npm - jbrowse-plugin-graphgenomeviewer - Versions diffs - 7.4.2 → 7.4.4 - Mend

jbrowse-plugin-graphgenomeviewer 7.4.2 → 7.4.4

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package/README.md CHANGED Viewed

@@ -1,9 +1,16 @@
 # jbrowse-plugin-graphgenomeviewer
-Pangenome graphs in JBrowse 2.
-- **In:** a GFA, rGFA, GBZ or walk-indexed graph
-- **Out:** a graph track in a linear view, or a view of its own, with
+- **In:** one of
+  - a [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix) walk file
+    (`<prefix>.<sample>.walks.bed.gz` beside its `.tbi`), opened with File →
+    **Open track**
+  - a gfa-to-tabix segments index (`<prefix>.segs.bed.gz` beside
+    `<prefix>.links.bed.gz` and a `.tbi` for each), opened the same way
+  - a [gbz-base](https://github.com/jltsiren/gbz-base) database (`.gbz.db`),
+    opened the same way
+  - a GFA file (`.gfa` or `.gfa.gz`), opened whole with Add → **Graph genome
+    view**
+- **Out:** a graph track in a linear view, or a separate graph genome view, with
   haplotypes, bubbles and genes marked
 ![KIV-2 as a graph track under RefSeq genes and the curated KIV-2 annotation, its reference segments on a strip at their bp](img/force_kiv2.png)
@@ -23,14 +30,19 @@ Pangenome graphs in JBrowse 2.
    }
    ```
-2. Open a graph:
-   - **A small GFA:** Add → **Graph genome view** opens the whole file
-   - **A large graph:** index it with
-     [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix) or build a gbz-base
-     database, then File → **Open track**. The track redraws the graph for the
-     view's window as you pan. See [docs/data.md](docs/data.md)
+2. Write a walk file from a base-level GFA with W or P lines
+   (`vg convert -f graph.gbz` writes one):
+   ```console
+   gfa-to-tabix chr22.gfa --walks --refs GRCh38 -o chr22
+   ```
+3. In an hg38 session, File → **Open track** on the url of
+   `chr22.GRCh38.walks.bed.gz`. The track redraws the graph for the view's
+   window as you pan. [docs/data.md](docs/data.md) covers the other formats and
+   the track config
-3. Explore:
+4. Explore:
    - Pick a layout from the track menu: force-directed, ordered, anchored,
      sample rows, walk rows or tube map ([docs/layouts.md](docs/layouts.md))
    - Lift haplotypes or show a panel per haplotype
@@ -42,14 +54,6 @@ Pangenome graphs in JBrowse 2.
 The [JBrowse tutorials](#tutorials) walk through the whole process with commands
 you can run.
-## What it draws
-![The KIV-2 array side by side: GRCh38, HG00097, HG01960 and HG00133 each followed start to end](img/force_kiv2_facet.png)
-![KIV-2 walk rows under LPA and the curated KIV-2 annotation](img/walk_rows_kiv2.png)
-![C4A and C4B as a tube per route coloured by superpopulation](img/tube_map_c4_routes_by_population.png)
 ## Tutorials
 In the [JBrowse 2 docs](https://jbrowse.org/jb2/docs/tutorials/):
@@ -71,11 +75,33 @@ In the [JBrowse 2 docs](https://jbrowse.org/jb2/docs/tutorials/):
 In reading order:
 1. [Data and track config](docs/data.md): index a graph and write the track
-2. [Layouts](docs/layouts.md): the seven layouts, colour, the reference strip
+2. [Layouts, bubbles and genes](docs/layouts.md): the seven layouts, the
+   reference strip, bubble halos, gene outlines, export
 3. [Haplotypes](docs/haplotypes.md): lifting, panels, colouring, walk rows
-4. [Tube maps](docs/tube-maps.md): panels, routes, reads
-5. [Bubbles](docs/bubbles.md) and [genes](docs/genes.md)
-6. [Developing](docs/developing.md): build, test, release
+4. [Tube maps](docs/tube-maps.md): axes, box colour, panels, routes, reads
+5. [Maize NAM founders](docs/maize.md): MaizeGDB's graph of one gene and a
+   Minigraph-Cactus graph of chr8, with links that open each view
+6. [syng graphs from impg](docs/syng.md): build C4 as a syng graph and draw it
+   with `bandage-figure`
+7. [Developing](docs/developing.md): build, test, release
+## Gallery
+<table>
+<tr>
+<td><a href="docs/haplotypes.md#facets"><img src="img/force_kiv2_facet.png" width="260" alt="KIV-2, a panel per haplotype"></a><br>KIV-2, a panel per haplotype</td>
+<td><a href="docs/haplotypes.md#walk-rows"><img src="img/walk_rows_kiv2.png" width="260" alt="KIV-2 walk rows tiled by kringle"></a><br>KIV-2 walk rows tiled by kringle</td>
+<td><a href="docs/tube-maps.md#routes-and-tube-colour"><img src="img/tube_map_c4_routes_by_population.png" width="260" alt="C4, a tube per route by superpopulation"></a><br>C4, a tube per route by superpopulation</td>
+</tr>
+<tr>
+<td><a href="docs/tube-maps.md#panels"><img src="img/tube_map_cfhr_samples.png" width="260" alt="The CFHR3–CFHR1 deletion, a panel per sample"></a><br>The CFHR3–CFHR1 deletion, a panel per sample</td>
+<td><a href="docs/layouts.md#bubbles"><img src="img/force_kiv2_bubbles.png" width="260" alt="KIV-2 bubbles under the HPRC bubbles track"></a><br>KIV-2 bubbles under the HPRC bubbles track</td>
+<td><a href="docs/maize.md"><img src="docs/maize/walk_rows_200kb.png" width="260" alt="Maize NAM founders as walk rows"></a><br>Maize NAM founders as walk rows</td>
+</tr>
+<tr>
+<td><a href="docs/syng.md"><img src="img/syng_c4.png" width="260" alt="C4 as a syng graph from impg"></a><br>C4 as a syng graph from impg</td>
+</tr>
+</table>
 ## See also
@@ -90,6 +116,8 @@ Supporting utility libraries
   layout and drawing engine
 - [@jbrowse/tubemap-core](https://github.com/GMOD/tubemap-core) (npm): tube map
   layout
+- [@jbrowse/graph-walks](https://github.com/GMOD/graph-walks) (npm): walk file
+  reader
 - [@gmod/gbz-base](https://github.com/GMOD/gbz-base-js) (npm): `.gbz.db` reader
 Supporting graph layout libraries
@@ -99,7 +127,8 @@ Supporting graph layout libraries
 Supporting data preparation toolkits
-- [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix): indexes a GFA
+- [gfa-to-tabix](https://github.com/GMOD/gfa-to-tabix): writes walk files and
+  segment indexes from a GFA
 - [gbz-haplotype-index](https://github.com/GMOD/gbz-haplotype-index): names
   every walk in a gbz-base cut
 - [gfa-to-pairwise-paf](https://github.com/cmdcolin/gfa-to-pairwise-paf-rs):

package/dist/chunks/{AddTrackWorkflow-LK25EC3H.js → AddTrackWorkflow-NLSZYK56.js} RENAMED Viewed

@@ -1,2 +1,2 @@
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-//# sourceMappingURL=AddTrackWorkflow-LK25EC3H.js.map
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+//# sourceMappingURL=AddTrackWorkflow-NLSZYK56.js.map

package/dist/chunks/{GbzBaseSyntenyAdapter-BVLBK4OO.js → GbzBaseSyntenyAdapter-A5MNPCKX.js} RENAMED Viewed

