@sjcrh/proteinpaint-client 2.74.2 → 2.76.0

package/dist/{block.mds.svcnv.share-81e62600.js → block.mds.svcnv.share-886d9479.js}

@@ -1 +1 @@
-import{k as e}from"./app-a8c4854a.js";function t(e){if(!e.dna_mintotalreads)e.dna_mintotalreads=8;if(!e.rna_mintotalreads)e.rna_mintotalreads=8;if(!e.hetsnp_minbaf)e.hetsnp_minbaf=.3;if(!e.hetsnp_maxbaf)e.hetsnp_maxbaf=.7;if(e.rnapileup_q==undefined)e.rnapileup_q=0;if(!e.rnapileup_Q)e.rnapileup_Q=13;if(!e.binompvaluecutoff)e.binompvaluecutoff=.05;if(!e.clientcolor_snpinuse)e.clientcolor_snpinuse="blue";if(!e.clientcolor_markernotinuse)e.clientcolor_markernotinuse="#bbb"}function n(t,n,p){const a=t.checkrnabam;if(!a)return;t.tkconfigtip.d.append("hr");const i=t.tkconfigtip.d.append("div").style("margin","15px 0px");i.append("div").style("opacity",.5).style("font-size",".9em").text("Finding heterozygous SNPs in DNA");{const r=i.append("div").style("margin-top","5px");r.append("span").html("DNA minimum total read count&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.dna_mintotalreads).on("keyup",(i=>{if(!e(i))return;let r=Number.parseInt(i.target.value);if(!r||r<=0)return;if(a.dna_mintotalreads==r){return}a.dna_mintotalreads=r;p(t,n)}));r.append("div").style("opacity",".5").style("font-size",".8em").text("If a SNP's total coverage is below cutoff, it will be skipped.")}{const r=i.append("div").style("margin-top","5px");r.append("span").html("Heterozygous SNP BAF range&nbsp;&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.hetsnp_minbaf).on("keyup",(i=>{if(!e(i))return;let r=Number.parseFloat(i.target.value);if(!r||r<=0)return;if(a.hetsnp_minbaf==r){return}a.hetsnp_minbaf=r;p(t,n)}));r.append("span").style("opacity",".5").style("font-size",".8em").html("&nbsp;&leq; BAF &leq;&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.hetsnp_maxbaf).on("keyup",(i=>{if(!e(i))return;let r=Number.parseFloat(i.target.value);if(!r||r<=0)return;if(a.hetsnp_maxbaf==r){return}a.hetsnp_maxbaf=r;p(t,n)}));r.append("div").style("opacity",".5").style("font-size",".8em").text("If a SNP's BAF (B-allele fraction) is within this range, it is heterozygous.")}i.append("div").style("margin-top","20px").style("opacity",.5).style("font-size",".9em").text("Counting alleles in RNA-seq BAM file");{const r=i.append("div").style("margin-top","5px");r.append("span").html("Skip alignments with mapQ smaller than&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.rnapileup_q).on("keyup",(i=>{if(!e(i))return;let r=Number.parseInt(i.target.value);if(!r||r<0)return;if(a.rnapileup_q==r){return}a.rnapileup_q=r;p(t,n)}))}{const r=i.append("div").style("margin-top","5px");r.append("span").html("Skip bases with baseQ/BAQ smaller than&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.rnapileup_Q).on("keyup",(i=>{if(!e(i))return;let r=Number.parseInt(i.target.value);if(!r||r<=0)return;if(a.rnapileup_Q==r){return}a.rnapileup_Q=r;p(t,n)}))}i.append("div").style("margin-top","20px").style("opacity",.5).style("font-size",".9em").text("Binomial test on whether a heterozygous SNP shows allelic bias in RNA");{const r=i.append("div").style("margin-top","5px");r.append("span").html("P-value cutoff&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.binompvaluecutoff).on("keyup",(i=>{if(!e(i))return;let r=Number.parseFloat(i.target.value);if(!r||r<=0||r>=1)return;if(a.binompvaluecutoff==r){return}a.binompvaluecutoff=r;p(t,n)}))}{const r=i.append("div").style("margin-top","5px");r.append("span").html("RNA minimum total read count&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.rna_mintotalreads).on("keyup",(i=>{if(!e(i))return;let r=Number.parseInt(i.target.value);if(!r||r<=0)return;if(a.rna_mintotalreads==r){return}a.rna_mintotalreads=r;p(t,n)}));r.append("div").style("opacity",".5").style("font-size",".8em").text("If a SNP's total read count from RNA is below cutoff, it won't do binomial test.")}}export{n as c,t as r};
+import{k as e}from"./app-b369b169.js";function t(e){if(!e.dna_mintotalreads)e.dna_mintotalreads=8;if(!e.rna_mintotalreads)e.rna_mintotalreads=8;if(!e.hetsnp_minbaf)e.hetsnp_minbaf=.3;if(!e.hetsnp_maxbaf)e.hetsnp_maxbaf=.7;if(e.rnapileup_q==undefined)e.rnapileup_q=0;if(!e.rnapileup_Q)e.rnapileup_Q=13;if(!e.binompvaluecutoff)e.binompvaluecutoff=.05;if(!e.clientcolor_snpinuse)e.clientcolor_snpinuse="blue";if(!e.clientcolor_markernotinuse)e.clientcolor_markernotinuse="#bbb"}function n(t,n,p){const a=t.checkrnabam;if(!a)return;t.tkconfigtip.d.append("hr");const i=t.tkconfigtip.d.append("div").style("margin","15px 0px");i.append("div").style("opacity",.5).style("font-size",".9em").text("Finding heterozygous SNPs in DNA");{const r=i.append("div").style("margin-top","5px");r.append("span").html("DNA minimum total read count&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.dna_mintotalreads).on("keyup",(i=>{if(!e(i))return;let r=Number.parseInt(i.target.value);if(!r||r<=0)return;if(a.dna_mintotalreads==r){return}a.dna_mintotalreads=r;p(t,n)}));r.append("div").style("opacity",".5").style("font-size",".8em").text("If a SNP's total coverage is below cutoff, it will be skipped.")}{const r=i.append("div").style("margin-top","5px");r.append("span").html("Heterozygous SNP BAF range&nbsp;&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.hetsnp_minbaf).on("keyup",(i=>{if(!e(i))return;let r=Number.parseFloat(i.target.value);if(!r||r<=0)return;if(a.hetsnp_minbaf==r){return}a.hetsnp_minbaf=r;p(t,n)}));r.append("span").style("opacity",".5").style("font-size",".8em").html("&nbsp;&leq; BAF &leq;&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.hetsnp_maxbaf).on("keyup",(i=>{if(!e(i))return;let r=Number.parseFloat(i.target.value);if(!r||r<=0)return;if(a.hetsnp_maxbaf==r){return}a.hetsnp_maxbaf=r;p(t,n)}));r.append("div").style("opacity",".5").style("font-size",".8em").text("If a SNP's BAF (B-allele fraction) is within this range, it is heterozygous.")}i.append("div").style("margin-top","20px").style("opacity",.5).style("font-size",".9em").text("Counting alleles in RNA-seq BAM file");{const r=i.append("div").style("margin-top","5px");r.append("span").html("Skip alignments with mapQ smaller than&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.rnapileup_q).on("keyup",(i=>{if(!e(i))return;let r=Number.parseInt(i.target.value);if(!r||r<0)return;if(a.rnapileup_q==r){return}a.rnapileup_q=r;p(t,n)}))}{const r=i.append("div").style("margin-top","5px");r.append("span").html("Skip bases with baseQ/BAQ smaller than&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.rnapileup_Q).on("keyup",(i=>{if(!e(i))return;let r=Number.parseInt(i.target.value);if(!r||r<=0)return;if(a.rnapileup_Q==r){return}a.rnapileup_Q=r;p(t,n)}))}i.append("div").style("margin-top","20px").style("opacity",.5).style("font-size",".9em").text("Binomial test on whether a heterozygous SNP shows allelic bias in RNA");{const r=i.append("div").style("margin-top","5px");r.append("span").html("P-value cutoff&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.binompvaluecutoff).on("keyup",(i=>{if(!e(i))return;let r=Number.parseFloat(i.target.value);if(!r||r<=0||r>=1)return;if(a.binompvaluecutoff==r){return}a.binompvaluecutoff=r;p(t,n)}))}{const r=i.append("div").style("margin-top","5px");r.append("span").html("RNA minimum total read count&nbsp;");r.append("input").attr("type","number").style("width","50px").property("value",a.rna_mintotalreads).on("keyup",(i=>{if(!e(i))return;let r=Number.parseInt(i.target.value);if(!r||r<=0)return;if(a.rna_mintotalreads==r){return}a.rna_mintotalreads=r;p(t,n)}));r.append("div").style("opacity",".5").style("font-size",".8em").text("If a SNP's total read count from RNA is below cutoff, it won't do binomial test.")}}export{n as c,t as r};

package/dist/block.mds2-7852c1ee.js

@@ -0,0 +1 @@
