 2:if(n=e.sent,a=this.createLayoutInWorker(t),o=t.regions,i=t.bpPerPx,c=this.layoutFeats(J(J({},t),{},{features:n,layout:a})),l=ie(o,1),u=l[0],!n.size||!Oe(null===(r=t.colorBy)||void 0===r?void 0:r.type)){e.next=13;break}return e.next=10,this.fetchSequence(t);case 10:e.t0=e.sent,e.next=14;break;case 13:e.t0=void 0;case 14:return p=e.t0,f=(u.end-u.start)/i,d=Math.max(a.getTotalHeight(),1),e.next=20,h.renderToAbstractCanvas(f,d,t,(function(e){return m.makeImageData(e,c,J(J({},t),{},{layout:a,features:n,regionSequence:p}))}));case 20:return 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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,userFeatureScreenDensity:o.types.maybe(o.types.number)})).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")," 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this.setHeight(e.height+t)-r}}})).actions((function(e){return{afterAttach:function(){o.addDisposer(e,_.autorun((function(){e.SNPCoverageDisplay?v(e.snpCoverageDisplayConfig,o.getSnapshot(e.SNPCoverageDisplay.configuration))||(e.SNPCoverageDisplay.setHeight(e.snpCovHeight),e.SNPCoverageDisplay.setConfig(e.snpCoverageDisplayConfig)):e.setSNPCoverageDisplay(e.snpCoverageDisplayConfig),e.PileupDisplay?v(e.pileupDisplayConfig,o.getSnapshot(e.PileupDisplay.configuration))||e.PileupDisplay.setConfig(e.pileupDisplayConfig):e.setPileupDisplay(e.pileupDisplayConfig),e.PileupDisplay.filterBy&&!v(o.getSnapshot(e.PileupDisplay.filterBy),o.getSnapshot(e.SNPCoverageDisplay.filterBy))&&e.SNPCoverageDisplay.setFilterBy(o.getSnapshot(e.PileupDisplay.filterBy)),e.PileupDisplay.colorBy&&!v(o.getSnapshot(e.PileupDisplay.colorBy),e.SNPCoverageDisplay.colorBy?o.getSnapshot(e.SNPCoverageDisplay.colorBy):{})&&e.SNPCoverageDisplay.setColorBy(o.getSnapshot(e.PileupDisplay.colorBy))}))),o.addDisposer(e,_.autorun((function(){e.setSNPCoverageHeight(e.SNPCoverageDisplay.height)})))},renderSvg:function(t){return Q(he.mark((function r(){var n;return he.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=C,r.t1=C.Fragment,r.t2=C,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=C,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)})))()}}}))},ct=E.makeStyles((function(){return{resizeHandle:{height:2,position:"absolute",zIndex:2}}}));function lt(e){var t=e.model,r=t.PileupDisplay,n=t.SNPCoverageDisplay,o=t.showPileup,i=t.showCoverage,s=ct(),c=n.height;return C.createElement("div",{"data-testid":"display-".concat(a.getConf(t,"displayId")),style:{position:"relative"}},i?C.createElement(C.Fragment,null,C.createElement("div",{"data-testid":"Blockset-snpcoverage"},C.createElement(n.RenderingComponent,{model:n})),C.createElement(u.ResizeHandle,{onDrag:function(e){return n.setHeight(n.height+e),e},className:s.resizeHandle,style:{top:c}})):null,o?C.createElement("div",{"data-testid":"Blockset-pileup",style:{position:"absolute",top:i?n.height:0}},C.createElement(r.RenderingComponent,{model:r})):null)}var ut=b.observer(lt);function pt(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 S({name:"LinearAlignmentsDisplay",configSchema:t,stateModel:st(e,t),trackType:"AlignmentsTrack",viewType:"LinearGenomeView",ReactComponent:ut})}))}var ft=function(e){return e.toLocaleString("en-US")},dt=C.forwardRef((function(e,t){var r=e.feature,n=r.get("start"),a=r.get("end"),o=r.get("refName"),i=r.get("snpinfo"),s=[o,n===a?ft(n):"".concat(ft(n),"..").concat(ft(a))].filter((function(e){return!!e})).join(":"),c=null==i?void 0:i.total;return C.createElement("div",{ref:t},C.createElement("table",null,C.createElement("caption",null,s),C.createElement("thead",null,C.createElement("tr",null,C.createElement("th",null,"Base"),C.createElement("th",null,"Count"),C.createElement("th",null,"% of Total"),C.createElement("th",null,"Strands"),C.createElement("th",null,"Source"))),C.createElement("tbody",null,C.createElement("tr",null,C.createElement("td",null,"Total"),C.createElement("td",null,c),C.createElement("td",null)),Object.entries(i).map((function(e){var t=ie(e,2),r=t[0];return Object.entries(t[1]).map((function(e){var t=ie(e,2),n=t[0],a=t[1],o=a.strands;return C.createElement("tr",{key:n},C.createElement("td",null,n.toUpperCase()),C.createElement("td",null,a.total),C.createElement("td",null,"total"===n||"skip"===n?"