@@ -1,2 +1,2 @@
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c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=e.get(p);l?l.push([o,s]):e.set(p,[[o,s]])}}let t=0;for(let a of e.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Le&&(t=Math.max(t,o))}}return t}function fe(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${_(n.fitsBp)} to see ${i}`),n}var le=(n,i,e)=>ie(fe(W(n,i,e)??n,"lanes"),e),me=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),T=class extends ae{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let e=this.getConf("gbzDbLocation"),t=this.getConf("haplotypeIndexLocation"),a=G(t)?{location:t}:await ce(e,this.pluginManager),r=a.location,o=await D.open({source:P(e,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await M(o),p=j({configured:this.getConf("referenceSample"),anchorPrefix:N(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let e=this.getConf("readsLocation"),t=this.getConf(["readsIndex","location"]);return G(e)?new v(P(e,this.pluginManager),G(t)?V(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(e,t){let{db:a,referenceSample:r}=await this.graph(t);return $(a,r,e)}async getHaplotypes(e={}){let{db:t,referenceSamples:a}=await this.graph(e),r=new Map;for(let o of await t.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(e={}){let{anchor:t,referenceSample:a}=await this.graph(e),r=C(this),o=[];for(let s of await this.getHaplotypes(e))s.sample!==a&&o.push({name:O(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:t,lanes:o}}async getRefNames(e={}){let{db:t,anchor:a,referenceSample:r}=await this.graph(e),{assemblyName:o}=e,s=o===a?void 0:N(this,o),c=(await t.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(e,t){let a=e===void 0||e.length===0?void 0:e.map(r=>N(this,r));return a===void 0&&t===void 0?void 0:r=>k(r,a)&&(t===void 0||F(u(r),t))}async getSubgraph(e,t={}){let{signal:a}=t,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:g}=me(e);if(p!==o)throw new q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let b=this.keepPredicate(t.haplotypes);if(b!==void 0&&!r.hasHaplotypeIndex)throw new I(c);let d=await U(r,y,f,g,{context:this.getConf("context"),snarls:t.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:t.signal,keep:b}).catch(w=>{throw fe(w,"the graph")});return typeof d=="string"?d:te(d,{start:f,end:g},t.walkRows)}async getReads(e,t={}){let a=await this.gaf(t);return a?a.readsOver(new Set(e),t):{records:[],total:0}}async laneHaplotypes(e,t){let a=N(this,e);return(await this.getHaplotypes(t)).filter(r=>F(r.prefix,a))}async anchorFeatures(e,t){let{db:a}=await this.graph(t),{assemblyName:r,refName:o,start:s,end:c}=e,p=N(this,t.targetAssemblyName),l=C(this),f=this.keepPredicate(t.haplotypes,p),g=await this.referenceQuery(o,t),y=this.getConf("nodeLimit");return(g?await B(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,t.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:t.signal,keep:f}).catch(d=>{throw le(d,y,c-s)})):[]).flatMap(d=>{let w=d.resolved?Ne({alignment:d,assemblyName:r,refName:o,lane:O(l,u(d.name))}):void 0;return w===void 0?[]:[w]})}async pairFeatures(e,t,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=e,l=(await Promise.all(t.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),b=this.getConf("context"),d=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:x=>f.has(u(x))}),w=async m=>{let h=await d(m,b).catch(S=>{throw le(S,y,c-s)}),x=Re(h,f),R=Math.ceil(x/2)+2e3;return x>0&&R>b?d(m,R).catch(S=>{if(S instanceof Q)return h;throw S}):h};return(g&&l.length>0?await B(oe(t),a.statusCallback,()=>w(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:x,mateSide:R})=>x.flatMap(S=>R.flatMap(de=>m.pairAlignments({target:S,query:de,bases:!1}).map(he=>Pe({pair:he,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(e,t={}){let a=me(e);return ee(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(t);if(!o.hasHaplotypeIndex)throw new I(c);if(a.assemblyName===s){let p=re(t),l=p.length>0?await this.pairFeatures(a,p,t):await this.anchorFeatures(a,t);for(let f of l)r.next(f)}r.complete()},t.signal)}};export{I as NoHaplotypeIndexError,ue as PairTargetError,T as default,Re as widestWalkGap};
-//# sourceMappingURL=GbzBaseSyntenyAdapter-BVLBK4OO.js.map
+import{a as ne,b as ae,c as ue,d as re,e as oe,f as O,g as ie,h as se}from"./chunk-HF4H6LQI.js";import{a as te}from"./chunk-QV7SSOMJ.js";import{a as ee}from"./chunk-KOB7YIMR.js";import{a as Q,b as D,c as Z,d as u,e as k,f as M,g as j,h as $,i as W,k as U}from"./chunk-XXBE4IFZ.js";import"./chunk-M2D7NUOY.js";import"./chunk-6WUWQX2P.js";import{b as z,c as E}from"./chunk-KIYRMZWP.js";import"./chunk-YBLNN5FU.js";import"./chunk-G53BI7VK.js";import"./chunk-LE7FZM6Y.js";import{C as V,a as K,c as L}from"./chunk-FTXDTU27.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import{g as F,h as N,i as C}from"./chunk-6SWXMRAV.js";import"./chunk-T4R3ZVEM.js";import"./chunk-7WIBGKBU.js";import{d as G,g as X,h as Y,i as J}from"./chunk-IKJZPPOA.js";import{a as P}from"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{e as _,o as B}from"./chunk-TENPGIPX.js";function A(n){let i=/\.gbz\.db$/i;return i.test(n)?n.replace(i,".haplotype-index.db"):void 0}function ge(n){return Y(n)&&A(X(n))?J(n,i=>A(i)):void 0}function ye(n){return n instanceof Error&&(/\bHTTP 40[34]\b/.test(n.message)||n.code==="ENOENT")}async function ce(n,i){let e=ge(n);if(!e)return{};try{return await P(e,i).stat(),{location:e}}catch(t){return ye(t)?{}:{unreadable:String(t)}}}var be=5e3,we=50*2**20,H=class extends Error{constructor(e){super(`this GAF is ${(e/2**20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`);this.name="UnindexedGafTooLargeError"}};function xe(n,i){if(n.length<=i)return n;let e=n.length/i;return Array.from({length:i},(t,a)=>n[Math.floor(a*e)])}var pe=(n,i)=>n.path.some(e=>i.has(e.name)),v=class{constructor(i,e){this.file=i;this.tabix=e;this.whole=L({setup:async({signal:i})=>{let{size:e}=await this.file.stat();if(e>we)throw new H(e);let t=await this.file.readFile({signal:i}),a=new TextDecoder().decode(t[0]===31&&t[1]===139?await K(t):t);return E(a)}})}async readIndexed(i,e,t){let a=1/0,r=-1/0;for(let s of e){let c=Number(s);Number.isInteger(c)&&(a=Math.min(a,c),r=Math.max(r,c))}let o=[];return a<=r&&await i.getLines("{node}",a,r+1,{signal:t,lineCallback:s=>{let c=z(s);c&&pe(c,e)&&o.push(c)}}),o}async readsOver(i,{signal:e}={}){let t=this.tabix?await this.readIndexed(this.tabix,i,e):(await this.whole({signal:e})).filter(a=>pe(a,i));return{records:xe(t,be),total:t.length}}};var I=class extends Error{constructor(e){super(e===void 0?"no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation":`the haplotype index beside the graph database could not be checked (${e}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`);this.name="NoHaplotypeIndexError"}},q=class extends Error{constructor(e,t){super(`the graph is cut on its reference, ${t}; a window on ${e} has no reference coordinates to cut at. Open the graph from a ${t} view, and find this haplotype's lane there`);this.name="HaplotypeWindowError"}};function Se(n,i){return`${u(n)}#${n.contig}@${i.start.node}.${i.start.offset}`}function Ne({alignment:n,assemblyName:i,refName:e,lane:t}){let{refStart:a,refEnd:r,strand:o,cigar:s}=n;if(!(r<=a)){let{name:c,hapStart:p,hapEnd:l}=n,f=Se(c,n),g={uniqueId:f,assemblyName:i,refName:e,start:a,end:r,type:"match",strand:o==="-"?-1:1,CIGAR:s,syntenyId:f,mate:{refName:c.contig,start:p,end:l,assemblyName:t}};return new ne(g)}}function Pe({pair:n,lane:i,mateLane:e}){return se({target:{name:`${u(n.target)}#${n.target.contig}`,assemblyName:i,refName:n.target.contig,start:n.targetStart,end:n.targetEnd},query:{name:`${u(n.query)}#${n.query.contig}`,assemblyName:e,refName:n.query.contig,start:n.queryStart,end:n.queryEnd},strand:n.strand,cigar:n.cigar,matches:n.matches,columns:n.columns})}var Le=12e4;function Re(n,i){let e=new Map;for(let a of n)for(let{name:r,start:o,end:s}of a.walkSpans()){let c=u(r);if(i.has(c)){let p=`${c}#${r.contig}`,l=e.get(p);l?l.push([o,s]):e.set(p,[[o,s]])}}let t=0;for(let a of e.values()){a.sort((r,o)=>r[0]-o[0]);for(let r=1;r<a.length;r++){let o=a[r][0]-a[r-1][1];o>0&&o<=Le&&(t=Math.max(t,o))}}return t}function fe(n,i){return n instanceof Z&&(n.message=`Zoom in to about ${_(n.fitsBp)} to see ${i}`),n}var le=(n,i,e)=>ie(fe(W(n,i,e)??n,"lanes"),e),me=n=>({...n,start:Math.floor(n.start),end:Math.ceil(n.end)}),T=class extends ae{constructor(){super(...arguments);this.graph=L({label:"Opening pangenome database",setup:async()=>{let e=this.getConf("gbzDbLocation"),t=this.getConf("haplotypeIndexLocation"),a=G(t)?{location:t}:await ce(e,this.pluginManager),r=a.location,o=await D.open({source:P(e,this.pluginManager),haplotypeIndex:r?P(r,this.pluginManager):void 0}),s=this.getConf("assemblyNames")[0];if(s===void 0)throw new Error("GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");let c=await M(o),p=j({configured:this.getConf("referenceSample"),anchorPrefix:N(this,s),referenceSamples:c});return{db:o,anchor:s,referenceSample:p,referenceSamples:c,unreadableIndex:a.unreadable}}});this.gaf=L({label:"Opening reads",setup:async()=>{let e=this.getConf("readsLocation"),t=this.getConf(["readsIndex","location"]);return G(e)?new v(P(e,this.pluginManager),G(t)?V(this,["readsLocation"],["readsIndex"]):void 0):void 0}})}async referenceQuery(e,t){let{db:a,referenceSample:r}=await this.graph(t);return $(a,r,e)}async getHaplotypes(e={}){let{db:t,referenceSamples:a}=await this.graph(e),r=new Map;for(let o of await t.paths()){let s=u(o.name),c=r.get(s);c?c.contigs.includes(o.name.contig)||c.contigs.push(o.name.contig):r.set(s,{prefix:s,sample:o.name.sample,haplotype:o.name.haplotype,contigs:[o.name.contig],isReference:a.includes(o.name.sample)})}return[...r.values()]}async getHeader(e={}){let{anchor:t,referenceSample:a}=await this.graph(e),r=C(this),o=[];for(let s of await this.getHaplotypes(e))s.sample!==a&&o.push({name:O(r,s.prefix),label:s.prefix,group:s.sample});return{hasCoarseTier:!1,anchorAssemblyName:t,lanes:o}}async getRefNames(e={}){let{db:t,anchor:a,referenceSample:r}=await this.graph(e),{assemblyName:o}=e,s=o===a?void 0:N(this,o),c=(await t.paths()).filter(p=>o===a?p.isIndexed&&p.name.sample===r:F(u(p.name),s)).map(p=>p.name.contig);return[...new Set(c)]}keepPredicate(e,t){let a=e===void 0||e.length===0?void 0:e.map(r=>N(this,r));return a===void 0&&t===void 0?void 0:r=>k(r,a)&&(t===void 0||F(u(r),t))}async getSubgraph(e,t={}){let{signal:a}=t,{db:r,anchor:o,referenceSample:s,unreadableIndex:c}=await this.graph({signal:a}),{assemblyName:p,refName:l,start:f,end:g}=me(e);if(p!==o)throw new q(p,o);let y=await this.referenceQuery(l,{signal:a});if(!y)throw new Error(`${s} has no indexed path ${l} in this graph`);let b=this.keepPredicate(t.haplotypes);if(b!==void 0&&!r.hasHaplotypeIndex)throw new I(c);let d=await U(r,y,f,g,{context:this.getConf("context"),snarls:t.snarls??this.getConf("subgraphSnarls"),limit:this.getConf("nodeLimit"),signal:t.signal,keep:b}).catch(w=>{throw fe(w,"the graph")});return typeof d=="string"?d:te(d,{start:f,end:g},t.walkRows)}async getReads(e,t={}){let a=await this.gaf(t);return a?a.readsOver(new Set(e),t):{records:[],total:0}}async laneHaplotypes(e,t){let a=N(this,e);return(await this.getHaplotypes(t)).filter(r=>F(r.prefix,a))}async anchorFeatures(e,t){let{db:a}=await this.graph(t),{assemblyName:r,refName:o,start:s,end:c}=e,p=N(this,t.targetAssemblyName),l=C(this),f=this.keepPredicate(t.haplotypes,p),g=await this.referenceQuery(o,t),y=this.getConf("nodeLimit");return(g?await B(`Reading graph ${o}:${s.toLocaleString()}-${c.toLocaleString()}`,t.statusCallback,()=>a.getAlignments({path:g,start:s,end:c,context:this.getConf("context"),haplotypes:"all",limit:y,signal:t.signal,keep:f}).catch(d=>{throw le(d,y,c-s)})):[]).flatMap(d=>{let w=d.resolved?Ne({alignment:d,assemblyName:r,refName:o,lane:O(l,u(d.name))}):void 0;return w===void 0?[]:[w]})}async pairFeatures(e,t,a){let{db:r}=await this.graph(a),{refName:o,start:s,end:c}=e,l=(await Promise.all(t.map(async m=>({pair:m,featureSide:await this.laneHaplotypes(m.queryAssemblyName,a),mateSide:await this.laneHaplotypes(m.targetAssemblyName,a)})))).filter(({featureSide:m,mateSide:h})=>m.length>0&&h.length>0),f=new Set(l.flatMap(({featureSide:m,mateSide:h})=>[...m,...h].map(u))),g=await this.referenceQuery(o,a),y=this.getConf("nodeLimit"),b=this.getConf("context"),d=(m,h)=>r.getSubgraphs({path:m,start:s,end:c,context:h,snarls:this.getConf("subgraphSnarls"),haplotypes:"all",limit:y,signal:a.signal,keep:x=>f.has(u(x))}),w=async m=>{let h=await d(m,b).catch(S=>{throw le(S,y,c-s)}),x=Re(h,f),R=Math.ceil(x/2)+2e3;return x>0&&R>b?d(m,R).catch(S=>{if(S instanceof Q)return h;throw S}):h};return(g&&l.length>0?await B(oe(t),a.statusCallback,()=>w(g)):[]).flatMap(m=>l.flatMap(({pair:h,featureSide:x,mateSide:R})=>x.flatMap(S=>R.flatMap(de=>m.pairAlignments({target:S,query:de,bases:!1}).map(he=>Pe({pair:he,lane:h.queryAssemblyName,mateLane:h.targetAssemblyName}))))))}getFeatures(e,t={}){let a=me(e);return ee(async r=>{let{db:o,anchor:s,unreadableIndex:c}=await this.graph(t);if(!o.hasHaplotypeIndex)throw new I(c);if(a.assemblyName===s){let p=re(t),l=p.length>0?await this.pairFeatures(a,p,t):await this.anchorFeatures(a,t);for(let f of l)r.next(f)}r.complete()},t.signal)}};export{I as NoHaplotypeIndexError,ue as PairTargetError,T as default,Re as widestWalkGap};
+//# sourceMappingURL=GbzBaseSyntenyAdapter-A5MNPCKX.js.map

package/dist/chunks/{GbzBaseSyntenyAdapter-BVLBK4OO.js.map → GbzBaseSyntenyAdapter-A5MNPCKX.js.map} RENAMED Viewed