+import{z as e,a7 as t,aF as n,aG as a,b as s,k as o,I as i,aN as l,ag as r,q as d,Z as p,b$ as c,v as f,p as u,ac as m,a9 as g,ah as h,d as y,W as x,M as _,B as b,ap as v,aq as k,ar as w,an as A,as as F,at as j,bL as L}from"./app-b369b169.js";import{l as z}from"./block.legend-d3f61ef7.js";import{f as N}from"./FilterStateless-54c0b763.js";import{a as E,c as M}from"./FilterRxComp-701a1480.js";import"./termsetting-33ea66f1.js";import{v as I}from"./vcf-5cc55588.js";import{appInit as R}from"./app-3320ab6f.js";import{b as S,c as C}from"./axis-747c801e.js";import{m as O}from"./checkbox-96437f4d.js";import"./partition-db811f6b.js";import"./arc-3d6751aa.js";import"./constant-426a1483.js";import"./math-2fb199c6.js";import"./legacy-d3-polyfill-bdb2d792.js";import"./table-29d5a973.js";import"./tslib.es6-c3c2d88f.js";import"./partjson.esm-b3f1fc21.js";import"./termdb.bins-8b656cc3.js";import"path";import"./termInfo-bf99a37e.js";import"./toggleButtons-dbdbad01.js";function U(e){const t=e.append("div").attr("class","sja_filter_tag_btn").style("position","absolute");const n=e.append("select").style("opacity",0).on("mouseover",(()=>{t.style("opacity","0.8").style("cursor","default")})).on("mouseout",(()=>{t.style("opacity","1")}));return[n,t]}function T(e,t,n,a,s){const o=D(t,s);console.log(o);return 0}const P=4;function B(e,t,n){if(!t.vcf)return 0;if(!e.vcf)return 0;if(!e.vcf.rglst)return 0;let a=0;for(const s of e.vcf.rglst){const o=t.g_vcfrow.append("g").attr("transform","translate("+s.xoff+",0)");if(s.rangetoobig){s.text_rangetoobig=o.append("text").text(s.rangetoobig).attr("text-anchor","middle").attr("dominant-baseline","central").attr("x",s.width/2);a=Math.max(a,50);continue}if(s.imgsrc){o.append("image").attr("width",s.width).attr("height",s.imgheight).attr("xlink:href",s.imgsrc);a=Math.max(a,s.imgheight);continue}if(s.variants){const i=q(e,s,o,t,n);a=Math.max(a,i);continue}}for(const t of e.vcf.rglst){if(t.rangetoobig){t.text_rangetoobig.attr("y",a/2)}}{const n=e.vcf.rglst.reduce(((e,t)=>e+t.variants.length),0);t.vcfrow_label_numbervariants.text(n==0?"No variant":n+" variant"+(n>1?"s":""));if(n==0){t.__vcf_data=null}else{t.__vcf_data=e}}return a}function q(e,t,n,a,s){let o=50;if(a.vcf.numerical_axis&&a.vcf.numerical_axis.in_use){o=ge(e,t,n,a,s)}else{o=T(e,t,n,a,s)}return o}function J(t,n){return e[t.class].color}function G(e,n){const a=["genome="+n.name];if(e.file){a.push("file="+e.file)}else{a.push("url="+e.url);if(e.indexURL)a.push("indexURL="+e.indexURL)}return t("vcfheader?"+a.join("&")).then((t=>{if(t.error)throw t.error;const[n,a,s,o]=I(t.metastr.split("\n"));if(o)throw"Error parsing VCF meta lines: "+o.join("; ");e.info=n;e.format=a;e.samples=s;e.nochr=t.nochr}))}function D(e,t){const s=new Map;for(const n of e.variants){const e=t.seekcoord(n.chr,n.pos);if(e.length==0){continue}if(e.length==1){n.__x=e[0].x}else{n.__x=e[0].x}if(!s.has(n.__x)){s.set(n.__x,[])}s.get(n.__x).push(n)}const o=[];if(t.exonsf>=P){for(const[e,t]of s){o.push({chr:t[0].chr,pos:t[0].pos,mlst:t,x:e})}}else{if(t.usegm&&t.usegm.coding&&t.gmmode!=n.genomic){for(const e of s.values()){const n=a(e[0].pos,t.usegm);for(const t of e){t.aapos=n.aapos;t.rnapos=n.rnapos}}const e=new Map;for(const[n,a]of s){if(a[0].chr!=t.usegm.chr){continue}const o=a[0].aapos;if(o==undefined){console.error("data item cannot map to aaposition");console.log(a[0]);continue}s.delete(n);if(!e.has(o)){e.set(o,[])}let i=true;for(const n of e.get(o)){if(Math.abs(n[0].__x-a[0].__x)<=t.exonsf*3){for(const e of a){n.push(e)}i=false;break}}if(i){e.get(o).push(a)}}t.usegm.utr5?t.usegm.utr5.reduce(((e,t)=>e+t[1]-t[0]),0):0;for(const t of e.values()){for(const e of t){let t=null;for(const n of e){if(Number.isFinite(n.rnapos))t=n}if(t==null){console.log("trying to map mlst to codon, but no rnapos found");for(const t of e){console.log(t)}continue}o.push({chr:e[0].chr,pos:t.pos,mlst:e,x:e[0].__x})}}}const e=[];const i=2;for(const[t,n]of s){const a=Math.floor(t/i);if(!e[a]){e[a]=[]}e[a]=[...e[a],...n]}for(const t of e){if(!t)continue;const e=t.reduce(((e,t)=>e+t.__x),0);o.push({isbin:true,chr:t[0].chr,pos:t[0].pos,mlst:t,x:e/t.length})}}o.sort(((e,t)=>e.x-t.x));return o}async function V(e,t,n,a){const s={d:{svgdiv:e.append("div"),wait:e.append("div")},m:t,tk:n,block:a,overlay_term:n.vcf.plot_mafcov.overlay_term};if(n.mds&&n.mds.sample2bam){s.d.tempbbdiv=e.append("div")}await Y(s)}async function Y(e){const t={genome:e.block.genome.name,trigger_mafcovplot:1,m:{chr:e.m.chr,pos:e.m.pos,ref:e.m.ref,alt:e.m.alt}};if(e.tk.mds){t.dslabel=e.tk.mds.label}else{t.vcf={file:e.tk.vcf.file,url:e.tk.vcf.url,indexURL:e.tk.vcf.indexURL}}if(e.overlay_term&&e.overlay_term.term){t.overlay_term=e.overlay_term.term.id;t.overlay_term_q=e.overlay_term.term.q}e.d.wait.text("Loading...").style("display","block");try{const n=await s("mds2",{method:"POST",body:JSON.stringify(t)});if(n.error)throw n.error;if(n.plotgroups){H(e,n.plotgroups)}e.d.wait.style("display","none")}catch(t){e.d.wait.text("ERROR: "+(t.message||t));if(t.stack)console.log(t.stack)}}function H(e,t){import("./plot.vaf2cov-b2284c64.js").then((n=>{const a={};e.d.svgdiv.selectAll("*").remove();for(const s of t){let o=e.d.svgdiv.append("div").style("display","inline-block").style("vertical-align","top");if(t.length>1){o.style("margin-right","30px").append("div").style("margin-top","10px").style("padding","3px 10px").style("background-color","#aaa").style("color","white").style("display","inline-block").style("font-size",".8em").style("font-weight","bold").text(s.name.toUpperCase());o=o.append("div").style("border","solid 1px #aaa")}const i={holder:o,data:s.lst,name:s.name,tip:e.tk.tktip,automax:true,samplecolor:"#4888BF",mouseover:e=>{if(!e.sampleobj)return;for(const t in a){if(t==s.name)continue;a[t].filter((t=>t.sampleobj.patient==e.sampleobj.patient)).each((e=>{e.crosshair1.attr("transform","scale(2.5)");e.crosshair2.attr("transform","scale(2.5)")}))}},mouseout:e=>{if(!e.sampleobj)return;for(const t in a){if(t==s.name)continue;a[t].filter((t=>t.sampleobj.patient==e.sampleobj.patient)).each((e=>{e.crosshair1.attr("transform","scale(1)");e.crosshair2.attr("transform","scale(1)")}))}}};if(e.tk&&e.tk.mds&&e.tk.mds.sample2bam){i.click=t=>{if(!t.sampleobj)return;const n=e.tk.mds.sample2bam[t.sampleobj.name];if(!n)return;e.d.tempbbdiv.selectAll("*").remove();import("./block-6aedd569.js").then((function(e){return e.c})).then((a=>{new a.Block({hostURL:sessionStorage.getItem("hostURL"),holder:e.d.tempbbdiv,genome:e.block.genome,nobox:true,chr:e.m.chr,start:e.m.pos-30,stop:e.m.pos+30,nativetracks:[e.block.genome.tracks.find((e=>e.__isgene)).name.toLowerCase()],tklst:[{type:"bam",name:t.sampleobj.name,file:n}],hlregions:[{chr:e.m.chr,start:e.m.pos,stop:e.m.pos}]})}))}}a[s.name]=n.default(i)}}))}async function Q(e,t,n,a){const{ssid:s,groups:o}=await te(t,n.mds.label,a.genome.name);const i=e.append("div");const l=i.append("div");try{const e={ssid:s,tip:n.legend.tip,mds:n.mds,genome:a.genome,termfilter:{filter:W(n)},dom:{}};Z(e,i,n);await X(e);l.remove()}catch(e){l.text("Error: "+(e.message||e));if(e.stack)console.log(e.stack)}}function W(e){if(e.vcf&&e.vcf.numerical_axis&&e.vcf.numerical_axis.in_use&&e.vcf.numerical_axis.inuse_AFtest){const t=e.vcf.numerical_axis.AFtest;const n=t.groups.find((e=>e.is_termdb));if(n){return n.filterApi.getNormalRoot()}}if(e.mds&&e.mds.termdb&&e.mds.termdb.selectCohort){const t=e.mds.termdb.selectCohort;return{type:"tvslst",join:"",in:true,lst:[{type:"tvs",tag:"cohortFilter",renderAs:"htmlSelect",selectOptionsFrom:"selectCohort",tvs:{term:JSON.parse(JSON.stringify(t.term)),values:t.values[0].keys.map((e=>({key:e})))}}]}}}function $(e){const t=["genome="+e.genome.name,"dslabel="+e.mds.label,"ssid="+e.ssid,"phewas=1","intendwidth="+e.svg.intendwidth,"axisheight="+e.svg.axisheight,"groupnamefontsize="+e.svg.groupnamefontsize,"dotradius="+e.svg.dotradius,"groupxspace="+e.svg.groupxspace,"leftpad="+e.svg.leftpad,"rightpad="+e.svg.rightpad,"toppad="+e.svg.toppad,"bottompad="+e.svg.bottompad,"devicePixelRatio="+(window.devicePixelRatio>1?window.devicePixelRatio:1)];if(e.termfilter.filter)t.push("filter="+encodeURIComponent(JSON.stringify(e.termfilter.filter)));return t}async function X(e){e.dom.svg.selectAll("*").remove();const n=await t("/termdb?"