---":"".concat(Math.floor(a.total/(c||a.total||1)*100),"%")),C.createElement("td",null,o[-1]?"".concat(o[-1],"(-)"):"",o[1]?"".concat(o[1],"(+)"):""),C.createElement("td",null,r))}))})))))})),gt=b.observer((function(e){var t=e.model.featureUnderMouse;return t&&"skip"===t.get("type")?null:C.createElement(p.Tooltip,Object.assign({TooltipContents:dt},e))}));function ht(e,t,r,n){return mt.apply(this,arguments)}function mt(){return(mt=Q(he.mark((function e(t,n,a,o){var i,s,c,l;return he.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return 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o.types.compose("LinearSNPCoverageDisplay",p.linearWiggleDisplayModelFactory(e,t),o.types.model({type:o.types.literal("LinearSNPCoverageDisplay"),drawInterbaseCounts:o.types.maybe(o.types.boolean),drawIndicators:o.types.maybe(o.types.boolean),drawArcs:o.types.maybe(o.types.boolean),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}))}),{}),colorBy:o.types.maybe(o.types.model({type:o.types.string,tag:o.types.maybe(o.types.string)}))})).volatile((function(){return{modificationTagMap:_.observable.map({})}})).actions((function(e){return{setConfig:function(t){e.configuration=t},setFilterBy:function(t){e.filterBy=o.cast(t)},setColorBy:function(t){e.colorBy=o.cast(t)},updateModificationColorMap:function(t){var 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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(){var r=t();return J(J({},r),{},{notReady:r.notReady||!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(he.mark((function t(){var n,o,i;return he.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,yt(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 s=o.tag,c=o.value;t.push("jexl:get(feature,'snpinfo') != undefined ? true : "+'"'.concat(c,"\" =='*' ? getTag(feature,\"").concat(s,'") != undefined : ')+'getTag(feature,"'.concat(s,'") == "').concat(c,'"'))}i&&t.push("jexl:get(feature,'snpinfo') != undefined ? true : "+"get(feature,'name') == \"".concat(i,'"'))}return new T({filters:t})}}}))};function Ct(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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r?C.createElement("div",{"data-testid":"blurb-".concat(t.sortedBy),style:{backgroundColor:"white"}},C.createElement(F,{color:"secondary",variant:"caption"},t.sortedBy?"Sorted by ".concat(r.type.toLowerCase()," at ").concat(r.refName,":").concat(r.pos):null)):null}var xt=b.observer(St),kt=["uniqueId"],_t=w.lazy((function(){return Promise.resolve().then((function(){return Qt}))})),Et=w.lazy((function(){return Promise.resolve().then((function(){return er}))})),Tt=w.lazy((function(){return Promise.resolve().then((function(){return nr}))})),Pt=w.lazy((function(){return Promise.resolve().then((function(){return ir}))})),Rt=w.lazy((function(){return Promise.resolve().then((function(){return lr}))})),Mt=w.lazy((function(){return Promise.resolve().then((function(){return dr}))})),Nt=new Map([["pileup","PileupRenderer"],["svg","SvgFeatureRenderer"]]),At=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}})).actions((function(e){return{setReady:function(t){e.ready=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=se(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=se(e.colorTagMap.keys()).length;e.colorTagMap.set(t,r[n])}}))}}})).actions((function(e){return{afterAttach:function(){o.addDisposer(e,_.autorun(Q(he.mark((function t(){var n,o,i,s,c,l,u,p;return he.