@@ -1,6 +1,6 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.1/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FNDNSDKW.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.9.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-FNDNSDKW.js", "../../src/GbzBaseSyntenyAdapter/companion.ts", "../../src/gaf/gafFile.ts", "../../src/GbzBaseSyntenyAdapter/GbzBaseSyntenyAdapter.ts"],
   "sourcesContent": ["import {\n  GBZ_CUT_DEFAULTS,\n  NoReferenceSampleError,\n  aliasedSample,\n  cutWindowGFA,\n  haplotypeWanted,\n  referencePathQuery,\n  referenceSamplesOf\n} from \"./chunk-ZKSC7QVE.js\";\nimport {\n  panSNSample\n} from \"./chunk-2JL2JVZ2.js\";\n\n// src/gbzCut.ts\nimport { GBZBase } from \"@gmod/gbz-base\";\nvar HPRC_GBZ = {\n  db: \"https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.gbz.db\",\n  index: \"https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.f3.db\"\n};\nfunction gbzLocations({ db, index }) {\n  return db === \"hprc\" ? { db: HPRC_GBZ.db, index: index ?? HPRC_GBZ.index } : { db, index };\n}\nfunction haplotypeIndexBeside(db) {\n  const GBZ_DB = /\\.gbz\\.db$/i;\n  return GBZ_DB.test(db) ? db.replace(GBZ_DB, \".haplotype-index.db\") : void 0;\n}\nfunction parseRegion(text) {\n  const m = /^\\s*(\\S+?):([\\d,]+)-([\\d,]+)\\s*$/.exec(text);\n  if (!m) {\n    throw new Error(\n      `\"${text}\" is not a 0-based region like chr6:160,614,797-160,647,758`\n    );\n  }\n  const n = (s) => Number(s.replaceAll(\",\", \"\"));\n  const region = { refName: m[1], start: n(m[2]), end: n(m[3]) };\n  if (region.end <= region.start) {\n    throw new Error(`\"${text}\" ends at or before it starts`);\n  }\n  return region;\n}\nasync function openGbz(db, index) {\n  const base = await GBZBase.open({ source: db, haplotypeIndex: index });\n  return { base, referenceSamples: await referenceSamplesOf(base) };\n}\nfunction referenceSample(ref, samples) {\n  if (ref) {\n    return aliasedSample(panSNSample(ref), samples) ?? ref;\n  }\n  const first = samples[0];\n  if (first === void 0) {\n    throw new NoReferenceSampleError(\"\", samples);\n  }\n  return first;\n}\nasync function cutGbzRegion({ base, referenceSamples }, src, signal) {\n  const region = parseRegion(src.region);\n  const sample = referenceSample(src.referenceSample, referenceSamples);\n  const query = await referencePathQuery(base, sample, region.refName);\n  if (!query) {\n    throw new Error(`${sample} has no indexed path named ${region.refName}`);\n  }\n  signal?.throwIfAborted();\n  const wanted = src.haplotypes?.length ? src.haplotypes : void 0;\n  const text = await cutWindowGFA(base, query, region.start, region.end, {\n    context: src.context ?? GBZ_CUT_DEFAULTS.context,\n    snarls: src.snarls ?? GBZ_CUT_DEFAULTS.snarls,\n    limit: GBZ_CUT_DEFAULTS.limit,\n    signal,\n    keep: wanted ? (name) => haplotypeWanted(name, wanted) : void 0\n  });\n  return { text, region, sample };\n}\n\nexport {\n  HPRC_GBZ,\n  gbzLocations,\n  haplotypeIndexBeside,\n  parseRegion,\n  openGbz,\n  cutGbzRegion\n};\n", "import { haplotypeIndexBeside } from '@jbrowse/bandage-core/gbzCut'\nimport { openLocation } from '@jbrowse/core/util/io'\n\nimport { locationName, readsSiblings, renamed } from '../locationName'\n\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { FileLocation } from '@jbrowse/core/util/types'\n\nexport function siblingCompanion(gbzDb: FileLocation) {\n  return readsSiblings(gbzDb) && haplotypeIndexBeside(locationName(gbzDb))\n    ? renamed(gbzDb, name => haplotypeIndexBeside(name)!)\n    : undefined\n}\n\n// 404 is a missing file, and so is 403 from a bucket that does not let a\n// reader list it; anything else leaves the file's presence unknown\nfunction isMissing(error: unknown) {\n  return (\n    error instanceof Error &&\n    (/\\bHTTP 40[34]\\b/.test(error.message) ||\n      (error as { code?: unknown }).code === 'ENOENT')\n  )\n}\n\n// `unreadable` is why a companion that may be there could not be checked, such\n// as a network error, or a server that answers a missing file without CORS\nexport async function findCompanion(\n  gbzDb: FileLocation,\n  pluginManager?: PluginManager,\n): Promise<{ location?: FileLocation; unreadable?: string }> {\n  const candidate = siblingCompanion(gbzDb)\n  if (!candidate) {\n    return {}\n  }\n  try {\n    await openLocation(candidate, pluginManager).stat()\n    return { location: candidate }\n  } catch (error) {\n    return isMissing(error) ? {} : { unreadable: String(error) }\n  }\n}\n", "import { unzip } from '@gmod/bgzf-filehandle'\nimport { parseGaf, parseGafLine } from '@jbrowse/bandage-core/gaf/parseGaf'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\n\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type { GafRecord } from '@jbrowse/bandage-core/gaf/parseGaf'\n\ninterface WholeFile {\n  stat(): Promise<{ size: number }>\n  readFile(opts?: { signal?: AbortSignal }): Promise<Uint8Array>\n}\n\nexport interface GafReads {\n  records: GafRecord[]\n  // reads over the nodes before sampling\n  total: number\n}\n\n// The tube map lays reads out on the main thread at about 40 ms per thousand\nexport const MAX_READS = 5000\n\n// An unindexed GAF is read whole, once, into the worker\nconst MAX_UNINDEXED_BYTES = 50 * 2 ** 20\n\nexport class UnindexedGafTooLargeError extends Error {\n  override name = 'UnindexedGafTooLargeError'\n\n  constructor(size: number) {\n    super(\n      `this GAF is ${(size / 2 ** 20).toFixed(0)} MB without an index; bgzip it and index it with tabix -p gaf`,\n    )\n  }\n}\n\n// Evenly spaced, so a pileup thins out rather than losing its right half\nfunction sample(records: GafRecord[], max: number) {\n  if (records.length <= max) {\n    return records\n  }\n  const stride = records.length / max\n  return Array.from({ length: max }, (_, k) => records[Math.floor(k * stride)]!)\n}\n\nconst touches = (record: GafRecord, names: ReadonlySet<string>) =>\n  record.path.some(step => names.has(step.name))\n\n// A GAF over a graph's segments: bgzipped and indexed with `tabix -p gaf`,\n// which keys each line by its lowest and highest node id and so needs numeric\n// segment names, or plain or gzipped and read whole.\nexport class GafFile {\n  // Shared by every window, so the signal is cachedSetup's own, which aborts\n  // once no caller is left waiting\n  private whole = cachedSetup({\n    setup: async ({ signal }) => {\n      const { size } = await this.file.stat()\n      if (size > MAX_UNINDEXED_BYTES) {\n        throw new UnindexedGafTooLargeError(size)\n      }\n      const bytes = await this.file.readFile({ signal })\n      const text = new TextDecoder().decode(\n        bytes[0] === 0x1f && bytes[1] === 0x8b ? await unzip(bytes) : bytes,\n      )\n      return parseGaf(text)\n    },\n  })\n\n  constructor(\n    private file: WholeFile,\n    private tabix?: TabixIndexedFile,\n  ) {}\n\n  private async readIndexed(\n    tabix: TabixIndexedFile,\n    names: ReadonlySet<string>,\n    signal?: AbortSignal,\n  ) {\n    let lo = Infinity\n    let hi = -Infinity\n    for (const name of names) {\n      const id = Number(name)\n      if (Number.isInteger(id)) {\n        lo = Math.min(lo, id)\n        hi = Math.max(hi, id)\n      }\n    }\n    const records: GafRecord[] = []\n    if (lo <= hi) {\n      // a GAF index ignores the refName, and getLines keeps a read whose node\n      // ids span min..max when min < end && max >= start, hence hi + 1\n      await tabix.getLines('{node}', lo, hi + 1, {\n        signal,\n        lineCallback: line => {\n          const record = parseGafLine(line)\n          if (record && touches(record, names)) {\n            records.push(record)\n          }\n        },\n      })\n    }\n    return records\n  }\n\n  async readsOver(\n    names: ReadonlySet<string>,\n    { signal }: { signal?: AbortSignal } = {},\n  ): Promise<GafReads> {\n    const records = this.tabix\n      ? await this.readIndexed(this.tabix, names, signal)\n      : (await this.whole({ signal })).filter(r => touches(r, names))\n    return { records: sample(records, MAX_READS), total: records.length }\n  }\n}\n", "import { GBZBase, SubgraphLimitError } from '@gmod/gbz-base'\nimport {\n  NodeLimitError,\n  cutWindowTables,\n  haplotypePrefix,\n  haplotypeWanted,\n  nodeLimitError,\n  referencePathQuery,\n  referenceSamplesOf,\n  resolveReferenceSample,\n} from '@jbrowse/bandage-core/gbzWindow'\nimport {\n  assemblyByPanSNPrefix,\n  panSNMatchesPrefix,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { cachedSetup } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { getBpDisplayStr, updateStatus } from '@jbrowse/core/util'\nimport { openLocation } from '@jbrowse/core/util/io'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { findCompanion } from './companion.ts'\nimport { walkCutFor } from '../RgfaTabixAdapter/walkCut.ts'\nimport { GafFile } from '../gaf/gafFile.ts'\nimport { locationIsSet } from '../locationName.ts'\nimport { openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\nimport {\n  laneAssemblyName,\n  lanePairsStatus,\n  requestedPairs,\n} from '../synteny/lanePairs.ts'\nimport { laneZoomNotice } from '../synteny/laneZoomNotice.ts'\nimport { matchFeature } from '../synteny/matchFeature.ts'\n\nimport type { GbzBaseSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { GafReads } from '../gaf/gafFile.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type {\n  HaplotypeAlignment,\n  HaplotypeRef,\n  PairAlignment,\n  PathName,\n  PathQuery,\n  Subgraph,\n} from '@gmod/gbz-base'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature, SimpleFeatureSerialized } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\nexport class NoHaplotypeIndexError extends Error {\n  override name = 'NoHaplotypeIndexError'\n\n  constructor(unreadable?: string) {\n    super(\n      unreadable === undefined\n        ? 'no haplotype index is set, so the walks cannot be named; build one with gbz-haplotype-index (cargo install gbz-haplotype-index) and set it as haplotypeIndexLocation'\n        : `the haplotype index beside the graph database could not be checked (${unreadable}), so the walks cannot be named; if it is there, reload to try again, or set haplotypeIndexLocation`,\n    )\n  }\n}\n\ninterface GbzHaplotype {\n  prefix: string\n  sample: string\n  haplotype: number\n  contigs: string[]\n  isReference: boolean\n}\n\n/**\n * One lane the header declares, in the shape MultiWaySyntenyDisplay's lane\n * picker reads: `name` is the lane's assembly name, the same string the\n * fetched features' mates carry, `label` its PanSN prefix and `group` its\n * sample, so a diploid sample's two lanes sit together\n */\ninterface GbzHeaderLane {\n  name: string\n  label: string\n  group: string\n}\n\nexport { PairTargetError } from '../synteny/lanePairs.ts'\n\nclass HaplotypeWindowError extends Error {\n  override name = 'HaplotypeWindowError'\n\n  constructor(assemblyName: string, anchor: string) {\n    super(\n      `the graph is cut on its reference, ${anchor}; a window on ${assemblyName} has no reference coordinates to cut at. Open the graph from a ${anchor} view, and find this haplotype's lane there`,\n    )\n  }\n}\n\ntype ResolvedAlignment = Extract<HaplotypeAlignment, { resolved: true }>\n\n/**\n * The id of one haplotype fragment: the walk's GBWT position at its first node\n * in the window, which is a property of the graph, so the same fragment gets\n * the same id on a refetch of the same window and the display's hover and\n * selection survive it. `clipToRegion` suffixes the window.\n */\nfunction fragmentId(name: PathName, alignment: ResolvedAlignment) {\n  return `${haplotypePrefix(name)}#${name.contig}@${alignment.start.node}.${alignment.start.offset}`\n}\n\nfunction fragmentFeature({\n  alignment,\n  assemblyName,\n  refName,\n  lane,\n}: {\n  alignment: ResolvedAlignment\n  assemblyName: string\n  refName: string\n  lane: string\n}) {\n  const { refStart, refEnd, strand, cigar } = alignment\n  if (refEnd <= refStart) {\n    return undefined\n  } else {\n    const { name, hapStart, hapEnd } = alignment\n    const id = fragmentId(name, alignment)\n    const data: SimpleFeatureSerialized = {\n      uniqueId: id,\n      assemblyName,\n      refName,\n      start: refStart,\n      end: refEnd,\n      type: 'match',\n      strand: strand === '-' ? -1 : 1,\n      CIGAR: cigar,\n      syntenyId: id,\n      mate: {\n        refName: name.contig,\n        start: hapStart,\n        end: hapEnd,\n        assemblyName: lane,\n      },\n    }\n    return new SyntenyFeature(data)\n  }\n}\n\n// gbz-base writes the CIGAR along the target, which is the side a JBrowse\n// feature is, so it passes through unchanged\nfunction pairFeature({\n  pair,\n  lane,\n  mateLane,\n}: {\n  pair: PairAlignment\n  lane: string\n  mateLane: string\n}) {\n  return matchFeature({\n    target: {\n      name: `${haplotypePrefix(pair.target)}#${pair.target.contig}`,\n      assemblyName: lane,\n      refName: pair.target.contig,\n      start: pair.targetStart,\n      end: pair.targetEnd,\n    },\n    query: {\n      name: `${haplotypePrefix(pair.query)}#${pair.query.contig}`,\n      assemblyName: mateLane,\n      refName: pair.query.contig,\n      start: pair.queryStart,\n      end: pair.queryEnd,\n    },\n    strand: pair.strand,\n    cigar: pair.cigar,\n    matches: pair.matches,\n    columns: pair.columns,\n  })\n}\n\n// The longest detour a pair cut widens its context to take in\nconst BRIDGE_MAX_BP = 120_000\n\n/**\n * The widest gap, up to `BRIDGE_MAX_BP`, between two pieces of one kept walk:\n * a haplotype that left the cut's nodes for sequence the reference lacks and\n * came back. Two kept haplotypes that share that sequence only align across it\n * once its nodes are in the cut.