+$(e).join("&"));if(n.error)throw n.error;if(!n.tmpfile)throw"data.tmpfile missing";e.tmpfile=n.tmpfile;e.svg.ymax=n.maxlogp;e.dom.filter_says.text("n="+n.numberofsamples);K(n,e)}function Z(e,n,a){e.dom.row_filter=n.append("div").style("margin-bottom","5px");e.dom.row_message=n.append("div");e.dom.row_control=n.append("div").style("margin","10px 0px");e.dom.svg=n.append("svg");e.dom.row_details=n.append("div");e.svg={intendwidth:800,axisheight:300,groupnamefontsize:16,dotradius:2,groupxspace:3,leftpad:2,rightpad:2,toppad:20,bottompad:10};{e.dom.row_filter.append("div").style("display","inline-block").text("FILTER").style("font-size",".7em").style("opacity",.5);N({vocab:{route:"termdb",genome:e.genome.name,dslabel:e.mds.label},holder:e.dom.row_filter.append("div").style("display","inline-block").style("margin","0px 10px"),termdbConfig:e.mds.termdb,callback:async t=>{e.termfilter.filter=t;await X(e)}}).main(e.termfilter.filter);e.dom.filter_says=e.dom.row_filter.append("div").style("display","inline-block")}{const 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e.ld.overlaywith;s.style("display","none");e.skewer2.selectAll(".sja_aa_disk_fill").attr("fill",(e=>J(e)))}else{e.ld.overlaywith=e.ld.tracks[t-1].name;s.style("display","inline-block")}}));n.append("option").text("No overlay");for(const t of e.ld.tracks){n.append("option").text(t.name)}const s=t.append("div").style("display","none").style("margin-left","10px");const o=[];for(let t=0;t<=1;t+=.1){o.push(e.ld.overlay.r2_to_color(t))}const l=s.append("svg");const d=20;const p=15;const c=10;const f=150;r({axis:l.append("g").attr("transform","translate("+c+","+d+")").call(C().scale(i().domain([0,1]).range([0,f])).ticks(4)),fontsize:12});const u=l.append("defs").append("linearGradient").attr("id","grad");u.append("stop").attr("offset","0%").attr("stop-color",e.ld.overlay.color_0);u.append("stop").attr("offset","100%").attr("stop-color",e.ld.overlay.color_1);l.append("rect").attr("x",c).attr("y",d).attr("width",f).attr("height",p).attr("fill","url(#grad)");l.attr("width",c*2+f).attr("height",d+p)}}function ot(e,t){if(!e.legend)e.legend={};e.legend.tip=new _({padding:"0px"});const[n,a]=z(t,e.name);e.tr_legend=n;const s=a.append("table").style("border-spacing","5px").style("border-collapse","separate");e.legend.table=s;Ge(e,t);Ye(e,t);it(e);st(e,t);pt(e,t)}function it(e){if(!e.legend.mclass)e.legend.mclass={};if(!e.legend.mclass.hiddenvalues)e.legend.mclass.hiddenvalues=new Set;e.legend.mclass.row=e.legend.table.append("tr");e.legend.mclass.row.append("td").style("text-align","right").style("opacity",.8).text("Mutation");e.legend.mclass.holder=e.legend.mclass.row.append("td")}function lt(e,t,n){if(e.mclass2count){rt(e.mclass2count,t)}if(e.info_fields){dt(e.info_fields,t)}if(e.AFtest_termdbgroup){let n=t.vcf.numerical_axis.AFtest.groups[0];if(n.is_termdb){n.dom.samplehandle.text("n="+e.AFtest_termdbgroup[0].samplecount+", view stats");n.popsetaverage=e.AFtest_termdbgroup[0].popsetaverage}n=t.vcf.numerical_axis.AFtest.groups[1];if(n.is_termdb){n.dom.samplehandle.text("n="+e.AFtest_termdbgroup[1].samplecount+", view stats");n.popsetaverage=e.AFtest_termdbgroup[1].popsetaverage}}}function rt(t,n){n.legend.mclass.holder.selectAll("*").remove();const a=[],s=[];for(const e in t){const o={k:e,count:t[e]};if(n.legend.mclass.hiddenvalues.has(e)){s.push(o)}else{a.push(o)}}a.sort(((e,t)=>t.count-e.count));s.sort(((e,t)=>t.count-e.count));for(const t of a){let o,i,l="#858585";if(Number.isInteger(t.k)){o=b[t.k];if(t.dt==v){i="Copy number variation."}else if(t.dt==k){i="Loss of heterozygosity."}else if(t.dt==w){l=e[A].color;i="Internal tandem duplication."}else if(t.dt==F){i="Structural variation of DNA."}else if(t.dt==j){i="Fusion gene from RNA-seq."}}else{o=e[t.k].label;l=e[t.k].color;i=e[t.k].desc}const r=n.legend.mclass.holder.append("div").attr("class","sja_clb").style("display","inline-block").on("click",(()=>{n.legend.tip.clear().d.append("div").attr("class","sja_menuoption").text("Hide").on("click",(()=>{n.legend.mclass.hiddenvalues.add(t.k);n.legend.tip.hide();n.load()}));n.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show only").on("click",(()=>{for(const e of a){n.legend.mclass.hiddenvalues.add(e.k)}n.legend.mclass.hiddenvalues.delete(t.k);n.legend.tip.hide();n.load()}));if(s.length){n.legend.tip.d.append("div").attr("class","sja_menuoption").text("Show all").on("click",(()=>{n.legend.mclass.hiddenvalues.clear();n.legend.tip.hide();n.load()}))}n.legend.tip.d.append("div").style("padding","10px").style("font-size",".8em").style("width","150px").text(i);n.legend.tip.showunder(r.node())}));r.append("div").style("display","inline-block").attr("class","sja_mcdot").style("background",l).html(t.count>1?t.count:"&nbsp;");r.append("div").style("display","inline-block").style("color",l).html("&nbsp;"+o)}for(const t of s){let a=false;n.legend.mclass.holder.append("div").style("display","inline-block").attr("class","sja_clb").style("text-decoration","line-through").style("opacity",.3).text("("+t.count+") "+(Number.isInteger(t.k)?b[t.k]:e[t.k].label)).on("click",(async e=>{if(a)return;a=true;n.legend.mclass.hiddenvalues.delete(t.k);e.target.innerHTML="Updating...";await n.load()}))}}function dt(e,t){for(const n in e){const a=t.info_fields.find((e=>e.key==n));if(!a){console.log("info field not found by key: "+n);continue}a._data=e[n];if(a.isactivefilter){if(a.iscategorical){if(a.unannotated_htmlspan)a.unannotated_htmlspan.text("("+(a._data.unannotated_count||0)+") Unannotated");for(const e of a.values){if(e.htmlspan){e.htmlspan.text("("+(a._data.value2count[e.key]||0)+") "+e.label)}}}else if(a.isinteger||a.isfloat){if(a.htmlspan)a.htmlspan.text("("+a._data.filteredcount+" filtered)")}else if(a.isflag){if(a.htmlspan)a.htmlspan.text("("+(a.remove_yes?a._data.count_yes:a._data.count_no)+") "+(a.remove_no?"No":"Yes"))}else{throw"unknown info type"}}}}function pt(e,t){if(e.mds&&e.mds.hide_genotypedownload)return;const n=e.legend.table.append("tr").append("td").attr("colspan",2).append("button").text("Export genotype");n.on("click",(async()=>{n.property("disabled",true);const a=vt(e,t);a.exportgenotype=true;delete a.trigger_ld;delete a.AFtest;const s=await d("mds2",a);if(s.error)throw s.error;const o=document.createElement("a");document.body.appendChild(o);o.addEventListener("click",(function(){o.download="genotype.txt";const e=new Blob([s.exportgenotype],{type:"octet/stream"});o.href=URL.createObjectURL(e);document.body.removeChild(o)}),false);o.click();n.property("disabled",false)}))}function ct(e,t){return()=>xt(e,t)}async function ft(e,t){e.load=ct(e,t);e.tip2=new _({padding:"0px"});if(e.dslabel){const n=t.genome.datasets[e.dslabel];if(!n)throw"dataset not found for "+e.dslabel;if(n.mdsIsUninitiated){const e=await s(`getDataset?genome=${t.genome.name}&dsname=${n.label}`);if(e.error)throw e.error;if(!e.ds)throw"ds missing";Object.assign(n,e.ds);delete n.mdsIsUninitiated}e.mds=n;if(!e.mds.track)throw"mds.track{} missing: dataset not configured for mds2 track";ht(e)}else{if(!e.name)e.name="Unnamed";if(e.vcf){await G(e.vcf,t.genome)}}ut(e);yt(e);e.tklabel.text(e.name);mt(e,t);gt(e);e.clear=()=>{if(e.g_vcfrow)e.g_vcfrow.selectAll("*").remove();if(e.leftaxis_vcfrow)e.leftaxis_vcfrow.selectAll("*").remove();if(e.g_ldrow)e.g_ldrow.selectAll("*").remove();if(e.gleft_ldrow)e.gleft_ldrow.selectAll("*").remove()};e.config_handle=t.maketkconfighandle(e).on("click",(()=>{}));ot(e,t)}function ut(e){if(e.termdb2groupAF){if(!e.mds)throw".mds missing";if(!e.mds.termdb)throw".mds.termdb missing";if(!e.vcf)throw"tk.vcf missing";if(!e.vcf.numerical_axis){e.vcf.numerical_axis={}}e.vcf.numerical_axis.termdb2groupAF=e.termdb2groupAF;delete e.termdb2groupAF}if(e.numericaxis_inuse_ebgatest){if(!e.vcf)throw"tk.vcf missing";if(!e.vcf.numerical_axis){e.vcf.numerical_axis={}}e.vcf.numerical_axis.inuse_ebgatest=true;delete e.vcf.numerical_axis.inuse_infokey;delete e.vcf.numerical_axis.inuse_termdb2groupAF}}function mt(e,t){if(!e.vcf)return;e.g_vcfrow=e.glider.append("g");e.g_vcfrow_layer2=e.glider.append("g");e.leftaxis_vcfrow=e.gleft.append("g");e.vcfrow_label_numbervariants=t.maketklefthandle(e,15).on("click",(()=>{if(!e.__vcf_data||!e.__vcf_data.vcf||!e.__vcf_data.vcf.rglst)return;const t=[];for(const n of e.