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,s=e.colorBy,c=r.getContainingView(e),null==s||!s.tag){t.next=9;break}return t.next=7,ht(e,s,c.staticBlocks);case 7:e.updateColorTagMap(t.sent);case 9:if("modifications"!==(null==s?void 0:s.type)){t.next=14;break}return t.next=12,yt(e,a.getConf(e.parentTrack,["adapter"]),s,c.staticBlocks);case 12:e.updateModificationColorMap(t.sent);case 14:if(!i){t.next=23;break}return p={start:l=i.pos,end:l+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(c.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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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_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(){var e=this.record,t=this.adapter;return e.isPaired()?"".concat(t.refIdToName(e._next_refid()),":").concat(e._next_pos()+1):void 0}},{key:"_get_seq",value:function(){return this.record.getReadBases()}},{key:"qualRaw",value:function(){return this.record.qualRaw()}},{key:"set",value:function(){}},{key:"tags",value:function(){var t=Object.getOwnPropertyNames(e.prototype);return se(new Set(t.filter((function(e){return e.startsWith("_get_")&&"_get_mismatches"!==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_mismatches",value:function(){return Ce(this.get("CIGAR"),this.get("MD"),this.get("seq"),this.ref,this.qualRaw())}},{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}(),Gt=function(e){ee(g,i.BaseFeatureDataAdapter);var t,n,o,s,u,p,f,d=ne(g);function g(){return Z(this,g),d.apply(this,arguments)}return Y(g,[{key:"configure",value:(f=Q(he.mark((function e(){var t,r,n,o,i;return he.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return this.configured||(t=a.readConfObject(this.config,"bamLocation"),r=a.readConfObject(this.config,["index","location"]),n=a.readConfObject(this.config,["index","indexType"]),o=new V.BamFile({bamFilehandle:z.openLocation(t,this.pluginManager),csiFilehandle:"CSI"===n?z.openLocation(r,this.pluginManager):void 0,baiFilehandle:"CSI"!==n?z.openLocation(r,this.pluginManager):void 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he.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 o.apply(this,arguments)})},{key:"seqFetch",value:(n=Q(he.mark((function e(t,r,n){var a,o,i;return he.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(l.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),s=Math.min(n-t,a-t)-o,c=e.get("seq")||e.get("residues");i+=c.substr(o,s)})),i.length===n-r){e.next=17;break}throw new Error("sequence fetch failed: fetching 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e.next=20,n.seqFetch(s||a,h.get("start"),h.get("end"));case 20:m=e.sent;case 21:c.next(new Vt(h,n,m));case 22:e.next=14;break;case 24:e.next=29;break;case 26:e.prev=26,e.t0=e.catch(12),d.e(e.t0);case 29:return e.prev=29,d.f(),e.finish(29);case 32:f(""),c.complete();case 34:case"end":return e.stop()}}),e,null,[[12,26,29,32]])})));return function(t){return e.apply(this,arguments)}}(),u)}},{key:"estimateRegionsStats",value:(t=Q(he.mark((function e(t,n){var o,i,s;return he.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return e.next=2,this.configure();case 2:if("?"