\n */\nexport function widestWalkGap(subgraphs: Subgraph[], kept: Set<string>) {\n  const byPath = new Map<string, [number, number][]>()\n  for (const subgraph of subgraphs) {\n    for (const { name, start, end } of subgraph.walkSpans()) {\n      const prefix = haplotypePrefix(name)\n      if (kept.has(prefix)) {\n        const key = `${prefix}#${name.contig}`\n        const spans = byPath.get(key)\n        if (spans) {\n          spans.push([start, end])\n        } else {\n          byPath.set(key, [[start, end]])\n        }\n      }\n    }\n  }\n  let widest = 0\n  for (const spans of byPath.values()) {\n    spans.sort((a, b) => a[0] - b[0])\n    for (let i = 1; i < spans.length; i++) {\n      const gap = spans[i]![0] - spans[i - 1]![1]\n      if (gap > 0 && gap <= BRIDGE_MAX_BP) {\n        widest = Math.max(widest, gap)\n      }\n    }\n  }\n  return widest\n}\n\n// A window past the node limit fails as a zoom-in notice naming a span that\n// fits\nfunction zoomInNotice(error: unknown, what: string) {\n  if (error instanceof NodeLimitError) {\n    error.message = `Zoom in to about ${getBpDisplayStr(error.fitsBp)} to see ${what}`\n  }\n  return error\n}\n\nconst laneLimitNotice = (error: unknown, nodeLimit: number, windowBp: number) =>\n  laneZoomNotice(\n    zoomInNotice(nodeLimitError(error, nodeLimit, windowBp) ?? error, 'lanes'),\n    windowBp,\n  )\n\n// gbz-base reads whole bp; a view asks at fractional ones\nconst wholeBp = (region: Region) => ({\n  ...region,\n  start: Math.floor(region.start),\n  end: Math.ceil(region.end),\n})\n\nexport default class GbzBaseSyntenyAdapter extends ComparativeAdapterBase<GbzBaseSyntenyAdapterConfig> {\n  private graph = cachedSetup({\n    label: 'Opening pangenome database',\n    setup: async () => {\n      const gbzDb: FileLocation = this.getConf('gbzDbLocation')\n      const configured: FileLocation = this.getConf('haplotypeIndexLocation')\n      const companion = locationIsSet(configured)\n        ? { location: configured }\n        : await findCompanion(gbzDb, this.pluginManager)\n      const indexLocation = companion.location\n      const db = await GBZBase.open({\n        source: openLocation(gbzDb, this.pluginManager),\n        haplotypeIndex: indexLocation\n          ? openLocation(indexLocation, this.pluginManager)\n          : undefined,\n      })\n      const anchor = this.getConf('assemblyNames')[0]\n      if (anchor === undefined) {\n        throw new Error(\n          'GbzBaseSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n        )\n      }\n      const referenceSamples = await referenceSamplesOf(db)\n      const referenceSample = resolveReferenceSample({\n        configured: this.getConf('referenceSample'),\n        anchorPrefix: resolvePanSNPrefix(this, anchor),\n        referenceSamples,\n      })\n      return {\n        db,\n        anchor,\n        referenceSample,\n        referenceSamples,\n        unreadableIndex: companion.unreadable,\n      }\n    },\n  })\n\n  /**\n   * The indexed reference path a window on `refName` resolves against, or\n   * undefined when the reference sample has no indexed path by that contig.\n   */\n  private async referenceQuery(\n    refName: string,\n    opts: BaseOptions,\n  ): Promise<PathQuery | undefined> {\n    const { db, referenceSample } = await this.graph(opts)\n    return referencePathQuery(db, referenceSample, refName)\n  }\n\n  /**\n   * Every haplotype the graph carries a walk for, `sample#haplotype` with its\n   * contigs, from the Paths scan the adapter already makes; the lane picker's\n   * source list. Reference samples are included and flagged.\n   */\n  async getHaplotypes(opts: BaseOptions = {}): Promise<GbzHaplotype[]> {\n    const { db, referenceSamples } = await this.graph(opts)\n    const byPrefix = new Map<string, GbzHaplotype>()\n    for (const path of await db.paths()) {\n      const prefix = haplotypePrefix(path.name)\n      const entry = byPrefix.get(prefix)\n      if (entry) {\n        if (!entry.contigs.includes(path.name.contig)) {\n          entry.contigs.push(path.name.contig)\n        }\n      } else {\n        byPrefix.set(prefix, {\n          prefix,\n          sample: path.name.sample,\n          haplotype: path.name.haplotype,\n          contigs: [path.name.contig],\n          isReference: referenceSamples.includes(path.name.sample),\n        })\n      }\n    }\n    return [...byPrefix.values()]\n  }\n\n  /**\n   * `lanes` is every haplotype but the reference sample's own, which is the\n   * anchor rather than a lane, declared up front so the display can offer the\n   * whole graph's haplotypes before a fetch has placed any of them.\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { anchor, referenceSample } = await this.graph(opts)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const lanes: GbzHeaderLane[] = []\n    for (const haplotype of await this.getHaplotypes(opts)) {\n      if (haplotype.sample !== referenceSample) {\n        lanes.push({\n          name: laneAssemblyName(asmByPrefix, haplotype.prefix),\n          label: haplotype.prefix,\n          group: haplotype.sample,\n        })\n      }\n    }\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      lanes,\n    }\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    const { db, anchor, referenceSample } = await this.graph(opts)\n    const { assemblyName } = opts\n    const prefix =\n      assemblyName === anchor\n        ? undefined\n        : resolvePanSNPrefix(this, assemblyName)\n    const contigs = (await db.paths())\n      .filter(path =>\n        assemblyName === anchor\n          ? path.isIndexed && path.name.sample === referenceSample\n          : panSNMatchesPrefix(haplotypePrefix(path.name), prefix),\n      )\n      .map(path => path.name.contig)\n    return [...new Set(contigs)]\n  }\n\n  /**\n   * The predicate gbz-base builds a window for, from the lanes a fetch asks\n   * for. With a companion whose stray rows cover the window gbz-base walks\n   * only the wanted haplotypes; otherwise it names every walk and keeps the\n   * ones the predicate accepts, and throws rather than guess when a walk has\n   * no name. Either way a cut holds those walks, the reference, and the nodes\n   * they visit. Undefined when every haplotype is wanted.\n   */\n  //\n  // `targetPrefix` is a pairwise view's one lane, and it belongs in here: left\n  // to filter what came back, it handed gbz-base no predicate, and every\n  // haplotype in the graph was walked for one to be kept.\n  private keepPredicate(\n    haplotypes: string[] | undefined,\n    targetPrefix?: string,\n  ) {\n    const wantedPrefixes =\n      haplotypes === undefined || haplotypes.length === 0\n        ? undefined\n        : haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n    return wantedPrefixes === undefined && targetPrefix === undefined\n      ? undefined\n      : (name: PathName) =>\n          haplotypeWanted(name, wantedPrefixes) &&\n          (targetPrefix === undefined ||\n            panSNMatchesPrefix(haplotypePrefix(name), targetPrefix))\n  }\n\n  /**\n   * The graph view's cut of the window, as tables: the reference walk, every\n   * top-level snarl contained in it, and one walk per haplotype, PanSN-named\n   * when the database (or its companion) carries the haplotype index and\n   * `unknown#N` otherwise. The reference walk is the first, which is the one\n   * the view anchors on by default. With `haplotypes` the walks are that\n   * set's and the nodes those walks visit, the reference walk kept. With\n   * `walkRows` the rows' runs come along, as on a walk-file cut.\n   *\n   * Only a window on the anchor can be cut: a haplotype lane's coordinates\n   * are its own contig's, and the graph is indexed for random access on the\n   * reference sample's paths alone.\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { signal } = opts\n    const { db, anchor, referenceSample, unreadableIndex } = await this.graph({\n      signal,\n    })\n    const { assemblyName, refName, start, end } = wholeBp(region)\n    if (assemblyName !== anchor) {\n      throw new HaplotypeWindowError(assemblyName, anchor)\n    }\n    const query = await this.referenceQuery(refName, { signal })\n    if (!query) {\n      throw new Error(\n        `${referenceSample} has no indexed path ${refName} in this graph`,\n      )\n    }\n    const keep = this.keepPredicate(opts.haplotypes)\n    if (keep !== undefined && !db.hasHaplotypeIndex) {\n      throw new NoHaplotypeIndexError(unreadableIndex)\n    }\n    const cut = await cutWindowTables(db, query, start, end, {\n      context: this.getConf('context'),\n      snarls: opts.snarls ?? this.getConf('subgraphSnarls'),\n      limit: this.getConf('nodeLimit'),\n      signal: opts.signal,\n      keep,\n    }).catch((error: unknown) => {\n      throw zoomInNotice(error, 'the graph')\n    })\n    return typeof cut === 'string'\n      ? cut\n      : walkCutFor(cut, { start, end }, opts.walkRows)\n  }\n\n  private gaf = cachedSetup({\n    label: 'Opening reads',\n    setup: async () => {\n      const location: FileLocation = this.getConf('readsLocation')\n      const index: FileLocation = this.getConf(['readsIndex', 'location'])\n      return locationIsSet(location)\n        ? new GafFile(\n            openLocation(location, this.pluginManager),\n            locationIsSet(index)\n              ? openTabixSlot(this, ['readsLocation'], ['readsIndex'])\n              : undefined,\n          )\n        : undefined\n    },\n  })\n\n  /**\n   * The reads over a cut's segments, from `readsLocation`, sampled down to\n   * what the tube map lays out at interactive speed\n   */\n  async getReads(\n    nodeNames: string[],\n    opts: BaseOptions = {},\n  ): Promise<GafReads> {\n    const gaf = await this.gaf(opts)\n    return gaf\n      ? gaf.readsOver(new Set(nodeNames), opts)\n      : { records: [], total: 0 }\n  }\n\n  private async laneHaplotypes(\n    assemblyName: string,\n    opts: BaseOptions,\n  ): Promise<HaplotypeRef[]> {\n    const prefix = resolvePanSNPrefix(this, assemblyName)\n    return (await this.getHaplotypes(opts)).filter(haplotype =>\n      panSNMatchesPrefix(haplotype.prefix, prefix),\n    )\n  }\n\n  private async anchorFeatures(region: Region, opts: LaneFeatureOptions) {\n    const { db } = await this.graph(opts)\n    const { assemblyName, refName, start, end } = region\n    const targetPrefix = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const keep = this.keepPredicate(opts.haplotypes, targetPrefix)\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const alignments = query\n      ? await updateStatus(\n          `Reading graph ${refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n          opts.statusCallback,\n          () =>\n            db\n              .getAlignments({\n                path: query,\n                start,\n                end,\n                context: this.getConf('context'),\n                haplotypes: 'all',\n                limit: nodeLimit,\n                signal: opts.signal,\n                keep,\n              })\n              .catch((error: unknown) => {\n                throw laneLimitNotice(error, nodeLimit, end - start)\n              }),\n        )\n      : []\n    return alignments.flatMap(alignment => {\n      const feature = alignment.resolved\n        ? fragmentFeature({\n            alignment,\n            assemblyName,\n            refName,\n            lane: laneAssemblyName(\n              asmByPrefix,\n              haplotypePrefix(alignment.name),\n            ),\n          })\n        : undefined\n      return feature === undefined ? [] : [feature]\n    })\n  }\n\n  /**\n   * Each pair's two lanes cut out of the anchor window alone, all pairs in one\n   * cut, and each walk of a pair's query lane aligned to each walk of its\n   * target lane on the nodes both visit, with no base compared. A pair's\n   * records sit on its query lane's contigs, the lane the display draws on top.\n   *\n   * Whether the index has anchor rows changes only how fast gbz-base finds\n   * the walks: both routes cut the same pieces.\n   */\n  private async pairFeatures(\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const { db } = await this.graph(opts)\n    const { refName, start, end } = region\n    const sides = await Promise.all(\n      pairs.map(async pair => ({\n        pair,\n        featureSide: await this.laneHaplotypes(pair.queryAssemblyName, opts),\n        mateSide: await this.laneHaplotypes(pair.targetAssemblyName, opts),\n      })),\n    )\n    const answerable = sides.filter(\n      ({ featureSide, mateSide }) =>\n        featureSide.length > 0 && mateSide.length > 0,\n    )\n    const kept = new Set(\n      answerable.flatMap(({ featureSide, mateSide }) =>\n        [...featureSide, ...mateSide].map(haplotypePrefix),\n      ),\n    )\n    const query = await this.referenceQuery(refName, opts)\n    const nodeLimit: number = this.getConf('nodeLimit')\n    const baseContext: number = this.getConf('context')\n    const cut = (path: PathQuery, context: number) =>\n      db.getSubgraphs({\n        path,\n        start,\n        end,\n        context,\n        snarls: this.getConf('subgraphSnarls'),\n        haplotypes: 'all',\n        limit: nodeLimit,\n        signal: opts.signal,\n        keep: name => kept.has(haplotypePrefix(name)),\n      })\n    // a cut past the node limit for the wider context keeps the first one\n    const bridged = async (path: PathQuery) => {\n      const subgraphs = await cut(path, baseContext).catch((error: unknown) => {\n        throw laneLimitNotice(error, nodeLimit, end - start)\n      })\n      const gap = widestWalkGap(subgraphs, kept)\n      const context = Math.ceil(gap / 2) + 2000\n      return gap > 0 && context > baseContext\n        ? cut(path, context).catch((error: unknown) => {\n            if (error instanceof SubgraphLimitError) {\n              return subgraphs\n            }\n            throw error\n          })\n        : subgraphs\n    }\n    const subgraphs =\n      query && answerable.length > 0\n        ? await updateStatus(lanePairsStatus(pairs), opts.statusCallback, () =>\n            bridged(query),\n          )\n        : []\n    return subgraphs.flatMap(subgraph =>\n      answerable.flatMap(({ pair, featureSide, mateSide }) =>\n        featureSide.flatMap(target =>\n          mateSide.flatMap(mate =>\n            subgraph\n              .pairAlignments({ target, query: mate, bases: false })\n              .map(alignment =>\n                pairFeature({\n                  pair: alignment,\n                  lane: pair.queryAssemblyName,\n                  mateLane: pair.targetAssemblyName,\n                }),\n              ),\n          ),\n        ),\n      ),\n    )\n  }\n\n  getFeatures(asked: Region, opts: LaneFeatureOptions = {}) {\n    const region = wholeBp(asked)\n    return ObservableCreate<Feature>(async observer => {\n      const { db, anchor, unreadableIndex } = await this.graph(opts)\n      if (!db.hasHaplotypeIndex) {\n        throw new NoHaplotypeIndexError(unreadableIndex)\n      }\n      // the graph is indexed on its reference alone, so a window on a\n      // haplotype lane has no answer: a lane pair is read inside the anchor's\n      if (region.assemblyName === anchor) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(region, pairs, opts)\n            : await this.anchorFeatures(region, opts)\n        for (const feature of features) {\n          observer.next(feature)\n        }\n      }\n      observer.complete()\n    }, opts.signal)\n  }\n}\n"],
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package/dist/chunks/{GraphGenomeView-UCOAMRF7.js → GraphGenomeView-SEAPDRXS.js} RENAMED Viewed