__vcf_data.vcf.rglst){if(!n.variants)continue;for(const e of n.variants){t.push(e.chr+":"+(e.pos+1)+" "+e.ref+">"+e.altstr)}}e.tktip.showunder(e.vcfrow_label_numbervariants.node());e.tktip.clear().d.append("textarea").attr("cols",25).attr("rows",20).text(t.join("\n"))}));try{Fe(e)}catch(e){throw"numerical axis error: "+e}}function gt(e){if(!e.ld)return;e.g_ldrow=e.glider.append("g");e.gleft_ldrow=e.gleft.append("g");if(e.g_vcfrow_layer2){e.ld.overlay.vcfcircle=e.g_vcfrow_layer2.append("circle").attr("fill","none").attr("stroke","black").attr("stroke-width",2).attr("stroke-opacity",0)}}function ht(e){if(!e.mds)return;e.name=e.mds.track.name;if(e.mds.track.vcf){if(!e.vcf)e.vcf={};const t=JSON.parse(JSON.stringify(e.mds.track.vcf));for(const n in t){if(e.vcf[n]==undefined)e.vcf[n]=t[n]}if(t.numerical_axis){for(const n in t.numerical_axis){if(e.vcf.numerical_axis[n]==undefined)e.vcf.numerical_axis[n]=t.numerical_axis[n]}if(t.numerical_axis.AFtest){for(const n in t.numerical_axis.AFtest){if(e.vcf.numerical_axis.AFtest[n]==undefined)e.vcf.numerical_axis.AFtest[n]=t.numerical_axis.AFtest[n]}}}}if(e.mds.track.ld){if(!e.ld)e.ld={};if(!e.ld.connheight)e.ld.connheight=50;const t=JSON.parse(JSON.stringify(e.mds.track.ld));for(const n in t){if(e.ld[n]==undefined)e.ld[n]=t[n]}e.ld.overlay.r2_to_color=L(e.ld.overlay.color_0,e.ld.overlay.color_1)}if(e.mds.track.info_fields){e.info_fields=JSON.parse(JSON.stringify(e.mds.track.info_fields))}if(e.mds.track.populations){e.populations=JSON.parse(JSON.stringify(e.mds.track.populations))}if(e.mds.track.sample_termfilter)e.sample_termfilter=JSON.parse(JSON.stringify(e.mds.track.sample_termfilter))}function yt(e){if(!e.info_fields)return;if(!Array.isArray(e.info_fields))throw"info_fields should be an array";for(const t of e.info_fields){if(!t.key)throw"key missing from one of info_fields";if(!t.label)t.label=t.key;if(!t.isfilter)continue;if(t.iscategorical){if(!t.values)throw".values[] missing from a categorical info field "+t.label;if(!Array.isArray(t.values))throw".values[] not an array from info field "+t.label;for(const e of t.values){if(!e.key)throw".key missing from a value of info field "+t.label;if(!e.label)e.label=e.key}}else if(t.isinteger||t.isfloat){if(!t.range)throw".range{} missing from a numeric info field "+t.label}else if(t.isflag);else{throw"info field "+t.label+" neither numerical or categorical"}}}async function xt(e,t){t.tkcloakon(e);t.block_setheight();const n=bt(e,t);try{if(e.uninitialized){await ft(e,t);delete e.uninitialized}e.tklabel.each((function(){e.leftLabelMaxwidth=this.getBBox().width}));const a=await _t(e,t);e.clear();const s=B(a,e,t);const o=at(a,e,t);if(e.g_ldrow){e.g_ldrow.transition().attr("transform","translate(0,"+s+")");e.gleft_ldrow.transition().attr("transform","translate(0,"+s+")")}e.height_main=s+o;n(a)}catch(t){if(e.clear)e.clear();e.height_main=50;n({error:t.message||t});if(t.stack)console.log(t.stack);return}}async function _t(e,t){const n=vt(e,t);return d("mds2",n).then((e=>{if(e.error)throw e.error;return e}))}function bt(e,t){return n=>{lt(n,e);t.tkcloakoff(e,{error:n.error});t.block_setheight();t.setllabel()}}function vt(e,t){const n={genome:t.genome.name};kt(n,e);if(e.legend.mclass.hiddenvalues.size){n.hidden_mclass=[...e.legend.mclass.hiddenvalues]}if(e.mds){n.dslabel=e.mds.label}else{if(e.vcf){n.vcf={file:e.vcf.file,url:e.vcf.url,indexURL:e.vcf.indexURL}}}if(e.vcf){n.trigger_vcfbyrange=1;Ne(e,n)}if(e.ld){const t=e.ld.tracks.filter((e=>e.shown));if(t.length){n.trigger_ld={tracks:t,connheight:e.ld.connheight}}}n.rglst=t.tkarg_rglst(e);if(t.usegm){const e=n.rglst[0];e.usegm_isoform=t.usegm.isoform;for(let a=1;a<n.rglst.length;a++){const s=n.rglst[a];e.width+=s.width+t.regionspace;e.start=Math.min(e.start,s.start);e.stop=Math.max(e.stop,s.stop)}n.rglst=[e]}let a=0;for(const e of n.rglst){e.xoff=0;a+=e.width+t.regionspace}if(t.subpanels.length==e.subpanels.length){for(const e of t.subpanels){n.rglst.push({chr:e.chr,start:e.start,stop:e.stop,width:e.width,exonsf:e.exonsf,xoff:a});a+=e.width+e.leftpad}}return n}function kt(e,t){if(t.info_fields){e.info_fields=t.info_fields.reduce(((e,t)=>{if(t.isfilter){if(t.iscategorical){const n={key:t.key,iscategorical:true,unannotated_ishidden:t.unannotated_ishidden,hiddenvalues:{}};for(const e of t.values){if(e.ishidden)n.hiddenvalues[e.key]=1}e.push(n)}else if(t.isinteger||t.isfloat){if(t.isactivefilter){e.push({key:t.key,isnumerical:true,missing_value:t.missing_value,range:t.range})}}else if(t.isflag){e.push({key:t.key,isflag:true,remove_no:t.remove_no,remove_yes:t.remove_yes})}else{throw"unknown type of info filter"}}return e}),[])}}export{vt as addparameter_rangequery,xt as loadTk};

package/dist/{block.svg-9121e8e7.js → block.svg-9b916fa6.js}

@@ -1 +1 @@
-import{U as t,aH as e,ah as n,z as a,O as s}from"./app-a8c4854a.js";const r=20;const o=2;const l=20;const i=3;const f=16;function c(e){for(const t of e.tklst){if(t.config_handle)t.config_handle.text("");if(t.label_close)t.label_close.text("")}const n=e.totalheight();let a;const[s,o]=d(e,n+r);const[l,i]=g(e,n+r);a=n+r+Math.max(s,l)+r;e.svg.attr("height",a);const f=[];if(e.usegm&&e.usegm.name)f.push(e.usegm.name);if(e.usegm&&e.usegm.isoform)f.push(e.usegm.isoform);t(e.svg.node(),f.length?f.join("_"):"screenshot");for(const t of e.tklst){if(t.config_handle)t.config_handle.text("CONFIG");if(t.label_close)t.label_close.text("Close")}if(o)o.remove();if(i)i.remove();e.svg.attr("height",n)}function d(t,a){const s=t.usegm;if(!s){return[0,null]}const r=e(s);if(r.length==0){return[0,null]}const c=[];for(const t of r){if(!s.domain_hidden[t.name+t.description]){c.push(t)}}if(c.length==0)return[0,null];const d=t.svg.append("g").attr("transform","translate("+(o+t.leftheadw)+","+a+")");let g=0;for(const t of c){const e=d.append("g").attr("transform","translate(0,"+g+")");e.append("rect").attr("width",15).attr("height",l).attr("stroke",t.stroke).attr("fill",t.fill).attr("shape-rendering","crispEdges");let a;e.append("text").attr("x",20).attr("y",l/2).attr("dominant-baseline","central").attr("font-size",f).attr("font-family",n).attr("fill","black").text(t.name).each((function(){a=this.getBBox().width}));if(t.description){e.append("text").attr("x",30+a).attr("y",l/2).attr("dominant-baseline","central").attr("font-size",12).attr("font-family",n).attr("fill","#858585").text(t.description.length>80?t.description.substr(0,70)+" ...":t.description)}g+=l+i}return[g,d]}function g(t,e){if(!t.legend){return[0,null]}let r=0;const c=m(t);r+=c.length;if(t.legend.morigins&&t.legend.morigins.size>0){for(const[e,n]of t.legend.morigins){if(!n.hidden){r++}}}if(r==0)return[0,null];let d=0;const g=t.svg.append("g").attr("transform","translate("+(o+t.leftheadw+t.lpad+t.width-200)+","+e+")");for(const[t,e]of c){const s=g.append("g").attr("transform","translate(0,"+d+")");s.append("circle").attr("cx",l/2).attr("cy",l/2).attr("r",l/2).attr("fill",a[t].color);s.append("text").text(a[t].label+", n="+e).attr("x",l+10).attr("y",l/2).attr("dominant-baseline","central").attr("font-size",f).attr("font-family",n).attr("fill",a[t].color);d+=l+i}if(t.legend.morigins&&t.legend.morigins.size>0){for(const[e,a]of t.legend.morigins){if(a.hidden){continue}const t=g.append("g").attr("transform","translate(0,"+d+")");const r=t.append("g").attr("transform","translate(5,0)");r.html(s[e].legend);t.append("text").text(s[e].label+", n="+a.count).attr("x",l+10).attr("y",l/2).attr("dominant-baseline","central").attr("font-size",f).attr("font-family",n).attr("fill","black");d+=l+i}}return[d,g]}function m(t){const e=[];if(t.legend.mclasses&&t.legend.mclasses.size>0){for(const[n,a]of t.legend.mclasses){if(!a.hidden)e.push([n,a.count])}}const n=t.tklst.find((t=>t.type=="mds3"));if(n&&n.legend?.mclass?.currentData){for(const t of n.legend.mclass.currentData){if(!n.legend.mclass.hiddenvalues.has(t[0])){e.push(t)}}}return e}export{c as default};