===(o=e.sent.bam).index.filehandle){e.next=12;break}return e.next=7,r.bytesForRegions(t,o);case 7:return i=e.sent,s=a.readConfObject(this.config,"fetchSizeLimit"),e.abrupt("return",{bytes:i,fetchSizeLimit:s});case 12:return e.abrupt("return",oe(te(g.prototype),"estimateRegionsStats",this).call(this,t,n));case 13:case"end":return e.stop()}}),e,this)}))),function(e,r){return t.apply(this,arguments)})},{key:"freeResources",value:function(){}},{key:"refIdToName",value:function(e){var t;return null===(t=this.samHeader)||void 0===t?void 0:t.idToName[e]}}]),g}(),Wt={__proto__:null,default:Gt},Ut={__proto__:null,default:function(e){ee(n,Gt);var t,r=ne(n);function n(){return Z(this,n),r.apply(this,arguments)}return Y(n,[{key:"configure",value:(t=Q(he.mark((function e(){var t,r,n,o;return he.wrap((function(e){for(;;)switch(e.prev=e.next){case 0:return this.configured||(t=a.readConfObject(this.config,"htsgetBase"),r=a.readConfObject(this.config,"htsgetTrackId"),n=new V.HtsgetFile({baseUrl:t,trackId:r}),(o=a.readConfObject(this.config,"sequenceAdapter"))&&this.getSubAdapter&&(this.configured=this.getSubAdapter(o).then((function(e){return{bam:n,sequenceAdapter:e.dataAdapter}}))),this.configured=Promise.resolve({bam:n})),e.abrupt("return",this.configured);case 2:case"end":return e.stop()}}),e,this)}))),function(){return t.apply(this,arguments)})}]),n}()},Jt=E.makeStyles((function(e){return{root:{width:300},closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]}}}));function Xt(e){var t=Jt(),r=e.model,n=e.handleClose,a=ie(w.useState(""),2),o=a[0],i=a[1],s=o.match(/^[A-Za-z][A-Za-z0-9]$/);return C.createElement(E.Dialog,{open:!0,onClose:n},C.createElement(E.DialogTitle,null,"Color by tag",C.createElement(E.IconButton,{"aria-label":"close",className:t.closeButton,onClick:n},C.createElement(G,null))),C.createElement(E.DialogContent,{style:{overflowX:"hidden"}},C.createElement(E.Typography,null,"Enter tag to color by: "),C.createElement(E.Typography,{color:"textSecondary"},"Examples: XS or TS for RNA-seq inferred read strand, ts (lower-case) for minimap2 read strand, HP for haplotype, RG for read group, etc."),C.createElement(E.TextField,{value:o,onChange:function(e){return i(e.target.value)},placeholder:"Enter tag 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alignment"];function Yt(e){var t=e.flag,r=void 0===t?0:t,n=e.setFlag;return C.createElement(C.Fragment,null,C.createElement(E.TextField,{type:"number",value:r,onChange:function(e){return n(+e.target.value)}}),$t.map((function(e,t){var a=r&1<<t,o="".concat(e,"_").concat(a);return C.createElement("div",{key:o},C.createElement("input",{type:"checkbox",checked:Boolean(a),onChange:function(e){n(e.target.checked?r|1<<t:r&~(1<<t))}}),C.createElement("label",{htmlFor:o},e))})))}function Kt(e){var t,r,n=e.model,a=e.handleClose,o=Zt(),i=n.filterBy,s=ie(w.useState(null==i?void 0:i.flagInclude),2),c=s[0],l=s[1],u=ie(w.useState(null==i?void 0:i.flagExclude),2),p=u[0],f=u[1],d=ie(w.useState((null==i||null===(t=i.tagFilter)||void 0===t?void 0:t.tag)||""),2),g=d[0],h=d[1],m=ie(w.useState((null==i||null===(r=i.tagFilter)||void 0===r?void 0:r.value)||""),2),y=m[0],v=m[1],b=ie(w.useState((null==i?void 0:i.readName)||""),2),S=b[0],x=b[1],k=g.match(/^[A-Za-z][A-Za-z0-9]$/),_="https://broadinstitute.github.io/picard/explain-flags.html";return C.createElement(E.Dialog,{open:!0,onClose:a},C.createElement(E.DialogTitle,null,"Filter options",C.createElement(E.IconButton,{"aria-label":"close",className:o.closeButton,onClick:a},C.createElement(G,null))),C.createElement(E.DialogContent,null,C.createElement(E.Typography,null,"Set filter bitmask options. Refer to ",C.createElement(E.Link,{href:_},_)," ","for details"),C.createElement(E.Paper,{className:o.paper,variant:"outlined"},C.createElement("div",{style:{display:"flex"}},C.createElement("div",null,C.createElement(E.Typography,null,"Read must have ALL these flags"),C.createElement(Yt,{flag:c,setFlag:l})),C.createElement("div",null,C.createElement(E.Typography,null,"Read must have NONE of these