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package/dist/chunks/{GraphTrackSettingsDialog-MR7X75EY.js → GraphTrackSettingsDialog-EVIIGC5G.js} RENAMED Viewed

@@ -1,6 +1,6 @@
-import{a as G,b as L}from"./chunk-WY5W5X62.js";import{b as v,c as x,n as d}from"./chunk-ZG2CQXOW.js";import"./chunk-2XZYJLCE.js";import"./chunk-Q3BXNKEL.js";import"./chunk-U5PIXAF2.js";import"./chunk-MVVXRZXV.js";import"./chunk-RCXOOBLX.js";import"./chunk-IKJZPPOA.js";import{g,h}from"./chunk-YU7T5WOQ.js";import{F as m,H as u,n as C}from"./chunk-UGCNPRKC.js";import{b as r,c as i,d as c}from"./chunk-JMBDTNUR.js";var P=d()({section:{marginBottom:24}}),T=[{value:"0",label:"None"},{value:"1",label:"1 hop"},{value:"2",label:"2 hops"}],w=c(function({model:t}){let{classes:l}=P(),o=t.sourceAdapter;return o?.type==="RgfaTabixAdapter"&&!v(o)?i("div",{className:l.section,children:[r(G,{label:"Graph context",sx:{minWidth:200},value:String(t.subgraphContext),options:T,testId:"graph-context-select",onChange:a=>{t.setSubgraphContext(Number(a)),t.recut()}}),r(u,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),k=w;var F=d()({section:{marginBottom:24}});function M(n){return n.split(/[\s,]+/).filter(t=>t!=="")}var I=c(function({model:t}){let[l,o]=h(t.cutHaplotypes?.join(", ")??""),a=()=>{let e=M(l);e.join(`
+import{a as G,b as L}from"./chunk-6VNU7SD4.js";import{b as v,c as x,n as d}from"./chunk-7RJMG6I2.js";import"./chunk-2KVE7YAS.js";import"./chunk-S333HOG5.js";import"./chunk-LE7FZM6Y.js";import"./chunk-JRJHXLGP.js";import"./chunk-6SWXMRAV.js";import"./chunk-IKJZPPOA.js";import{g,h}from"./chunk-YU7T5WOQ.js";import{F as m,H as u,n as C}from"./chunk-UGCNPRKC.js";import{b as r,c as i,d as c}from"./chunk-JMBDTNUR.js";var P=d()({section:{marginBottom:24}}),T=[{value:"0",label:"None"},{value:"1",label:"1 hop"},{value:"2",label:"2 hops"}],w=c(function({model:t}){let{classes:l}=P(),o=t.sourceAdapter;return o?.type==="RgfaTabixAdapter"&&!v(o)?i("div",{className:l.section,children:[r(G,{label:"Graph context",sx:{minWidth:200},value:String(t.subgraphContext),options:T,testId:"graph-context-select",onChange:a=>{t.setSubgraphContext(Number(a)),t.recut()}}),r(u,{variant:"caption",component:"div",color:"text.secondary",children:"How far the cut follows links out of the region. At none, a detour that leaves the window draws as two stubs. No effect on gfa-to-tabix's default anchored index."})]}):null}),k=w;var F=d()({section:{marginBottom:24}});function M(n){return n.split(/[\s,]+/).filter(t=>t!=="")}var I=c(function({model:t}){let[l,o]=h(t.cutHaplotypes?.join(", ")??""),a=()=>{let e=M(l);e.join(`
 `)===(t.cutHaplotypes??[]).join(`
 `)||(t.setSubgraphHaplotypes(e),t.recut())};return r(m,{fullWidth:!0,label:"Haplotypes",placeholder:"every haplotype",value:l,slotProps:{htmlInput:{"data-testid":"graph-haplotypes-field"}},onChange:e=>{o(e.target.value)},onBlur:()=>{a()},onKeyDown:e=>{e.key==="Enter"&&a()}})}),A=c(function({model:t,names:l}){let[o,a]=h(t.cutHaplotypes??[]),e=g(o),f=g(""),[b,S]=h(!1),H=p=>{p.join(`
 `)!==(t.cutHaplotypes??[]).join(`
 `)&&(t.setSubgraphHaplotypes(p),t.recut())};return r(C,{multiple:!0,freeSolo:!0,disableCloseOnSelect:!0,options:l,value:o,open:b,onOpen:()=>{S(!0)},onInputChange:(p,s)=>{f.current=s},onClose:(p,s)=>{S(!1);let y=f.current.trim();s==="blur"&&y&&!e.current.includes(y)&&(e.current=[...e.current,y],a(e.current)),H(e.current)},onChange:(p,s)=>{e.current=s,a(s),b||H(s)},renderInput:p=>r(m,{...p,label:"Haplotypes",placeholder:o.length===0?"every haplotype":void 0,slotProps:{...p.slotProps,htmlInput:{...p.slotProps.htmlInput,"data-testid":"graph-haplotypes-field"}}})})}),D=c(function({model:t}){let{classes:l}=F(),o=t.haplotypeNames,a=t.cutHaplotypes?.join(",")??"",e=t.sourceAdapter;return e&&x(e)?i("div",{className:l.section,children:[o?r(A,{model:t,names:o},a):r(I,{model:t},a),i(u,{variant:"caption",component:"div",color:"text.secondary",children:[o?`Which of the graph's ${o.length.toLocaleString()} haplotypes to cut, or a PanSN prefix (HG002 for both).`:"Which haplotypes to cut, as lane assembly names or PanSN prefixes (HG002#1, or HG002 for both) separated by commas."," ","Empty is every haplotype."]})]}):null}),N=D;function B({model:n,onClose:t}){return i(L,{model:n,onClose:t,children:[r(k,{model:n}),r(N,{model:n})]})}export{B as default};
-//# sourceMappingURL=GraphTrackSettingsDialog-MR7X75EY.js.map
+//# sourceMappingURL=GraphTrackSettingsDialog-EVIIGC5G.js.map

package/dist/chunks/{HighlightColorDialog-ZBAZDYIR.js → HighlightColorDialog-QAYWLO5I.js} RENAMED Viewed