+import{U as t,aH as e,ah as n,z as a,O as s}from"./app-b369b169.js";const r=20;const o=2;const l=20;const i=3;const f=16;function c(e){for(const t of e.tklst){if(t.config_handle)t.config_handle.text("");if(t.label_close)t.label_close.text("")}const n=e.totalheight();let a;const[s,o]=d(e,n+r);const[l,i]=g(e,n+r);a=n+r+Math.max(s,l)+r;e.svg.attr("height",a);const f=[];if(e.usegm&&e.usegm.name)f.push(e.usegm.name);if(e.usegm&&e.usegm.isoform)f.push(e.usegm.isoform);t(e.svg.node(),f.length?f.join("_"):"screenshot");for(const t of e.tklst){if(t.config_handle)t.config_handle.text("CONFIG");if(t.label_close)t.label_close.text("Close")}if(o)o.remove();if(i)i.remove();e.svg.attr("height",n)}function d(t,a){const s=t.usegm;if(!s){return[0,null]}const r=e(s);if(r.length==0){return[0,null]}const c=[];for(const t of r){if(!s.domain_hidden[t.name+t.description]){c.push(t)}}if(c.length==0)return[0,null];const d=t.svg.append("g").attr("transform","translate("+(o+t.leftheadw)+","+a+")");let g=0;for(const t of c){const e=d.append("g").attr("transform","translate(0,"+g+")");e.append("rect").attr("width",15).attr("height",l).attr("stroke",t.stroke).attr("fill",t.fill).attr("shape-rendering","crispEdges");let a;e.append("text").attr("x",20).attr("y",l/2).attr("dominant-baseline","central").attr("font-size",f).attr("font-family",n).attr("fill","black").text(t.name).each((function(){a=this.getBBox().width}));if(t.description){e.append("text").attr("x",30+a).attr("y",l/2).attr("dominant-baseline","central").attr("font-size",12).attr("font-family",n).attr("fill","#858585").text(t.description.length>80?t.description.substr(0,70)+" ...":t.description)}g+=l+i}return[g,d]}function g(t,e){if(!t.legend){return[0,null]}let r=0;const c=m(t);r+=c.length;if(t.legend.morigins&&t.legend.morigins.size>0){for(const[e,n]of t.legend.morigins){if(!n.hidden){r++}}}if(r==0)return[0,null];let d=0;const g=t.svg.append("g").attr("transform","translate("+(o+t.leftheadw+t.lpad+t.width-200)+","+e+")");for(const[t,e]of c){const s=g.append("g").attr("transform","translate(0,"+d+")");s.append("circle").attr("cx",l/2).attr("cy",l/2).attr("r",l/2).attr("fill",a[t].color);s.append("text").text(a[t].label+", n="+e).attr("x",l+10).attr("y",l/2).attr("dominant-baseline","central").attr("font-size",f).attr("font-family",n).attr("fill",a[t].color);d+=l+i}if(t.legend.morigins&&t.legend.morigins.size>0){for(const[e,a]of t.legend.morigins){if(a.hidden){continue}const t=g.append("g").attr("transform","translate(0,"+d+")");const r=t.append("g").attr("transform","translate(5,0)");r.html(s[e].legend);t.append("text").text(s[e].label+", n="+a.count).attr("x",l+10).attr("y",l/2).attr("dominant-baseline","central").attr("font-size",f).attr("font-family",n).attr("fill","black");d+=l+i}}return[d,g]}function m(t){const e=[];if(t.legend.mclasses&&t.legend.mclasses.size>0){for(const[n,a]of t.legend.mclasses){if(!a.hidden)e.push([n,a.count])}}const n=t.tklst.find((t=>t.type=="mds3"));if(n&&n.legend?.mclass?.currentData){for(const t of n.legend.mclass.currentData){if(!n.legend.mclass.hiddenvalues.has(t[0])){e.push(t)}}}return e}export{c as default};

package/dist/{block.tk.aicheck-c1b478e9.js → block.tk.aicheck-6770e333.js}

@@ -1 +1 @@
-import{a7 as t,I as e,ag as a,ah as r,k as i}from"./app-a8c4854a.js";import{m as o}from"./radiobutton-09bff425.js";import{b as n,d as l}from"./axis-747c801e.js";function s(t,e){t.img=t.glider.append("image");if(!t.dotsize){t.dotsize=1}if(!t.coveragemax){t.coveragemax=100}if(!t.vafheight){t.vafheight=50}if(!t.coverageheight){t.coverageheight=30}if(!t.rowspace){t.rowspace=5}t.tklabel.attr("y",20);t.Tvafaxis=t.gleft.append("g");t.Nvafaxis=t.gleft.append("g");t.aiaxis=t.gleft.append("g");t.label_tumor=t.gleft.append("text").attr("font-family",r).attr("font-size",e.labelfontsize).attr("dominant-baseline","central").attr("text-anchor","end").attr("x",e.tkleftlabel_xshift).attr("fill-opacity",.6).text("Tumor");t.label_germline=t.gleft.append("text").attr("font-family",r).attr("font-size",e.labelfontsize).attr("dominant-baseline","central").attr("text-anchor","end").attr("x",e.tkleftlabel_xshift).attr("fill-opacity",.6).text("Germline");t.label_ai=t.gleft.append("text").attr("font-family",r).attr("font-size",e.labelfontsize).attr("dominant-baseline","central").attr("text-anchor","end").attr("x",e.tkleftlabel_xshift).attr("fill-opacity",.6).text("abs(T-G)");t.Tcovaxis=t.gright.append("g");t.Ncovaxis=t.gright.append("g");t.label_tumorcoverage=t.gright.append("text").attr("font-family",r).attr("font-size",e.labelfontsize).attr("dominant-baseline","central").attr("x",10).attr("fill-opacity",.6).text("T coverage");t.label_germlinecoverage=t.gright.append("text").attr("font-family",r).attr("font-size",e.labelfontsize).attr("dominant-baseline","central").attr("x",10).attr("fill-opacity",.6).text("G coverage");t.config_handle=e.maketkconfighandle(t).on("click",(a=>{t.tkconfigtip.clear().showunder(t.config_handle.node());p(t,e)}))}function c(t,e,a,r){const i=["rglst="+JSON.stringify(r||e.tkarg_rglst()),"regionspace="+e.regionspace,"width="+(a||e.width),"coveragemax="+t.coveragemax,"gtotalcutoff="+t.gtotalcutoff,"gmafrestrict="+t.gmafrestrict,"vafheight="+t.vafheight,"coverageheight="+t.coverageheight,"rowspace="+t.rowspace,"dotsize="+t.dotsize,"devicePixelRatio="+(window.devicePixelRatio>1?window.devicePixelRatio:1)];if(t.file){i.push("file="+t.file)}else{i.push("url="+t.url);if(t.indexURL)i.push("indexURL="+t.indexURL)}return i.join("&")}function g(r,i){if(r.uninitialized){s(r,i);delete r.uninitialized}i.tkcloakon(r);t("tkaicheck?"+c(r,i)).then((t=>{if(t.error)throw{message:t.error};const o=r.vafheight*3+r.rowspace*4+r.coverageheight*2;r.height_main=r.toppad+o+r.bottompad;r.img.attr("width",i.width).attr("height",o).attr("xlink:href",t.src);if(t.coveragemax){r.coveragemax=t.coveragemax}if(!t.nodata){const t=e().domain([0,1]).range([r.vafheight,0]);let i=0;a({axis:r.Tvafaxis.attr("transform","translate(0,"+i+")").call(n().scale(t).tickValues([0,1])),color:"black",showline:true});r.label_tumor.attr("y",i+r.vafheight*3/4);i=r.vafheight+r.rowspace+r.coverageheight+r.rowspace;a({axis:r.Nvafaxis.attr("transform","translate(0,"+i+")").call(n().scale(t).tickValues([0,1])),color:"black",showline:true});r.label_germline.attr("y",i+r.vafheight/2);i=2*(r.vafheight+r.rowspace+r.coverageheight+r.rowspace);a({axis:r.aiaxis.attr("transform","translate(0,"+i+")").call(n().scale(t).tickValues([0,1])),color:"black",showline:true});r.label_ai.attr("y",i+r.vafheight/2);const o=e().domain([0,r.coveragemax]).range([r.coverageheight,0]);i=r.vafheight+r.rowspace;a({axis:r.Tcovaxis.attr("transform","translate(0,"+i+")").call(l().scale(o).tickValues([0,r.coveragemax])),color:"black",showline:true});r.label_tumorcoverage.attr("y",i+r.coverageheight/2);i=2*(r.vafheight+r.rowspace)+r.coverageheight+r.rowspace;a({axis:r.Ncovaxis.attr("transform","translate(0,"+i+")").call(l().scale(o).tickValues([0,r.coveragemax])),color:"black",showline:true});r.label_germlinecoverage.attr("y",i+r.coverageheight/2)}return null})).catch((t=>{r.img.attr("width",1).attr("height",1);if(t.stack){console.log(t.stack)}return t.message})).then((t=>{i.tkcloakoff(r,{error:t});i.block_setheight();for(const t of r.subpanels){f(r,i,t)}}))}function f(e,a,r){a.tkcloakon_subpanel(r);const i=c(e,a,r.width,[{chr:r.chr,start:r.start,stop:r.stop,width:r.width}]);t("tkaicheck?"+i).then((t=>{if(t.error)throw{message:t.error};r.img.attr("width",r.width).attr("height",e.vafheight*3+e.rowspace*4+e.coverageheight*2).attr("xlink:href",t.src);return null})).catch((t=>{r.img.attr("width",1).attr("height",1);if(t.stack){console.log(t.stack)}return t.message})).then((t=>{a.tkcloakoff_subpanel(r,{error:t})}))}function p(t,e){t.tkconfigtip.clear();{const a=t.tkconfigtip.d.append("div").style("margin-bottom","15px");a.append("span").html("Coverage max:&nbsp;");a.append("input").attr("type","number").style("width","60px").property("value",t.coveragemax).on("keyup",(a=>{if(!i(a))return;const r=a.target.value;if(r=="")return;const o=Number.parseInt(r);if(Number.isNaN(o)||o<=1){alert("coverage max must be positive integer");return}t.coveragemax=o;g(t,e)}))}{const a=t.tkconfigtip.d.append("div").style("margin-bottom","15px");a.append("span").html("Marker dot size:&nbsp;");o({holder:a,options:[{label:"1 pixel",value:1,checked:t.dotsize==1},{label:"2 pixels",value:2,checked:t.dotsize==2},{label:"3 pixels",value:3,checked:t.dotsize==3}],callback:a=>{t.dotsize=a;g(t,e)},styles:{display:"inline-block","margin-right":"5px"}})}{const a=t.tkconfigtip.d.append("div").style("margin-bottom","15px");a.append("span").html("Filter markers by minimum total germline coverage:&nbsp;");a.append("input").attr("type","number").style("width","60px").property("value",t.gtotalcutoff||0).on("keyup",(a=>{if(!i(a))return;const r=a.target.value;if(r=="")return;const o=Number.parseInt(r);if(Number.isNaN(o)||o<0){alert("coverage max must be non-negative integer");return}if(o==t.gtotalcutoff)return;t.gtotalcutoff=o;g(t,e)}));a.append("div").style("font-size",".7em").style("opacity",.5).text("Set to 0 to use all markers")}{const a=t.tkconfigtip.d.append("div").style("margin-bottom","15px");a.append("span").html("Filter markers by narrowing range of germline B-allele fraction:&nbsp;");a.append("input").attr("type","number").style("width","60px").property("value",t.gmafrestrict||0).on("keyup",(a=>{if(!i(a))return;const r=a.target.value;if(r=="")return;const o=Number.parseFloat(r);if(Number.isNaN(o)||o<0||o>.5){alert("Must enter a value between 0 and 0.5");return}if(t.gmafrestrict==o)return;t.gmafrestrict=o;g(t,e);p(t,e)}));a.append("div").style("font-size",".7em").style("opacity",.5).text((t.gmafrestrict?"Keeping markers with BAF range "+t.gmafrestrict+" to "+(1-t.gmafrestrict)+". ":"")+"Set to 0 to use all markers")}}export{g as loadTk,f as loadTksubpanel};