flags"),C.createElement(Yt,{flag:p,setFlag:f})))),C.createElement(E.Paper,{className:o.paper,variant:"outlined"},C.createElement(E.Typography,null,"Filter by tag name and value. Use * in the value field to get all reads containing any value for that tag. Example: filter tag name SA with value * to get all split/supplementary reads. Other examples include HP for haplotype, or RG for read group"),C.createElement(E.TextField,{className:o.field,value:g,onChange:function(e){h(e.target.value)},placeholder:"Enter tag name",inputProps:{maxLength:2,"data-testid":"color-tag-name-input"},error:2===g.length&&!k,helperText:2!==g.length||k?"":"Not a valid tag","data-testid":"color-tag-name"}),C.createElement(E.TextField,{className:o.field,value:y,onChange:function(e){v(e.target.value)},placeholder:"Enter tag value",inputProps:{"data-testid":"color-tag-name-input"},"data-testid":"color-tag-value"})),C.createElement(E.Paper,{className:o.paper,variant:"outlined"},C.createElement(E.Typography,null,"Filter by read name"),C.createElement(E.TextField,{className:o.field,value:S,onChange:function(e){x(e.target.value)},placeholder:"Enter read name",inputProps:{"data-testid":"color-tag-readname-input"},"data-testid":"color-tag-readname"})),C.createElement(E.DialogActions,null,C.createElement(E.Button,{variant:"contained",color:"primary",autoFocus:!0,type:"submit",onClick:function(){n.setFilterBy({flagInclude:c,flagExclude:p,readName:S,tagFilter:""!==g?{tag:g,value:y}:void 0}),a()}},"Submit"),C.createElement(E.Button,{variant:"contained",color:"secondary",onClick:function(){return a()}},"Cancel"))))}var er={__proto__:null,default:b.observer(Kt)},tr=E.makeStyles((function(e){return{root:{margin:0,padding:e.spacing(2)},closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]}}}));function rr(e){var t=tr(),r=e.model,n=e.handleClose,a=ie(w.useState(""),2),o=a[0],i=a[1],s=o.match(/^[A-Za-z][A-Za-z0-9]$/);return C.createElement(E.Dialog,{open:!0,onClose:n},C.createElement(E.DialogTitle,null,"Sort by tag",C.createElement(E.IconButton,{"aria-label":"close",className:t.closeButton,onClick:n},C.createElement(G,null))),C.createElement(E.DialogContent,null,C.createElement(E.Typography,null,"Set the tag to sort by"),C.createElement(E.Typography,{color:"textSecondary"},"Examples: HP for haplotype, RG for read group, etc."),C.createElement(E.TextField,{value:o,onChange:function(e){return i(e.target.value)},placeholder:"Enter tag name",inputProps:{maxLength:2,"data-testid":"sort-tag-name-input"},error:2===o.length&&!s,helperText:2!==o.length||s?"":"Not a valid tag",autoComplete:"off","data-testid":"sort-tag-name"}),C.createElement(E.DialogActions,null,C.createElement(E.Button,{variant:"contained",color:"primary",type:"submit",autoFocus:!0,onClick:function(){r.setSortedBy("tag",o),n()}},"Submit"),C.createElement(E.Button,{variant:"contained",color:"secondary",onClick:function(){return n()}},"Cancel"))))}var nr={__proto__:null,default:b.observer(rr)},ar=E.makeStyles((function(e){return{closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]}}}));function or(e){var t=ar(),r=e.model,n=e.handleClose,a=r.noSpacing,o=ie(w.useState("".concat(r.featureHeightSetting)),2),i=o[0],s=o[1],c=ie(w.useState(a),2),l=c[0],u=c[1],p=""!==i&&!Number.isNaN(+i);return C.createElement(E.Dialog,{open:!0,onClose:n},C.createElement(E.DialogTitle,null,"Set feature height",C.createElement(E.IconButton,{className:t.closeButton,onClick:n},C.createElement(G,null))),C.createElement(E.DialogContent,null,C.createElement(E.Typography,null,"Adjust the feature height and whether there is any spacing between features. Setting feature height to 1 and removing spacing makes the display very compact."),C.createElement(E.TextField,{value:i,helperText:"Feature height",onChange:function(e){s(e.target.value)}}),C.createElement(E.FormControlLabel,{control:C.createElement(E.Checkbox,{checked:!!l,onChange:function(){return u((function(e){return!e}))}}),label:"Remove spacing between features in y-direction?"