@@ -1,2 +1,2 @@
-import{u as v,v as C}from"./chunk-S75MFZDE.js";import"./chunk-Q3BXNKEL.js";import"./chunk-U5PIXAF2.js";import"./chunk-RCXOOBLX.js";import{F as g,H as t,d as u,o as y,q as c,r as d,z as s}from"./chunk-UGCNPRKC.js";import{a as h,b as l,c as p,d as m}from"./chunk-JMBDTNUR.js";var b=m(function({model:o,onClose:r}){return p(u,{open:!0,onClose:r,title:"Color highlighted haplotypes",children:[p(d,{sx:{display:"grid",gridTemplateColumns:"auto 1fr 1fr",alignItems:"center",gap:1.5},children:[l(t,{variant:"subtitle2",children:"Haplotype"}),l(t,{variant:"subtitle2",children:"Color by"}),l(t,{variant:"subtitle2",children:"Palette"}),o.drawnWalks.map(({name:a,encoding:n})=>l(f,{label:o.walkLabel(a),field:n.field,scheme:n.scheme,onField:e=>{o.setWalkColor(a,{field:e})},onScheme:e=>{o.setWalkColor(a,{scheme:e})}},a))]}),l(c,{children:l(y,{variant:"contained",onClick:r,children:"Done"})})]})});function f({label:i,field:o,scheme:r,onField:a,onScheme:n}){return p(h,{children:[l(t,{variant:"body2",children:i}),l(g,{select:!0,size:"small",value:o,slotProps:{select:{SelectDisplayProps:{"aria-label":`Color ${i} by`}}},onChange:e=>{a(e.target.value)},children:v.map(e=>l(s,{value:e.value,children:e.label},e.value))}),l(g,{select:!0,size:"small",value:r,slotProps:{select:{SelectDisplayProps:{"aria-label":`Palette for ${i}`}}},onChange:e=>{n(e.target.value)},children:C.filter(e=>e.value!=="rainbow"||o==="reference").map(e=>l(s,{value:e.value,children:e.label},e.value))})]})}var P=b;export{P as default};
-//# sourceMappingURL=HighlightColorDialog-ZBAZDYIR.js.map
+import{x as v,y as C}from"./chunk-VZQ6VOUP.js";import"./chunk-S333HOG5.js";import"./chunk-LE7FZM6Y.js";import"./chunk-6SWXMRAV.js";import{F as g,H as t,d as u,o as y,q as c,r as d,z as s}from"./chunk-UGCNPRKC.js";import{a as h,b as l,c as p,d as m}from"./chunk-JMBDTNUR.js";var b=m(function({model:o,onClose:r}){return p(u,{open:!0,onClose:r,title:"Color highlighted haplotypes",children:[p(d,{sx:{display:"grid",gridTemplateColumns:"auto 1fr 1fr",alignItems:"center",gap:1.5},children:[l(t,{variant:"subtitle2",children:"Haplotype"}),l(t,{variant:"subtitle2",children:"Color by"}),l(t,{variant:"subtitle2",children:"Palette"}),o.drawnWalks.map(({name:a,encoding:n})=>l(f,{label:o.walkLabel(a),field:n.field,scheme:n.scheme,onField:e=>{o.setWalkColor(a,{field:e})},onScheme:e=>{o.setWalkColor(a,{scheme:e})}},a))]}),l(c,{children:l(y,{variant:"contained",onClick:r,children:"Done"})})]})});function f({label:i,field:o,scheme:r,onField:a,onScheme:n}){return p(h,{children:[l(t,{variant:"body2",children:i}),l(g,{select:!0,size:"small",value:o,slotProps:{select:{SelectDisplayProps:{"aria-label":`Color ${i} by`}}},onChange:e=>{a(e.target.value)},children:v.map(e=>l(s,{value:e.value,children:e.label},e.value))}),l(g,{select:!0,size:"small",value:r,slotProps:{select:{SelectDisplayProps:{"aria-label":`Palette for ${i}`}}},onChange:e=>{n(e.target.value)},children:C.filter(e=>e.value!=="rainbow"||o==="reference").map(e=>l(s,{value:e.value,children:e.label},e.value))})]})}var P=b;export{P as default};
+//# sourceMappingURL=HighlightColorDialog-QAYWLO5I.js.map

package/dist/chunks/{LinearGraphDisplay-AJ5OZN27.js → LinearGraphDisplay-ZC4BQ27J.js} RENAMED Viewed

@@ -1,2 +1,2 @@
-import{a as h}from"./chunk-62AHPP6H.js";import"./chunk-WY5W5X62.js";import"./chunk-WJGCVNGH.js";import"./chunk-FWVXBJ64.js";import"./chunk-ZG2CQXOW.js";import"./chunk-55DIX25J.js";import"./chunk-S75MFZDE.js";import"./chunk-2XZYJLCE.js";import"./chunk-Q3BXNKEL.js";import"./chunk-JSRGX4TC.js";import"./chunk-DXNE2CFX.js";import"./chunk-LFTZNUXB.js";import"./chunk-YBLNN5FU.js";import"./chunk-MEMUEG5Z.js";import"./chunk-U5PIXAF2.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-RCXOOBLX.js";import"./chunk-IKJZPPOA.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{h as T}from"./chunk-YU7T5WOQ.js";import"./chunk-UGCNPRKC.js";import{b as e,c as d,d as i}from"./chunk-JMBDTNUR.js";var n=JBrowseExports["@jbrowse/display-kit/DisplayBackgroundProgress"];var f=n&&n.__esModule?n.default:n;var l=JBrowseExports["@jbrowse/display-kit/DisplayErrorBar"];var v=l&&l.__esModule?l.default:l;var p=JBrowseExports["@jbrowse/display-kit/DisplayLoadingOverlay"];var O=p&&p.__esModule?p.default:p;var c=JBrowseExports["@jbrowse/display-kit/TooLargeMessage"];var L=c&&c.__esModule?c.default:c;var s=JBrowseExports["@jbrowse/display-ui"],u=r=>s!=null&&r in Object(s)?s[r]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+r+"' from '@jbrowse/display-ui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:r});var w=u("BottomRightCornerContext");var g=u("TrackOverlayPortal");var C=u("useChromeOverlayOverride");var U=s&&s.__esModule?s.default:s;var k={TooLarge:L,ErrorBar:v,Loading:O,BackgroundProgress:f},m="Zoom in to see features, or force load this track for the rest of the session (may be slow)",M="Force load this track for the rest of the session (may be slow)";function H(r){let o=r.error??r.renderError,t=o instanceof Error&&o.regionTooLarge===!0;return{error:{error:o,onRetry:t?void 0:()=>{r.reload()}},tooLarge:{message:[r.regionTooLargeReason,r.zoomCanReleaseGate?m:M].filter(Boolean).join(". "),onForceLoad:()=>{r.forceLoad()}},loading:{message:r.statusMessage,progress:r.statusProgress,canceled:r.fetchCanceled,onCancel:()=>{r.cancelFetchByUser()},onRetry:()=>{r.reload()}},background:{message:r.statusMessage,progress:r.statusProgress}}}var _=i(function({model:o,phase:t,drawn:x,testid:E,style:B,children:G,...S}){let{TooLarge:b,ErrorBar:P,Loading:A,BackgroundProgress:D}=C()??k,[R,I]=T(null),a=H(o),y={...S,"data-testid":E,"data-display-id":o.configuration.displayId,"data-display-drawn":x,"data-display-phase":t};return t==="tooLarge"?e("div",{style:{display:"contents"},...y,children:e(g,{children:e("div",{style:{pointerEvents:"auto"},children:e(b,{model:o,...a.tooLarge})})})}):d("div",{style:{position:"relative",height:o.height,...B},...y,children:[e(w,{value:R,children:G}),d(g,{children:[t==="error"?e(P,{model:o,visible:!0,...a.error}):null,e(A,{model:o,...a.loading,visible:t==="loading"||t==="canceled",immediate:!x}),e("div",{ref:I,style:{position:"absolute",bottom:2,right:2,display:"flex",flexDirection:"column",alignItems:"flex-end",gap:4,pointerEvents:"none"},children:t==="ready"&&o.statusMessage?e(D,{model:o,visible:!0,...a.background}):null})]})]})});var j=i(function({model:o}){return e(_,{model:o,phase:o.displayPhase,drawn:o.painted&&o.geometryPainted,testid:"linear-graph-display","data-layout":o.chosenLayoutMode,"data-cut-tier":o.cutTier,"data-recuts":o.recuts,"data-node-count":o.hasGraph?o.nodeCount:void 0,"data-loading":o.isLoading?"":void 0,style:{width:o.paneWidth,height:o.height,overflow:"hidden"},children:e(h,{model:o,ownChrome:!1})})}),so=j;export{so as default};
-//# sourceMappingURL=LinearGraphDisplay-AJ5OZN27.js.map
+import{a as h}from"./chunk-HCDKP3IP.js";import"./chunk-6VNU7SD4.js";import"./chunk-LE43I4PT.js";import"./chunk-GRTN25B6.js";import"./chunk-7RJMG6I2.js";import"./chunk-WLRRI35A.js";import"./chunk-VZQ6VOUP.js";import"./chunk-2KVE7YAS.js";import"./chunk-S333HOG5.js";import"./chunk-P3FBI5ML.js";import"./chunk-6WUWQX2P.js";import"./chunk-KIYRMZWP.js";import"./chunk-YBLNN5FU.js";import"./chunk-G53BI7VK.js";import"./chunk-LE7FZM6Y.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-6SWXMRAV.js";import"./chunk-IKJZPPOA.js";import"./chunk-NDRLCGPC.js";import"./chunk-TENPGIPX.js";import{h as T}from"./chunk-YU7T5WOQ.js";import"./chunk-UGCNPRKC.js";import{b as e,c as d,d as i}from"./chunk-JMBDTNUR.js";var n=JBrowseExports["@jbrowse/display-kit/DisplayBackgroundProgress"];var f=n&&n.__esModule?n.default:n;var l=JBrowseExports["@jbrowse/display-kit/DisplayErrorBar"];var v=l&&l.__esModule?l.default:l;var p=JBrowseExports["@jbrowse/display-kit/DisplayLoadingOverlay"];var O=p&&p.__esModule?p.default:p;var c=JBrowseExports["@jbrowse/display-kit/TooLargeMessage"];var L=c&&c.__esModule?c.default:c;var s=JBrowseExports["@jbrowse/display-ui"],u=r=>s!=null&&r in Object(s)?s[r]:Object.assign(function(){throw new Error("This JBrowse does not provide '"+r+"' from '@jbrowse/display-ui' to plugins: GraphGenomeView was built for a different JBrowse version, so update the plugin or JBrowse")},{jbrowseHostMissing:r});var w=u("BottomRightCornerContext");var g=u("TrackOverlayPortal");var C=u("useChromeOverlayOverride");var U=s&&s.__esModule?s.default:s;var k={TooLarge:L,ErrorBar:v,Loading:O,BackgroundProgress:f},m="Zoom in to see features, or force load this track for the rest of the session (may be slow)",M="Force load this track for the rest of the session (may be slow)";function H(r){let o=r.error??r.renderError,t=o instanceof Error&&o.regionTooLarge===!0;return{error:{error:o,onRetry:t?void 0:()=>{r.reload()}},tooLarge:{message:[r.regionTooLargeReason,r.zoomCanReleaseGate?m:M].filter(Boolean).join(". "),onForceLoad:()=>{r.forceLoad()}},loading:{message:r.statusMessage,progress:r.statusProgress,canceled:r.fetchCanceled,onCancel:()=>{r.cancelFetchByUser()},onRetry:()=>{r.reload()}},background:{message:r.statusMessage,progress:r.statusProgress}}}var _=i(function({model:o,phase:t,drawn:x,testid:E,style:B,children:G,...S}){let{TooLarge:b,ErrorBar:P,Loading:A,BackgroundProgress:D}=C()??k,[R,I]=T(null),a=H(o),y={...S,"data-testid":E,"data-display-id":o.configuration.displayId,"data-display-drawn":x,"data-display-phase":t};return t==="tooLarge"?e("div",{style:{display:"contents"},...y,children:e(g,{children:e("div",{style:{pointerEvents:"auto"},children:e(b,{model:o,...a.tooLarge})})})}):d("div",{style:{position:"relative",height:o.height,...B},...y,children:[e(w,{value:R,children:G}),d(g,{children:[t==="error"?e(P,{model:o,visible:!0,...a.error}):null,e(A,{model:o,...a.loading,visible:t==="loading"||t==="canceled",immediate:!x}),e("div",{ref:I,style:{position:"absolute",bottom:2,right:2,display:"flex",flexDirection:"column",alignItems:"flex-end",gap:4,pointerEvents:"none"},children:t==="ready"&&o.statusMessage?e(D,{model:o,visible:!0,...a.background}):null})]})]})});var j=i(function({model:o}){return e(_,{model:o,phase:o.displayPhase,drawn:o.painted&&o.geometryPainted,testid:"linear-graph-display","data-layout":o.chosenLayoutMode,"data-cut-tier":o.cutTier,"data-recuts":o.recuts,"data-node-count":o.hasGraph?o.nodeCount:void 0,"data-loading":o.isLoading?"":void 0,style:{width:o.paneWidth,height:o.height,overflow:"hidden"},children:e(h,{model:o,ownChrome:!1})})}),so=j;export{so as default};
+//# sourceMappingURL=LinearGraphDisplay-ZC4BQ27J.js.map

package/dist/chunks/MinigraphBubbleAdapter-3QM4XV47.js ADDED Viewed

	@@ -0,0 +1,2 @@
1	+ import{a as f,d as c,f as d}from"./chunk-P3FBI5ML.js";import{a as g}from"./chunk-KOB7YIMR.js";import{C as p,E as u,b,x as m}from"./chunk-FTXDTU27.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-6SWXMRAV.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as i,o as l}from"./chunk-TENPGIPX.js";var a=class extends b{constructor(){super(...arguments);this.bubbles=p(this,["bubblesLocation"],["index"]);this.refNames=new u(this.bubbles,this)}static{this.capabilities=["getFeatures","getRefNames"]}async getRefNames(t={}){return this.refNames.assemblyRefNames(t)}async getRegionByteSize(t,s={}){return this.refNames.regionBytes(t,s)}async hasDataForRefName(){return!0}getFeatures(t,s={}){let{signal:n,statusCallback:h}=s;return g(async r=>{let o=await this.refNames.resolveMapped(t,s);o!==void 0&&await l("Downloading bubbles",h,()=>m(this.bubbles,o,t.start,t.end,{signal:n,lineCallback:(N,y)=>{let e=f(N);r.next(new i({uniqueId:`bubble-${y}`,refName:t.refName,start:e.start,end:e.end,name:c(e),description:d(e),type:"bubble",score:e.segmentCount,segmentCount:e.segmentCount,pathCount:e.pathCount,inversion:e.inversion,shortestAlleleLength:e.shortestAlleleLength,longestAlleleLength:e.longestAlleleLength,segments:e.segments,shortestAllele:e.shortestAllele,longestAllele:e.longestAllele}))}})),r.complete()},n)}};export{a as default};
2	+ //# sourceMappingURL=MinigraphBubbleAdapter-3QM4XV47.js.map

package/dist/chunks/{MinigraphBubbleAdapter-PEQK5NII.js.map → MinigraphBubbleAdapter-3QM4XV47.js.map} RENAMED Viewed