+import{a7 as t,I as e,ag as a,ah as r,k as i}from"./app-b369b169.js";import{m as o}from"./radiobutton-09bff425.js";import{b as n,d as l}from"./axis-747c801e.js";function s(t,e){t.img=t.glider.append("image");if(!t.dotsize){t.dotsize=1}if(!t.coveragemax){t.coveragemax=100}if(!t.vafheight){t.vafheight=50}if(!t.coverageheight){t.coverageheight=30}if(!t.rowspace){t.rowspace=5}t.tklabel.attr("y",20);t.Tvafaxis=t.gleft.append("g");t.Nvafaxis=t.gleft.append("g");t.aiaxis=t.gleft.append("g");t.label_tumor=t.gleft.append("text").attr("font-family",r).attr("font-size",e.labelfontsize).attr("dominant-baseline","central").attr("text-anchor","end").attr("x",e.tkleftlabel_xshift).attr("fill-opacity",.6).text("Tumor");t.label_germline=t.gleft.append("text").attr("font-family",r).attr("font-size",e.labelfontsize).attr("dominant-baseline","central").attr("text-anchor","end").attr("x",e.tkleftlabel_xshift).attr("fill-opacity",.6).text("Germline");t.label_ai=t.gleft.append("text").attr("font-family",r).attr("font-size",e.labelfontsize).attr("dominant-baseline","central").attr("text-anchor","end").attr("x",e.tkleftlabel_xshift).attr("fill-opacity",.6).text("abs(T-G)");t.Tcovaxis=t.gright.append("g");t.Ncovaxis=t.gright.append("g");t.label_tumorcoverage=t.gright.append("text").attr("font-family",r).attr("font-size",e.labelfontsize).attr("dominant-baseline","central").attr("x",10).attr("fill-opacity",.6).text("T coverage");t.label_germlinecoverage=t.gright.append("text").attr("font-family",r).attr("font-size",e.labelfontsize).attr("dominant-baseline","central").attr("x",10).attr("fill-opacity",.6).text("G coverage");t.config_handle=e.maketkconfighandle(t).on("click",(a=>{t.tkconfigtip.clear().showunder(t.config_handle.node());p(t,e)}))}function c(t,e,a,r){const i=["rglst="+JSON.stringify(r||e.tkarg_rglst()),"regionspace="+e.regionspace,"width="+(a||e.width),"coveragemax="+t.coveragemax,"gtotalcutoff="+t.gtotalcutoff,"gmafrestrict="+t.gmafrestrict,"vafheight="+t.vafheight,"coverageheight="+t.coverageheight,"rowspace="+t.rowspace,"dotsize="+t.dotsize,"devicePixelRatio="+(window.devicePixelRatio>1?window.devicePixelRatio:1)];if(t.file){i.push("file="+t.file)}else{i.push("url="+t.url);if(t.indexURL)i.push("indexURL="+t.indexURL)}return i.join("&")}function g(r,i){if(r.uninitialized){s(r,i);delete r.uninitialized}i.tkcloakon(r);t("tkaicheck?"+c(r,i)).then((t=>{if(t.error)throw{message:t.error};const o=r.vafheight*3+r.rowspace*4+r.coverageheight*2;r.height_main=r.toppad+o+r.bottompad;r.img.attr("width",i.width).attr("height",o).attr("xlink:href",t.src);if(t.coveragemax){r.coveragemax=t.coveragemax}if(!t.nodata){const t=e().domain([0,1]).range([r.vafheight,0]);let i=0;a({axis:r.Tvafaxis.attr("transform","translate(0,"+i+")").call(n().scale(t).tickValues([0,1])),color:"black",showline:true});r.label_tumor.attr("y",i+r.vafheight*3/4);i=r.vafheight+r.rowspace+r.coverageheight+r.rowspace;a({axis:r.Nvafaxis.attr("transform","translate(0,"+i+")").call(n().scale(t).tickValues([0,1])),color:"black",showline:true});r.label_germline.attr("y",i+r.vafheight/2);i=2*(r.vafheight+r.rowspace+r.coverageheight+r.rowspace);a({axis:r.aiaxis.attr("transform","translate(0,"+i+")").call(n().scale(t).tickValues([0,1])),color:"black",showline:true});r.label_ai.attr("y",i+r.vafheight/2);const o=e().domain([0,r.coveragemax]).range([r.coverageheight,0]);i=r.vafheight+r.rowspace;a({axis:r.Tcovaxis.attr("transform","translate(0,"+i+")").call(l().scale(o).tickValues([0,r.coveragemax])),color:"black",showline:true});r.label_tumorcoverage.attr("y",i+r.coverageheight/2);i=2*(r.vafheight+r.rowspace)+r.coverageheight+r.rowspace;a({axis:r.Ncovaxis.attr("transform","translate(0,"+i+")").call(l().scale(o).tickValues([0,r.coveragemax])),color:"black",showline:true});r.label_germlinecoverage.attr("y",i+r.coverageheight/2)}return null})).catch((t=>{r.img.attr("width",1).attr("height",1);if(t.stack){console.log(t.stack)}return t.message})).then((t=>{i.tkcloakoff(r,{error:t});i.block_setheight();for(const t of r.subpanels){f(r,i,t)}}))}function f(e,a,r){a.tkcloakon_subpanel(r);const i=c(e,a,r.width,[{chr:r.chr,start:r.start,stop:r.stop,width:r.width}]);t("tkaicheck?"+i).then((t=>{if(t.error)throw{message:t.error};r.img.attr("width",r.width).attr("height",e.vafheight*3+e.rowspace*4+e.coverageheight*2).attr("xlink:href",t.src);return null})).catch((t=>{r.img.attr("width",1).attr("height",1);if(t.stack){console.log(t.stack)}return t.message})).then((t=>{a.tkcloakoff_subpanel(r,{error:t})}))}function p(t,e){t.tkconfigtip.clear();{const a=t.tkconfigtip.d.append("div").style("margin-bottom","15px");a.append("span").html("Coverage max:&nbsp;");a.append("input").attr("type","number").style("width","60px").property("value",t.coveragemax).on("keyup",(a=>{if(!i(a))return;const r=a.target.value;if(r=="")return;const o=Number.parseInt(r);if(Number.isNaN(o)||o<=1){alert("coverage max must be positive integer");return}t.coveragemax=o;g(t,e)}))}{const a=t.tkconfigtip.d.append("div").style("margin-bottom","15px");a.append("span").html("Marker dot size:&nbsp;");o({holder:a,options:[{label:"1 pixel",value:1,checked:t.dotsize==1},{label:"2 pixels",value:2,checked:t.dotsize==2},{label:"3 pixels",value:3,checked:t.dotsize==3}],callback:a=>{t.dotsize=a;g(t,e)},styles:{display:"inline-block","margin-right":"5px"}})}{const a=t.tkconfigtip.d.append("div").style("margin-bottom","15px");a.append("span").html("Filter markers by minimum total germline coverage:&nbsp;");a.append("input").attr("type","number").style("width","60px").property("value",t.gtotalcutoff||0).on("keyup",(a=>{if(!i(a))return;const r=a.target.value;if(r=="")return;const o=Number.parseInt(r);if(Number.isNaN(o)||o<0){alert("coverage max must be non-negative integer");return}if(o==t.gtotalcutoff)return;t.gtotalcutoff=o;g(t,e)}));a.append("div").style("font-size",".7em").style("opacity",.5).text("Set to 0 to use all markers")}{const a=t.tkconfigtip.d.append("div").style("margin-bottom","15px");a.append("span").html("Filter markers by narrowing range of germline B-allele fraction:&nbsp;");a.append("input").attr("type","number").style("width","60px").property("value",t.gmafrestrict||0).on("keyup",(a=>{if(!i(a))return;const r=a.target.value;if(r=="")return;const o=Number.parseFloat(r);if(Number.isNaN(o)||o<0||o>.5){alert("Must enter a value between 0 and 0.5");return}if(t.gmafrestrict==o)return;t.gmafrestrict=o;g(t,e);p(t,e)}));a.append("div").style("font-size",".7em").style("opacity",.5).text((t.gmafrestrict?"Keeping markers with BAF range "+t.gmafrestrict+" to "+(1-t.gmafrestrict)+". ":"")+"Set to 0 to use all markers")}}export{g as loadTk,f as loadTksubpanel};

package/dist/{block.tk.ase-0f6ded48.js → block.tk.ase-ee807e59.js}

@@ -1 +1 @@
-import{q as a,ag as e,I as t,ae as r,a9 as n,k as o}from"./app-a8c4854a.js";import{r as i,c as s}from"./block.mds.svcnv.share-81e62600.js";import{m as c,a as l,s as p,i as g}from"./block.mds.expressionstat-31dc5595.js";import{b as f}from"./axis-747c801e.js";async function d(a,e){e.tkcloakon(a);e.block_setheight();if(a.uninitialized){u(a,e)}const t=[];let r=0;for(let a=e.startidx;a<=e.stopidx;a++){const n=e.rglst[a];t.push({chr:n.chr,start:n.start,stop:n.stop,width:n.width,x:r});r+=n.width+e.regionspace}if(e.subpanels.length==a.subpanels.length){for(const[a,n]of e.subpanels.entries()){r+=n.leftpad;t.push({chr:n.chr,start:n.start,stop:n.stop,width:n.width,exonsf:n.exonsf,subpanelidx:a,x:r});r+=n.width}}a.regions=t;try{a.dna.coveragemax=0;if(a.rna.coverageauto)a.rna.coveragemax=0;for(const r of t){await m(r,a,e)}h(a,e);e.tkcloakoff(a,{})}catch(t){if(t.stack)console.log(t.stack);a.height_main=a.height=100;e.tkcloakoff(a,{error:t.message||t})}e.block_setheight()}function m(e,t,r){const n={genome:r.genome.name,samplename:t.samplename,rnabamfile:t.rnabamfile,rnabamurl:t.rnabamurl,rnabamindexURL:t.rnabamindexURL,rnabamtotalreads:t.rnabamtotalreads,rnabamispairedend:t.rnabamispairedend,vcffile:t.vcffile,vcfurl:t.vcfurl,vcfindexURL:t.vcfindexURL,rnabarheight:t.rna.coveragebarh,dnabarheight:t.dna.coveragebarh,barypad:t.barypad,chr:e.chr,start:e.start,stop:e.stop,width:e.width,checkrnabam:t.checkrnabam,refcolor:t.dna.refcolor,altcolor:t.dna.altcolor,devicePixelRatio:window.devicePixelRatio>1?window.devicePixelRatio:1};if(!t.rna.coverageauto){n.rnamax=t.rna.coveragemax}return