}),C.createElement(E.DialogActions,null,C.createElement(E.Button,{variant:"contained",color:"primary",type:"submit",autoFocus:!0,disabled:!p,onClick:function(){r.setFeatureHeight(""===i||Number.isNaN(+i)?void 0:+i),r.setNoSpacing(l),n()}},"Submit"),C.createElement(E.Button,{variant:"contained",color:"secondary",onClick:function(){return n()}},"Cancel"))))}var ir={__proto__:null,default:b.observer(or)},sr=E.makeStyles((function(e){return{root:{width:500},closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]},field:{margin:e.spacing(2)}}}));function cr(e){var t=e.model,r=e.handleClose,n=sr(),a=t.maxHeight,o=ie(w.useState("".concat(void 0===a?"":a)),2),i=o[0],s=o[1];return C.createElement(E.Dialog,{open:!0,onClose:r},C.createElement(E.DialogTitle,null,"Filter options",C.createElement(E.IconButton,{"aria-label":"close",className:n.closeButton,onClick:r},C.createElement(G,null))),C.createElement(E.DialogContent,{className:n.root},C.createElement(E.Typography,null,'Set max height for the track. For example, you can increase this if the layout says "Max height reached"'),C.createElement(E.TextField,{value:i,onChange:function(e){s(e.target.value)},placeholder:"Enter max height for layout"}),C.createElement(E.DialogActions,null,C.createElement(E.Button,{variant:"contained",color:"primary",type:"submit",autoFocus:!0,onClick:function(){t.setMaxHeight(""===i||Number.isNaN(+i)?void 0:+i),r()}},"Submit"),C.createElement(E.Button,{variant:"contained",color:"secondary",onClick:function(){return r()}},"Cancel"))))}var lr={__proto__:null,default:b.observer(cr)},ur=E.makeStyles((function(e){return{closeButton:{position:"absolute",right:e.spacing(1),top:e.spacing(1),color:e.palette.grey[500]},table:{border:"1px solid #888",margin:e.spacing(4),"& td":{padding:e.spacing(1)}}}}));function pr(e){var t=e.modifications,r=ur();return C.createElement("table",{className:r.table},C.createElement("tbody",null,t.map((function(e){var t=ie(e,2),r=t[0],n=t[1];return C.createElement("tr",{key:r},C.createElement("td",null,r),C.createElement("td",null,n),C.createElement("td",{style:{width:"1em",background:n}}))}))))}function fr(e){var t=ur(),r=e.model,n=e.handleClose,a=r.colorBy,o=r.modificationTagMap,i=se(o.entries());return C.createElement(E.Dialog,{open:!0,onClose:n},C.createElement(E.DialogTitle,null,"Color by modifications",C.createElement(E.IconButton,{"aria-label":"close",className:t.closeButton,onClick:n},C.createElement(G,null))),C.createElement(E.DialogContent,null,C.createElement(E.Typography,null,"You can choose to color the modifications in the BAM/CRAM MM/ML specification using this dialog. Choosing modifications colors the modified positions and can color multiple modification types. Choosing the methylation setting colors methylated and unmethylated CpG."),C.createElement(E.Typography,null,"Note: you can revisit this dialog to see the current mapping of colors to modification type for the modification coloring mode"),C.createElement("div",{style:{margin:20}},"modifications"===(null==a?void 0:a.type)?C.createElement("div",null,i.length?C.createElement(C.Fragment,null,"Current modification-type-to-color mapping",C.createElement(pr,{modifications:se(o.entries())})):C.createElement("div",null,C.createElement(E.Typography,null,"Note: color by modifications is already enabled. Loading current modifications..."),C.createElement(E.CircularProgress,{size:15}))):null,"methylation"===(null==a?void 