@@ -2,6 +2,6 @@
   "version": 3,
   "sources": ["../../src/MinigraphBubbleAdapter/MinigraphBubbleAdapter.ts"],
   "sourcesContent": ["import {\n  bubbleDescription,\n  bubbleLabel,\n  parseBubbleLine,\n} from '@jbrowse/bandage-core/bubbles/bubbleLine'\nimport { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\n\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { getLines } from '../tabixRange.ts'\n\nimport type { MinigraphBubbleAdapterConfig } from './configSchema.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\n\nexport default class MinigraphBubbleAdapter extends BaseFeatureDataAdapter<MinigraphBubbleAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly bubbles = openTabixSlot(this, ['bubblesLocation'], ['index'])\n  // `gfatools bubble` names each row after the graph's stable sequence, so a\n  // Minigraph-Cactus graph produces PanSN rows (`GRCh38#0#chr6`) where a plain\n  // minigraph graph produces bare ones (`chr6`). Same resolution the segment\n  // adapter does, through the same `assemblyNameToPanSN` slot.\n  private readonly refNames = new PanSNRefNames(this.bubbles, this)\n\n  async getRefNames(opts: BaseOptions = {}) {\n    return this.refNames.assemblyRefNames(opts)\n  }\n\n  async getRegionByteSize(regions: Region[], opts: BaseOptions = {}) {\n    return this.refNames.regionBytes(regions, opts)\n  }\n\n  public async hasDataForRefName() {\n    return true\n  }\n\n  getFeatures(query: Region, opts: BaseOptions = {}) {\n    const { signal, statusCallback } = opts\n    return ObservableCreate<Feature>(async observer => {\n      const tabixRefName = await this.refNames.resolveMapped(query, opts)\n      if (tabixRefName !== undefined) {\n        await updateStatus('Downloading bubbles', statusCallback, () =>\n          getLines(this.bubbles, tabixRefName, query.start, query.end, {\n            signal,\n            lineCallback: (line, fileOffset) => {\n              const bubble = parseBubbleLine(line)\n              observer.next(\n                new SimpleFeature({\n                  uniqueId: `bubble-${fileOffset}`,\n                  refName: query.refName,\n                  start: bubble.start,\n                  end: bubble.end,\n                  // How variable this spot is, in two words, since that is the\n                  // whole point of the track.\n                  name: bubbleLabel(bubble),\n                  description: bubbleDescription(bubble),\n                  type: 'bubble',\n                  score: bubble.segmentCount,\n                  segmentCount: bubble.segmentCount,\n                  pathCount: bubble.pathCount,\n                  inversion: bubble.inversion,\n                  shortestAlleleLength: bubble.shortestAlleleLength,\n                  longestAlleleLength: bubble.longestAlleleLength,\n                  segments: bubble.segments,\n                  shortestAllele: bubble.shortestAllele,\n                  longestAllele: bubble.longestAllele,\n                }),\n              )\n            },\n          }),\n        )\n      }\n      observer.complete()\n    }, signal)\n  }\n}\n"],
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   "names": ["MinigraphBubbleAdapter", "BaseFeatureDataAdapter", "openTabixSlot", "PanSNRefNames", "opts", "regions", "query", "signal", "statusCallback", "ObservableCreate", "observer", "tabixRefName", "updateStatus", "getLines", "line", "fileOffset", "bubble", "parseBubbleLine", "SimpleFeature", "bubbleLabel", "bubbleDescription"]
 }

package/dist/chunks/{RgfaTabixAdapter-Q63YLPK4.js → RgfaTabixAdapter-XSOIEWBK.js} RENAMED Viewed

@@ -1,2 +1,2 @@
-import{a as b}from"./chunk-SFYSQ52W.js";import"./chunk-J3AXN7JQ.js";import{a as N}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-MEMUEG5Z.js";import"./chunk-U5PIXAF2.js";import{b as g,h as c,i as u,j as h,k as w,p as m,q as k,r as x}from"./chunk-AWGMTI73.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import"./chunk-RCXOOBLX.js";import{d}from"./chunk-IKJZPPOA.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as p,o as f}from"./chunk-TENPGIPX.js";var l=class extends g{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let a=m(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),s=m(this,[...e,"linksLocation"],[...e,"linksIndex"]),n=this.getConf("walksLocation"),r=e.length===0&&d(n)?new b(m(this,["walksLocation"],["walksIndex"]),this):void 0;return{segments:a,links:s,walks:r,refNames:new x(r?.file??a,this)}}async getHaplotypeNames(e={}){return this.fine.walks?.haplotypeNames(e)}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async getRegionByteSize(e,a={}){let{walks:s,refNames:n}=this.fine;return n.regionBytes(e,a,s&&((r,{start:t,end:i})=>s.reader.queryStart(t,{...a,refName:r,end:i})))}async hasDataForRefName(){return!0}getFeatures(e,a={}){return N(async s=>{let n=await this.fine.refNames.resolveMapped(e,a);if(n!==void 0){let{walks:r}=this.fine,t=i=>{s.next(i)};await(r?this.walkFeatures(r,n,e,a,t):this.segmentFeatures(n,e,a,t))}s.complete()},a.signal)}async walkFeatures(e,a,s,n,r){let t=await f("Downloading walks",n.statusCallback,()=>e.referenceNodes(a,s,n));for(let i of t){let o=String(i.id);r(new p({uniqueId:o,refName:s.refName,start:i.start,end:i.end,name:o,type:"segment",rank:0,stableName:i.refName}))}}async segmentFeatures(e,a,s,n){await f("Downloading segments",s.statusCallback,()=>w(this.fine.segments,e,a.start,a.end,{signal:s.signal,lineCallback:r=>{let{segment:t,anchored:i}=c(r);if(i&&t.refName!==e)return;let o=u(t);n(new p({uniqueId:t.id,refName:a.refName,start:t.start,end:t.end,name:t.id,type:"segment",rank:t.rank,stableName:t.refName,...o&&{samples:o,sampleCount:o.length}}))}}))}async getSubgraph(e,a={}){let{hops:s,signal:n,tier:r}=a,t=this.index(r),i=await t.refNames.resolve(e,{signal:n});if(i===void 0)throw new Error(k(e));return t.walks?t.walks.subgraph(i,e,a):h(t,{refName:i,start:e.start,end:e.end},{hops:s,signal:n})}};export{l as default};
-//# sourceMappingURL=RgfaTabixAdapter-Q63YLPK4.js.map
+import{a as b}from"./chunk-OJWBLPPH.js";import"./chunk-QV7SSOMJ.js";import{a as N}from"./chunk-KOB7YIMR.js";import"./chunk-YBLNN5FU.js";import"./chunk-G53BI7VK.js";import"./chunk-LE7FZM6Y.js";import{C as m,D as k,E as x,b as g,u as c,v as u,w as h,x as w}from"./chunk-FTXDTU27.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import"./chunk-6SWXMRAV.js";import{d}from"./chunk-IKJZPPOA.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{a as p,o as f}from"./chunk-TENPGIPX.js";var l=class extends g{constructor(){super(...arguments);this.fine=this.openIndex([])}static{this.capabilities=["getFeatures","getRefNames"]}openIndex(e){let a=m(this,[...e,"segmentsLocation"],[...e,"segmentsIndex"]),s=m(this,[...e,"linksLocation"],[...e,"linksIndex"]),n=this.getConf("walksLocation"),r=e.length===0&&d(n)?new b(m(this,["walksLocation"],["walksIndex"]),this):void 0;return{segments:a,links:s,walks:r,refNames:new x(r?.file??a,this)}}async getHaplotypeNames(e={}){return this.fine.walks?.haplotypeNames(e)}index(e="fine"){return e==="fine"?this.fine:(this.coarse??=this.openIndex(["coarse"]),this.coarse)}async getRefNames(e={}){return this.fine.refNames.assemblyRefNames(e)}async getRegionByteSize(e,a={}){let{walks:s,refNames:n}=this.fine;return n.regionBytes(e,a,s&&((r,{start:t,end:i})=>s.reader.queryStart(t,{...a,refName:r,end:i})))}async hasDataForRefName(){return!0}getFeatures(e,a={}){return N(async s=>{let n=await this.fine.refNames.resolveMapped(e,a);if(n!==void 0){let{walks:r}=this.fine,t=i=>{s.next(i)};await(r?this.walkFeatures(r,n,e,a,t):this.segmentFeatures(n,e,a,t))}s.complete()},a.signal)}async walkFeatures(e,a,s,n,r){let t=await f("Downloading walks",n.statusCallback,()=>e.referenceNodes(a,s,n));for(let i of t){let o=String(i.id);r(new p({uniqueId:o,refName:s.refName,start:i.start,end:i.end,name:o,type:"segment",rank:0,stableName:i.refName}))}}async segmentFeatures(e,a,s,n){await f("Downloading segments",s.statusCallback,()=>w(this.fine.segments,e,a.start,a.end,{signal:s.signal,lineCallback:r=>{let{segment:t,anchored:i}=c(r);if(i&&t.refName!==e)return;let o=u(t);n(new p({uniqueId:t.id,refName:a.refName,start:t.start,end:t.end,name:t.id,type:"segment",rank:t.rank,stableName:t.refName,...o&&{samples:o,sampleCount:o.length}}))}}))}async getSubgraph(e,a={}){let{hops:s,signal:n,tier:r}=a,t=this.index(r),i=await t.refNames.resolve(e,{signal:n});if(i===void 0)throw new Error(k(e));return t.walks?t.walks.subgraph(i,e,a):h(t,{refName:i,start:e.start,end:e.end},{hops:s,signal:n})}};export{l as default};
+//# sourceMappingURL=RgfaTabixAdapter-XSOIEWBK.js.map

package/dist/chunks/WalkFormsAdapter-FT2SW4H6.js ADDED Viewed

	@@ -0,0 +1,2 @@
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2	+ //# sourceMappingURL=WalkFormsAdapter-FT2SW4H6.js.map

package/dist/chunks/WalkFormsAdapter-FT2SW4H6.js.map ADDED Viewed

@@ -0,0 +1,7 @@
+{
+  "version": 3,
+  "sources": ["../../src/WalkFormsAdapter/WalkFormsAdapter.ts"],
+  "sourcesContent": ["import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport {\n  ExpansionTooLargeError,\n  RegionTooLargeError,\n  WalkReader,\n  bpString,\n  formsCut,\n  panSNContig,\n  panSNMatchesPrefix,\n  structuralForms,\n} from '@jbrowse/graph-walks'\n\nimport {\n  formSources,\n  formVariants,\n  formWarnings,\n  referenceGenotypes,\n} from './formRows.ts'\nimport { floorOf, pinnedLocus, pinnedOf, warningPrefix } from './pinned.ts'\nimport { openTabixSlot } from '../panSNTabix.ts'\n\nimport type { WalkFormsAdapterConfig } from './configSchema.ts'\nimport type { Pinned } from './pinned.ts'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\nimport type { HaplotypeDepartures, StructuralForms } from '@jbrowse/graph-walks'\n\nconst megabytes = (bytes: number) => `${(bytes / 1_000_000).toFixed(1)} MB`\n\nconst millions = (n: number) => `${(n / 1_000_000).toFixed(1)} M`\n\n// A zoom-in notice would mislead, since the view's zoom does not move the\n// pinned window\nfunction pinnedTooLarge(error: unknown, pinned: Pinned) {\n  if (!(error instanceof RegionTooLargeError)) {\n    return error\n  }\n  const window = pinnedLocus(pinned)\n  if (error instanceof ExpansionTooLargeError) {\n    return new Error(\n      `The pinned window ${window} is too large to read every walk in full for structural forms: its walks take ${millions(error.steps)} steps, over the ${millions(error.limit)} step budget, and about ${bpString(error.fitsBp)} of it fits. Pin a narrower window`,\n    )\n  }\n  const budget = `walkByteBudget, ${megabytes(error.limit)}`\n  return new Error(\n    `The pinned window ${window} is too large to cut for structural forms: ${\n      error.zoomHelps\n        ? `about ${bpString(error.fitsBp)} of it fits in ${budget}. Pin a narrower window or raise walkByteBudget`\n        : `its cut fetches ${megabytes(error.bytes ?? 0)}, over ${budget}. 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+}

package/dist/chunks/{WalkTabixSyntenyAdapter-N5PFI4LS.js → WalkTabixSyntenyAdapter-3WRVNDLB.js} RENAMED Viewed