a("ase",n).then((a=>{if(a.error)throw a.error;e.genes=a.genes;e.fpkmrangelimit=a.fpkmrangelimit;if(a.covplotrangelimit){e.covplotrangelimit=a.covplotrangelimit}else{e.coveragesrc=a.coveragesrc;t.dna.coveragemax=Math.max(t.dna.coveragemax,a.dnamax);if(t.rna.coverageauto){t.rna.coveragemax=Math.max(t.rna.coveragemax,a.rnamax)}}}))}function h(a,e){a.glider.selectAll("*").remove();for(const e of a.subpanels){e.glider.attr("transform","translate(0,0)").selectAll("*").remove()}v(a,e);b(a,e);e.setllabel();a.height_main+=a.toppad+a.bottompad}function v(a,n){const o=30;const i=a.regions.find((a=>a.coveragesrc));if(i){e({axis:a.rna.coverageaxisg.attr("transform","scale(1) translate(0,0)").call(f().scale(t().domain([0,a.rna.coveragemax]).range([a.rna.coveragebarh,0])).tickValues([0,a.rna.coveragemax])),showline:true});a.tklabel.attr("y",a.rna.coveragebarh/2-7);a.rna.coveragelabel.attr("y",a.rna.coveragebarh/2+2).attr("transform","scale(1)");e({axis:a.dna.coverageaxisg.attr("transform","scale(1) translate(0,"+(a.rna.coveragebarh+a.barypad)+")").call(f().scale(t().domain([0,a.dna.coveragemax]).range([0,a.dna.coveragebarh])).tickValues([0,a.dna.coveragemax])),showline:true});a.dna.coveragelabel.attr("transform","scale(1)").attr("y",a.rna.coveragebarh+a.barypad+a.dna.coveragebarh/2).each((function(){a.leftLabelMaxwidth=Math.max(a.leftLabelMaxwidth,this.getBBox().width)}));a.height_main=a.rna.coveragebarh+a.barypad+a.dna.coveragebarh}else{a.dna.coverageaxisg.attr("transform","scale(0)");a.rna.coverageaxisg.attr("transform","scale(0)");a.dna.coveragelabel.attr("transform","scale(0)");a.rna.coveragelabel.attr("transform","scale(0)");a.height_main=o}for(const e of a.regions){if(e.covplotrangelimit){a.glider.append("text").text("Zoom in under "+r(e.covplotrangelimit)+" to show coverage plot").attr("font-size",n.laelfontsize).attr("text-anchor","middle").attr("x",e.x+e.width/2).attr("y",o/2);continue}a.glider.append("image").attr("x",e.x).attr("width",e.width).attr("height",a.rna.coveragebarh+a.barypad+a.dna.coveragebarh).attr("xlink:href",e.coveragesrc)}}function b(a,n){const o=30;const i=a.regions.find((a=>!a.fpkmrangelimit));let s=0;for(const e of a.regions){if(e.fpkmrangelimit)continue;if(e.genes){for(const t of e.genes){if(Number.isFinite(t.fpkm))s=Math.max(s,t.fpkm);c(t,a.gecfg)}}}const p=a.height_main+a.yspace1;if(i&&s>0){e({axis:a.fpkm.axisg.attr("transform","scale(1) translate(0,"+p+")").call(f().scale(t().domain([0,s]).range([a.fpkm.barh,0])).tickValues([0,s])),showline:true});a.fpkm.label.attr("y",p+a.fpkm.barh/2).attr("transform","scale(1)");a.height_main+=a.yspace1+a.fpkm.barh}else{a.fpkm.axisg.attr("transform","scale(0)");a.fpkm.label.attr("transform","scale(0)");a.height_main+=o}for(const e of a.regions){if(e.fpkmrangelimit){a.glider.append("text").text("Zoom in under "+r(e.fpkmrangelimit)+" to show gene "+a.gecfg.datatype+" values").attr("font-size",n.laelfontsize).attr("text-anchor","middle").attr("x",e.x+e.width/2).attr("y",p+o/2);continue}if(!e.genes)continue;if(s==0){continue}const t=e.width/(e.stop-e.start);for(const r of e.genes){if(!Number.isFinite(r.fpkm))continue;const n=l(r,a.gecfg);const o=a.fpkm.barh*r.fpkm/s;let i,c;if(e.reverse){i=e.x+t*(e.stop-Math.min(e.stop,r.stop));c=e.x+t*(e.stop-Math.max(e.start,r.start))}else{i=e.x+t*(Math.max(e.start,r.start)-e.start);c=e.x+t*(Math.min(e.stop,r.stop)-e.start)}const g=a.glider.append("line").attr("x1",i).attr("x2",c).attr("y1",p+a.fpkm.barh-o).attr("y2",p+a.fpkm.barh-o).attr("stroke",n).attr("stroke-width",2).attr("stroke-opacity",.4);const f=a.glider.append("rect").attr("x",i).attr("y",p+a.fpkm.barh-o).attr("width",c-i).attr("height",o).attr("fill",n).attr("fill-opacity",.2);a.glider.append("rect").attr("x",i).attr("y",p+a.fpkm.barh-o-2).attr("width",c-i).attr("height",o+2).attr("fill","white").attr("fill-opacity",0).on("mouseover",(e=>{g.attr("stroke-opacity",.5);f.attr("fill-opacity",.3);x(r,a)})).on("mouseout",(e=>{g.attr("stroke-opacity",.4);f.attr("fill-opacity",.2);a.tktip.hide()}))}}}function x(a,e){e.tktip.clear().show(event.clientX,event.clientY);const t=[{k:a.gene+" "+e.gecfg.datatype,v:a.fpkm}];const r=n(e.tktip.d,t);p(a,e.gecfg,r)}function u(a,e){delete a.uninitialized;if(!a.barypad)a.barypad=0;if(!a.rna)a.rna={};a.rna.coverageaxisg=a.gleft.append("g");a.rna.coveragelabel=e.maketklefthandle(a).attr("class",null).attr("dominant-baseline","hanging").text("RNA coverage");a.rna.coverageauto=true;if(!a.rna.coveragebarh)a.rna.coveragebarh=50;if(!a.dna)a.dna={};a.dna.coverageaxisg=a.gleft.append("g");a.dna.coveragelabel=e.maketklefthandle(a).attr("class",null).text("DNA coverage");a.dna.coveragemax=0;if(!a.dna.coveragebarh)a.dna.coveragebarh=50;if(!a.dna.refcolor)a.dna.refcolor="#188FF5";if(!a.dna.altcolor)a.dna.altcolor="#F51818";if(!a.yspace1)a.yspace1=15;a.gecfg={datatype:"FPKM"};g(a.gecfg);if(!a.fpkm)a.fpkm={};a.fpkm.axisg=a.gleft.append("g");a.fpkm.label=e.maketklefthandle(a).attr("class",null).text("Gene "+a.gecfg.datatype);if(!a.fpkm.barh)a.fpkm.barh=50;a.config_handle=e.maketkconfighandle(a).attr("y",10+e.labelfontsize).on("click",(t=>{k(a,e)}));if(!a.checkrnabam)a.checkrnabam={};i(a.checkrnabam)}function k(a,e){a.tkconfigtip.clear().showunder(a.config_handle.node());const t=a.tkconfigtip.d.append("div");t.append("div").text("RNA-seq coverage is shown at all covered bases.").style("font-size",".8em").style("opacity",.5);{const r=t.append("div").style("margin","5px 0px");r.append("span").html("Bar height&nbsp;");r.append("input").attr("type","numeric").property("value",a.rna.coveragebarh).style("width","80px").on("keyup",(t=>{if(!o(t))return;const r=Number.parseInt(t.target.value);if(r<=20)return;if(r==a.rna.coveragebarh)return;a.rna.coveragebarh=r;d(a,e)}))}{const r=t.append("div").style("margin","5px 0px");const n=Math.random();r.append("input").attr("type","checkbox").attr("id",n).property("checked",a.rna.coverageauto).on("change",(t=>{a.rna.coverageauto=t.target.checked;i.style("display",a.rna.coverageauto?"none":"inline");d(a,e)}));r.append("label").html("&nbsp;automatic scale").attr("for",n);const i=r.append("div").style("display",a.rna.coverageauto?"none":"inline").style("margin-left","20px");i.append("span").html("Fixed max&nbsp");i.append("input").attr("value","numeric").property("value",a.rna.coveragemax).style("width","50px").on("keyup",(t=>{if(!o(t))return;const r=Number.parseInt(t.target.value);if(r<=0)return;if(r==a.rna.coveragemax)return;a.rna.coveragemax=r;d(a,e)}))}t.append("div").text("SNPs are only shown for those heterozygous in DNA.").style("font-size",".8em").style("opacity",.5).style("margin-top","25px");{const r=t.append("div").style("margin","5px 0px");r.append("span").html("Bar height&nbsp;");r.append("input").attr("type","numeric").property("value",a.dna.coveragebarh).style("width","80px").on("keyup",(t=>{if(!o(t))return;const r=Number.parseInt(t.target.value);if(r<=20)return;if(r==a.dna.coveragebarh)return;a.dna.coveragebarh=r;d(a,e)}))}{const r=t.append("div").style("margin","5px 0px 25px 0px");r.append("span").html("Allele color&nbsp;&nbsp;Ref:&nbsp;");r.append("input").attr("type","color").property("value",a.dna.refcolor).on("change",(t=>{a.dna.refcolor=t.target.value;d(a,e)}));r.append("span").html("&nbsp;Alt:&nbsp;");r.append("input").attr("type","color").property("value",a.dna.altcolor).on("change",(t=>{a.dna.altcolor=t.target.value;d(a,e)}))}s(a,e,d)}export{d as loadTk};