0:a.type)?C.createElement(pr,{modifications:[["methylated","red"],["unmethylated","blue"]]}):null),C.createElement(E.DialogActions,null,C.createElement(E.Button,{variant:"contained",color:"primary",style:{margin:5},onClick:function(){r.setColorScheme({type:"modifications"}),n()}},"Modifications"),C.createElement(E.Button,{variant:"contained",color:"primary",style:{margin:5},onClick:function(){r.setColorScheme({type:"methylation"}),n()}},"Methylation"),C.createElement(E.Button,{variant:"contained",color:"secondary",style:{margin:5},onClick:function(){return n()}},"Cancel"))))}var dr={__proto__:null,default:b.observer(fr)},gr=E.makeStyles((function(){return{compact:{paddingRight:0,paddingTop:0,paddingBottom:0}}})),hr=["clipPos","flags"];function mr(e){var t=gr(),r=e.feature.flags;return C.createElement(W.BaseCard,Object.assign({},e,{title:"Flags"}),C.createElement(W.SimpleValue,{name:"Flag",value:r}),C.createElement(E.FormGroup,null,["read paired","read mapped in proper pair","read unmapped","mate unmapped","read reverse strand","mate reverse strand","first in pair","second in pair","not primary alignment","read fails platform/vendor quality checks","read is PCR or optical duplicate","supplementary alignment"].map((function(e,n){var a=r&1<<n,o="".concat(e,"_").concat(a);return C.createElement(E.FormControlLabel,{key:o,control:C.createElement(E.Checkbox,{className:t.compact,checked:Boolean(a),name:e,readOnly:!0}),label:e})}))))}function yr(e){var t=e.value,r=ie(w.useState(!1),2),n=r[0],a=r[1],o=String(t);return o.length>100?C.createElement(C.Fragment,null,C.createElement("button",{type:"button",onClick:function(){return N(o)}},"Copy"),C.createElement("button",{type:"button",onClick:function(){return a((function(e){return!e}))}},n?"Show less":"Show more"),C.createElement("div",null,n?o:"".concat(o.slice(0,100),"..."))):C.createElement("div",null,o)}function vr(e){var t=e.tag,n=e.model,a=r.getSession(n);return C.createElement(W.BaseCard,Object.assign({},e,{title:"Supplementary alignments"}),C.createElement(E.Typography,null,"List of supplementary alignment locations"),C.createElement("ul",null,t.split(";").filter((function(e){return!!e})).map((function(e,t){var r=ie(e.split(","),4),o=r[0],i=r[1],s=r[2],c=function(e){for(var t=ve(e),r=0,n=0;n<t.length;n+=2){var a=t[n+1];"H"!==a&&"S"!==a&&"I"!==a&&(r+=+t[n])}return r}(r[3]),l=Math.floor(c/5),u=+i,p=+i+c,f="".concat(o,":").concat(Math.max(1,u-l),"-").concat(p+l),d=u.toLocaleString("en-US"),g=p.toLocaleString("en-US"),h="".concat(o,":").concat(d,"-").concat(g," (").concat(s,")");return C.createElement("li",{key:"".concat(f,"-").concat(t)},C.createElement(E.Link,{onClick:function(){var e=n.view;try{if(!e)throw new Error("No view associated with this view anymore");e.navToLocString(f)}catch(e){console.error(e),a.notify("".concat(e))}},href:"#"},h))}))))}function br(e){var t=e.locString,n=e.model,a=r.getSession(n);return C.createElement(E.Link,{onClick:function(){var e=n.view;try{e?e.navToLocString(t):a.notify("No view associated with this feature detail panel anymore","warning")}catch(e){console.error(e),a.notify("".concat(e))}},href:"#"},t)}function wr(e){var t=e.model,r=JSON.parse(JSON.stringify(t.featureData)),n=r.tags&&r.tags.SA||r.SA;return C.createElement(E.Paper,{"data-testid":"alignment-side-drawer"},C.createElement(W.FeatureDetails,Object.assign({},e,{omit:hr,feature:r,formatter:function(e,r){return"next_segment_position"===r?C.createElement(br,{model:t,locString:e}):C.createElement(yr,{value:e})}})),n?C.createElement(vr,{model:t,tag:n}):null,C.createElement(mr,Object.assign({feature:r},e)))}var Cr={__proto__:null,default:b.observer(wr)};exports.MismatchParser=_e,exports.default=jt;
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