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+import{a as K}from"./chunk-OJWBLPPH.js";import{b as q,d as U,e as X,f as O,g as z,h as G}from"./chunk-HF4H6LQI.js";import"./chunk-QV7SSOMJ.js";import{a as H}from"./chunk-KOB7YIMR.js";import{p as M,q as _,r as T}from"./chunk-M2D7NUOY.js";import"./chunk-YBLNN5FU.js";import"./chunk-G53BI7VK.js";import"./chunk-LE7FZM6Y.js";import{C as j,E as D,i as $}from"./chunk-FTXDTU27.js";import"./chunk-YBLNN5FU.js";import"./chunk-JRJHXLGP.js";import{a as A,c as I,d as W,g as F,h as w,i as x}from"./chunk-6SWXMRAV.js";import"./chunk-T4R3ZVEM.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{o as R}from"./chunk-TENPGIPX.js";var se=50;function re(r){let i=[];for(let e=0;e<r.length;e++){let[t,a]=r[e],[s,n]=r[e+1]??[];a===n&&a<=se&&(t==="I"&&s==="D"||t==="D"&&s==="I")?(i.push(["X",a]),e++):i.push([t,a])}return i}function v(r){return Array.from(r.ids,(i,e)=>2*i+r.rev[e])}function P(r,i){let e=r.get(i);return e===void 0?0:e.end-e.start}function V(r){let i=new Map,e=s=>{let n=P(r,s),o=i.get(n);return o===void 0&&(o="N".repeat(n),i.set(n,o)),o},t=new Map,a=s=>{let n=t.get(s);return n===void 0&&(n=v(s),t.set(s,n)),n};return(s,n)=>_({query:a(s),target:a(n),sequenceOf:e,bases:!1})}var B=100;function E(r,i,e){let t=r.at(-1);e>0&&(t?.[0]===i?t[1]+=e:r.push([i,e]))}function Z(r){let i=t=>P(r,t>>1),e=t=>{let a=new Float64Array(t.length+1);return t.forEach((s,n)=>{a[n+1]=a[n]+i(s)}),a};return(t,a)=>{let s=v(a),n=v(t),[o,l]=M(n,s,i),[u,f]=M(n.map(g=>g^1).reverse(),s,i),c=f>l,p=c?u:o,N=Math.max(l,f);if(N<B)return[];let d=e(s),h=e(n),y=g=>c?n.length-1-p[g][0]:p[g][0],m=[];p.forEach(([,g],k)=>{if(k>0){let[ee,te]=[y(k-1),y(k)].sort((ae,ne)=>ae-ne);E(m,"I",h[te]-h[ee+1]),E(m,"D",d[g]-d[p[k-1][1]+1])}E(m,"=",i(s[g]))});let[b,S]=[y(0),y(p.length-1)].sort((g,k)=>g-k);return[{queryStart:h[b],queryEnd:h[S+1],targetStart:d[p[0][1]],targetEnd:d[p.at(-1)[1]+1],strand:c?"-":"+",edits:m,sharedBases:N}]}}function oe(r){let i=new Map,e=new Set;r.ids.forEach((t,a)=>{i.has(t)?e.add(t):i.set(t,r.rev[a])});for(let t of e)i.delete(t);return i}function J(r){let i=new Map,e=t=>{let a=i.get(t);return a===void 0&&(a=oe(t),i.set(t,a)),a};return(t,a)=>{let s=e(a),n=0,o=0;for(let[l,u]of e(t)){let f=s.get(l);f===u?n+=P(r,l):f!==void 0&&(o+=P(r,l))}return{same:n,opposite:o}}}function Q(r){let i=Z(r),e=V(r),t=J(r);return(a,s)=>{let{same:n,opposite:o}=t(a,s);return n>=B&&o>=B?e(a,s):i(a,s)}}var ie=1e4;function Y(r){let i=Z(r),e=V(r),t=J(r);return(a,s)=>{let n=i(a,s),o=n[0]?.strand,{same:l,opposite:u}=t(a,s);return o===void 0||Math.min(l,u)<ie?n:[...n,...e(a,s).filter(f=>f.strand!==o)]}}function C({chain:r,target:i,query:e,assemblyName:t,refName:a,mateAssemblyName:s}){let n=re(r.edits);return G({target:{name:i.name,assemblyName:t,refName:a,start:i.hapStart+r.targetStart,end:i.hapStart+r.targetEnd},query:{name:e.name,assemblyName:s,refName:W(e.name),start:e.hapStart+r.queryStart,end:e.hapStart+r.queryEnd},strand:r.strand,cigar:T(n),matches:n.reduce((o,[l,u])=>o+(l==="="?u:0),0),columns:n.reduce((o,[,l])=>o+l,0)})}var me=r=>I(r.name)??r.name,L=class extends q{constructor(){super(...arguments);this.walks=new K(j(this,["walksLocation"],["walksIndex"]),this);this.refNames=new D(this.walks.file,this)}get anchor(){let e=this.getConf("assemblyNames")[0];if(e===void 0)throw new Error("WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as");return e}async getHaplotypeNames(e={}){return this.walks.haplotypeNames(e)}async getHeader(e={}){let{haplotypes:t}=await this.walks.reader.header(e),{anchor:a}=this,s=w(this,a),n=x(this);return{hasCoarseTier:!1,anchorAssemblyName:a,lanes:t.filter(o=>o!==s&&A(o)!==s).map(o=>({name:O(n,o),label:o,group:A(o)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}async getSubgraph(e,t={}){let a=await this.refNames.resolve(e,{signal:t.signal});if(a===void 0)throw new Error(`${e.assemblyName} ${e.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`);return this.walks.subgraph(a,e,t)}async laneWalks(e,t,a,s,n){let o=$(a,e);return R(n,s.statusCallback,()=>this.walks.reader.cut(e,t,{...this.walks.budgets(),signal:s.signal,keep:o,expand:o,links:!1}).catch(l=>{throw z(l,t.end-t.start)}))}async anchorFeatures(e,t,a){let s=a.haplotypes?.length?a.haplotypes.map(m=>w(this,m)):void 0,n=w(this,a.targetAssemblyName),o=n===void 0?s:s===void 0||s.some(m=>F(n,m)||F(m,n))?[n]:[];if(o?.length===0)return[];let{start:l,end:u}=t,{graph:f,fragments:c}=await this.laneWalks(e,t,o,a,`Reading walks ${t.refName}:${l.toLocaleString()}-${u.toLocaleString()}`),p=Y(f.nodes),N=x(this),d=c.filter(m=>m.name===e),h=m=>o===void 0?0:o.findIndex(b=>F(m.name,b));return c.filter(m=>m.name!==e&&h(m)>=0).sort((m,b)=>h(m)-h(b)).flatMap(m=>d.flatMap(b=>p(m,b).map(S=>C({chain:S,target:b,query:m,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:O(N,me(m))}))))}async pairFeatures(e,t,a,s){let n=a.map(c=>({pair:c,featurePrefix:w(this,c.queryAssemblyName),matePrefix:w(this,c.targetAssemblyName)})),{graph:o,fragments:l}=await this.laneWalks(e,t,n.flatMap(c=>[c.featurePrefix,c.matePrefix]),s,X(a)),u=Q(o.nodes),f=c=>l.filter(p=>F(p.name,c));return n.flatMap(({pair:c,featurePrefix:p,matePrefix:N})=>f(p).flatMap(d=>f(N).flatMap(h=>u(h,d).map(y=>C({chain:y,target:d,query:h,assemblyName:c.queryAssemblyName,refName:W(d.name),mateAssemblyName:c.targetAssemblyName})))))}getFeatures(e,t={}){return H(async a=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=U(t),o=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let l of o)a.next(l)}a.complete()},t.signal)}};export{L as default};
+//# sourceMappingURL=WalkTabixSyntenyAdapter-3WRVNDLB.js.map

package/dist/chunks/{chunk-2XZYJLCE.js → chunk-2KVE7YAS.js} RENAMED Viewed

@@ -1,2 +1,2 @@
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i=e+s>>1;n[i]<t?e=i+1:s=i}return e}fraction(t,n){let e=this.arc[t]-this.arc[t-1];return e>0?(n-this.arc[t-1])/e:0}pointAt(t){let{pts:n}=this,e=n.length-1;if(e===0)return{...n[0]};if(t<=0){let i=lt(n[0],n[1]);return{x:n[0].x+i.x*t,y:n[0].y+i.y*t}}if(t>=this.total){let i=lt(n[e-1],n[e]),r=t-this.total;return{x:n[e].x+i.x*r,y:n[e].y+i.y*r}}let s=this.segment(t);return gt(n[s-1],n[s],this.fraction(s,t))}normalAt(t){let{normals:n}=this;if(n.length===1||t<=0)return n[0];if(t>=this.total)return n[n.length-1];let e=this.segment(t),{x:s,y:i}=gt(n[e-1],n[e],this.fraction(e,t)),r=Math.hypot(s,i)||1;return{x:s/r,y:i/r}}};function cn(o,t){let n=Ut(o);return o.map((e,s)=>{let i=lt(o[Math.max(0,s-1)],o[Math.min(o.length-1,s+1)]),r={x:-i.y,y:i.x},l=e.x-n.x,d=e.y-n.y,a=Math.hypot(l,d),c=r.x*l+r.y*d,h=t[s],f=a>1e-9&&Math.abs(c)>.3*a?Math.sign(c):Math.sign(r.x*h.x+r.y*h.y)||1;return{x:r.x*f,y:r.y*f}})}function xt(o,t,n,e,s){let i=Math.min(s,Math.max(e.length/24,.5)),r=[],l=[];for(let 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")})).sort((e,s)=>e.span-s.span||(e.feet===s.feet?s.drawn-e.drawn:e.drawn-s.drawn));for(let e of n)this.placePiece(e.members,this.backboneCentroid)}write(t,n){let{first:e}=this.c;this.points.forEach((s,i)=>{s?.forEach((r,l)=>{t[e[i]+l]=r.x,n[e[i]+l]=r.y})})}drawn(t){return this.c.per[t]*(this.c.count[t]-1)}endIndex(t,n){return n?this.c.count[t]-1:0}occupy(t,n){for(let e of t){let s=Rt(Math.floor(e.x/10.5),Math.floor(e.y/10.5)),i=this.grid.get(s),r={x:e.x,y:e.y,curve:n};i?i.push(r):this.grid.set(s,[r])}}violations(t,n,e,s){var i;let r=0;for(let l of t){if(e.some(c=>Math.hypot(l.x-c.x,l.y-c.y)<15))continue;let d=Math.floor(l.x/10.5),a=Math.floor(l.y/10.5);for(let c=d-1;c<=d+1;c++)for(let h=a-1;h<=a+1;h++)for(let f of(i=this.grid.get(Rt(c,h)))!==null&&i!==void 0?i:[])if(f.curve!==n&&Math.hypot(l.x-f.x,l.y-f.y)<10.5&&(r++,r>=s))return r}return r}choose(t,n,e){let s,i=1/0;for(let r of t){let l=this.violations(r(an).pts,n,e,i);if(l===0)return r(Tt);l<i&&(i=l,s=r)}return 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