+import{q as a,ag as e,I as t,ae as r,a9 as n,k as o}from"./app-b369b169.js";import{r as i,c as s}from"./block.mds.svcnv.share-886d9479.js";import{m as c,a as l,s as p,i as g}from"./block.mds.expressionstat-f2d31c86.js";import{b as f}from"./axis-747c801e.js";async function d(a,e){e.tkcloakon(a);e.block_setheight();if(a.uninitialized){u(a,e)}const t=[];let r=0;for(let a=e.startidx;a<=e.stopidx;a++){const n=e.rglst[a];t.push({chr:n.chr,start:n.start,stop:n.stop,width:n.width,x:r});r+=n.width+e.regionspace}if(e.subpanels.length==a.subpanels.length){for(const[a,n]of e.subpanels.entries()){r+=n.leftpad;t.push({chr:n.chr,start:n.start,stop:n.stop,width:n.width,exonsf:n.exonsf,subpanelidx:a,x:r});r+=n.width}}a.regions=t;try{a.dna.coveragemax=0;if(a.rna.coverageauto)a.rna.coveragemax=0;for(const r of t){await m(r,a,e)}h(a,e);e.tkcloakoff(a,{})}catch(t){if(t.stack)console.log(t.stack);a.height_main=a.height=100;e.tkcloakoff(a,{error:t.message||t})}e.block_setheight()}function m(e,t,r){const n={genome:r.genome.name,samplename:t.samplename,rnabamfile:t.rnabamfile,rnabamurl:t.rnabamurl,rnabamindexURL:t.rnabamindexURL,rnabamtotalreads:t.rnabamtotalreads,rnabamispairedend:t.rnabamispairedend,vcffile:t.vcffile,vcfurl:t.vcfurl,vcfindexURL:t.vcfindexURL,rnabarheight:t.rna.coveragebarh,dnabarheight:t.dna.coveragebarh,barypad:t.barypad,chr:e.chr,start:e.start,stop:e.stop,width:e.width,checkrnabam:t.checkrnabam,refcolor:t.dna.refcolor,altcolor:t.dna.altcolor,devicePixelRatio:window.devicePixelRatio>1?window.devicePixelRatio:1};if(!t.rna.coverageauto){n.rnamax=t.rna.coveragemax}return a("ase",n).then((a=>{if(a.error)throw a.error;e.genes=a.genes;e.fpkmrangelimit=a.fpkmrangelimit;if(a.covplotrangelimit){e.covplotrangelimit=a.covplotrangelimit}else{e.coveragesrc=a.coveragesrc;t.dna.coveragemax=Math.max(t.dna.coveragemax,a.dnamax);if(t.rna.coverageauto){t.rna.coveragemax=Math.max(t.rna.coveragemax,a.rnamax)}}}))}function h(a,e){a.glider.selectAll("*").remove();for(const e of a.subpanels){e.glider.attr("transform","translate(0,0)").selectAll("*").remove()}v(a,e);b(a,e);e.setllabel();a.height_main+=a.toppad+a.bottompad}function v(a,n){const o=30;const i=a.regions.find((a=>a.coveragesrc));if(i){e({axis:a.rna.coverageaxisg.attr("transform","scale(1) translate(0,0)").call(f().scale(t().domain([0,a.rna.coveragemax]).range([a.rna.coveragebarh,0])).tickValues([0,a.rna.coveragemax])),showline:true});a.tklabel.attr("y",a.rna.coveragebarh/2-7);a.rna.coveragelabel.attr("y",a.rna.coveragebarh/2+2).attr("transform","scale(1)");e({axis:a.dna.coverageaxisg.attr("transform","scale(1) translate(0,"+(a.rna.coveragebarh+a.barypad)+")").call(f().scale(t().domain([0,a.dna.coveragemax]).range([0,a.dna.coveragebarh])).tickValues([0,a.dna.coveragemax])),showline:true});a.dna.coveragelabel.attr("transform","scale(1)").attr("y",a.rna.coveragebarh+a.barypad+a.dna.coveragebarh/2).each((function(){a.leftLabelMaxwidth=Math.max(a.leftLabelMaxwidth,this.getBBox().width)}));a.height_main=a.rna.coveragebarh+a.barypad+a.dna.coveragebarh}else{a.dna.coverageaxisg.attr("transform","scale(0)");a.rna.coverageaxisg.attr("transform","scale(0)");a.dna.coveragelabel.attr("transform","scale(0)");a.rna.coveragelabel.attr("transform","scale(0)");a.height_main=o}for(const e of a.regions){if(e.covplotrangelimit){a.glider.append("text").text("Zoom in under "+r(e.covplotrangelimit)+" to show coverage plot").attr("font-size",n.laelfontsize).attr("text-anchor","middle").attr("x",e.x+e.width/2).attr("y",o/2);continue}a.glider.append("image").attr("x",e.x).attr("width",e.width).attr("height",a.rna.coveragebarh+a.barypad+a.dna.coveragebarh).attr("xlink:href",e.coveragesrc)}}function b(a,n){const o=30;const i=a.regions.find((a=>!a.fpkmrangelimit));let s=0;for(const e of a.regions){if(e.fpkmrangelimit)continue;if(e.genes){for(const t of e.genes){if(Number.isFinite(t.fpkm))s=Math.max(s,t.fpkm);c(t,a.gecfg)}}}const p=a.height_main+a.yspace1;if(i&&s>0){e({axis:a.fpkm.axisg.attr("transform","scale(1) translate(0,"+p+")").call(f().scale(t().domain([0,s]).range([a.fpkm.barh,0])).tickValues([0,s])),showline:true});a.fpkm.label.attr("y",p+a.fpkm.barh/2).attr("transform","scale(1)");a.height_main+=a.yspace1+a.fpkm.barh}else{a.fpkm.axisg.attr("transform","scale(0)");a.fpkm.label.attr("transform","scale(0)");a.height_main+=o}for(const e of a.regions){if(e.fpkmrangelimit){a.glider.append("text").text("Zoom in under "+r(e.fpkmrangelimit)+" to show gene "+a.gecfg.datatype+" values").attr("font-size",n.laelfontsize).attr("text-anchor","middle").attr("x",e.x+e.width/2).attr("y",p+o/2);continue}if(!e.genes)continue;if(s==0){continue}const t=e.width/(e.stop-e.start);for(const r of e.genes){if(!Number.isFinite(r.fpkm))continue;const n=l(r,a.gecfg);const o=a.fpkm.barh*r.fpkm/s;let i,c;if(e.reverse){i=e.x+t*(e.stop-Math.min(e.stop,r.stop));c=e.x+t*(e.stop-Math.max(e.start,r.start))}else{i=e.x+t*(Math.max(e.start,r.start)-e.start);c=e.x+t*(Math.min(e.stop,r.stop)-e.start)}const g=a.glider.append("line").attr("x1",i).attr("x2",c).attr("y1",p+a.fpkm.barh-o).attr("y2",p+a.fpkm.barh-o).attr("stroke",n).attr("stroke-width",2).attr("stroke-opacity",.4);const f=a.glider.append("rect").attr("x",i).attr("y",p+a.fpkm.barh-o).attr("width",c-i).attr("height",o).attr("fill",n).attr("fill-opacity",.2);a.glider.append("rect").attr("x",i).attr("y",p+a.fpkm.barh-o-2).attr("width",c-i).attr("height",o+2).attr("fill","white").attr("fill-opacity",0).on("mouseover",(e=>{g.attr("stroke-opacity",.5);f.attr("fill-opacity",.3);x(r,a)})).on("mouseout",(e=>{g.attr("stroke-opacity",.4);f.attr("fill-opacity",.2);a.tktip.hide()}))}}}function x(a,e){e.tktip.clear().show(event.clientX,event.clientY);const t=[{k:a.gene+" "+e.gecfg.datatype,v:a.fpkm}];const r=n(e.tktip.d,t);p(a,e.gecfg,r)}function u(a,e){delete a.uninitialized;if(!a.barypad)a.barypad=0;if(!a.rna)a.rna={};a.rna.coverageaxisg=a.gleft.append("g");a.rna.coveragelabel=e.maketklefthandle(a).attr("class",null).attr("dominant-baseline","hanging").text("RNA coverage");a.rna.coverageauto=true;if(!a.rna.coveragebarh)a.rna.coveragebarh=50;if(!a.dna)a.dna={};a.dna.coverageaxisg=a.gleft.append("g");a.dna.coveragelabel=e.maketklefthandle(a).attr("class",null).text("DNA coverage");a.dna.coveragemax=0;if(!a.dna.coveragebarh)a.dna.coveragebarh=50;if(!a.dna.refcolor)a.dna.refcolor="#188FF5";if(!a.dna.altcolor)a.dna.altcolor="#F51818";if(!a.yspace1)a.yspace1=15;a.gecfg={datatype:"FPKM"};g(a.gecfg);if(!a.fpkm)a.fpkm={};a.fpkm.axisg=a.gleft.append("g");a.fpkm.label=e.maketklefthandle(a).attr("class",null).text("Gene "+a.gecfg.datatype);if(!a.fpkm.barh)a.fpkm.barh=50;a.config_handle=e.maketkconfighandle(a).attr("y",10+e.labelfontsize).on("click",(t=>{k(a,e)}));if(!a.checkrnabam)a.checkrnabam={};i(a.checkrnabam)}function k(a,e){a.tkconfigtip.clear().showunder(a.config_handle.node());const t=a.tkconfigtip.d.append("div");t.append("div").text("RNA-seq coverage is shown at all covered bases.").style("font-size",".8em").style("opacity",.5);{const r=t.append("div").style("margin","5px 0px");r.append("span").html("Bar height&nbsp;");r.append("input").attr("type","numeric").property("value",a.rna.coveragebarh).style("width","80px").on("keyup",(t=>{if(!o(t))return;const r=Number.parseInt(t.target.value);if(r<=20)return;if(r==a.rna.coveragebarh)return;a.rna.coveragebarh=r;d(a,e)}))}{const r=t.append("div").style("margin","5px 0px");const n=Math.random();r.append("input").attr("type","checkbox").attr("id",n).property("checked",a.rna.coverageauto).on("change",(t=>{a.rna.coverageauto=t.target.checked;i.style("display",a.rna.coverageauto?"none":"inline");d(a,e)}));r.append("label").html("&nbsp;automatic scale").attr("for",n);const i=r.append("div").style("display",a.rna.coverageauto?"none":"inline").style("margin-left","20px");i.append("span").html("Fixed max&nbsp");i.append("input").attr("value","numeric").property("value",a.rna.coveragemax).style("width","50px").on("keyup",(t=>{if(!o(t))return;const r=Number.parseInt(t.target.value);if(r<=0)return;if(r==a.rna.coveragemax)return;a.rna.coveragemax=r;d(a,e)}))}t.append("div").text("SNPs are only shown for those heterozygous in DNA.").style("font-size",".8em").style("opacity",.5).style("margin-top","25px");{const r=t.append("div").style("margin","5px 0px");r.append("span").html("Bar height&nbsp;");r.append("input").attr("type","numeric").property("value",a.dna.coveragebarh).style("width","80px").on("keyup",(t=>{if(!o(t))return;const r=Number.parseInt(t.target.value);if(r<=20)return;if(r==a.dna.coveragebarh)return;a.dna.coveragebarh=r;d(a,e)}))}{const r=t.append("div").style("margin","5px 0px 25px 0px");r.append("span").html("Allele color&nbsp;&nbsp;Ref:&nbsp;");r.append("input").attr("type","color").property("value",a.dna.refcolor).on("change",(t=>{a.dna.refcolor=t.target.value;d(a,e)}));r.append("span").html("&nbsp;Alt:&nbsp;");r.append("input").attr("type","color").property("value",a.dna.altcolor).on("change",(t=>{a.dna.altcolor=t.target.value;d(a,e)}))}s(a,e,d)}export{d as loadTk};