jbrowse-plugin-graphgenomeviewer 4.0.21 → 4.0.22

package/dist/chunks/chunk-XK7OPCRQ.js

@@ -1,2 +0,0 @@
-import{a as f,b as m}from"./chunk-FY3BTKY4.js";var l=f((y,b)=>{b.exports=JBrowseExports["@jbrowse/core/util/tracks"]});var u=m(l(),1),A={RgfaTabixAdapter:"rGFA segments (tabix BED pair)",MinigraphBubbleAdapter:"Minigraph bubbles (tabix BED)"},I={RgfaTabixAdapter:"Path to segments BED (.segs.bed.gz from build_rgfa_tabix.sh; the .links.bed.gz and both .tbi are assumed beside it)",MinigraphBubbleAdapter:"Path to bubbles BED (.bed.gz from gfatools bubble; the .tbi is assumed beside it)"},o=".segs.bed.gz";function g(e){let i=e.search(/[?#]/);return i===-1?{name:e,query:""}:{name:e.slice(0,i),query:e.slice(i)}}function r(e){return"uri"in e?g(e.uri).name:"localPath"in e?e.localPath:""}function h(e,i){if("uri"in e){let{name:n,query:t}=g(e.uri);return{...e,uri:i(n)+t}}return"localPath"in e?{...e,localPath:i(e.localPath)}:e}function s(e,i){return h(e,n=>n+i)}function x(e){return r(e).endsWith(o)}function F(e){if(!x(e))throw new Error(`Expected a segments BED ending in ${o}, got ${r(e)||"a blob"}`);return h(e,i=>`${i.slice(0,-o.length)}.links.bed.gz`)}function d(e,i){return i?{location:i,indexType:(0,u.makeIndexType)(r(i),"CSI","TBI")}:{location:s(e,".tbi"),indexType:"TBI"}}function L(e,i){return i!==void 0&&r(i).endsWith(".csi")?{location:s(e,".csi"),indexType:"CSI"}:{location:s(e,".tbi"),indexType:"TBI"}}function p(e,i){let n=i.trim();return n?{assemblyNameToPanSN:{[e]:n}}:{}}function T({choice:e,loc:i,indexLoc:n,assembly:t,sample:a}){if(e==="MinigraphBubbleAdapter")return{type:"MinigraphBubbleAdapter",bubblesLocation:i,index:d(i,n),...p(t,a)};let c=F(i);return{type:"RgfaTabixAdapter",segmentsLocation:i,segmentsIndex:d(i,n),linksLocation:c,linksIndex:L(c,n),...p(t,a)}}function B(e){let{choice:i,assembly:n,trackId:t,name:a}=e;return{type:i==="RgfaTabixAdapter"?"GraphTrack":"FeatureTrack",trackId:t,name:a,assemblyNames:[n],adapter:T(e),...i==="RgfaTabixAdapter"?{displayDefaults:{showLabels:"none"}}:{}}}export{l as a,A as b,I as c,g as d,r as e,h as f,x as g,T as h,B as i};
-//# sourceMappingURL=chunk-XK7OPCRQ.js.map

package/dist/chunks/chunk-XK7OPCRQ.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["global-externals:@jbrowse/core/util/tracks", "../../src/GraphAddTrackWorkflow/buildTrackConfig.ts"],
-  "sourcesContent": ["module.exports = JBrowseExports[\"@jbrowse/core/util/tracks\"];", "import { makeIndexType } from '@jbrowse/core/util/tracks'\n\nimport type { FileLocation } from '@jbrowse/core/util'\n\nexport type GraphFileChoice = 'RgfaTabixAdapter' | 'MinigraphBubbleAdapter'\n\nexport const GRAPH_FILE_LABELS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter: 'rGFA segments (tabix BED pair)',\n  MinigraphBubbleAdapter: 'Minigraph bubbles (tabix BED)',\n}\n\nexport const GRAPH_FILE_FIELDS: Record<GraphFileChoice, string> = {\n  RgfaTabixAdapter:\n    'Path to segments BED (.segs.bed.gz from build_rgfa_tabix.sh; the .links.bed.gz and both .tbi are assumed beside it)',\n  MinigraphBubbleAdapter:\n    'Path to bubbles BED (.bed.gz from gfatools bubble; the .tbi is assumed beside it)',\n}\n\nconst SEGMENTS_SUFFIX = '.segs.bed.gz'\n\n// A url's query string (a presigned signature, a token) follows the file name\nexport function splitUri(uri: string) {\n  const end = uri.search(/[?#]/)\n  return end === -1\n    ? { name: uri, query: '' }\n    : { name: uri.slice(0, end), query: uri.slice(end) }\n}\n\nexport function locationName(loc: FileLocation) {\n  return 'uri' in loc\n    ? splitUri(loc.uri).name\n    : 'localPath' in loc\n      ? loc.localPath\n      : ''\n}\n\nexport function renamed(loc: FileLocation, rename: (name: string) => string) {\n  if ('uri' in loc) {\n    const { name, query } = splitUri(loc.uri)\n    return { ...loc, uri: rename(name) + query }\n  }\n  return 'localPath' in loc ? { ...loc, localPath: rename(loc.localPath) } : loc\n}\n\nfunction sibling(loc: FileLocation, suffix: string) {\n  return renamed(loc, name => name + suffix)\n}\n\nexport function isSegmentsLocation(loc: FileLocation) {\n  return locationName(loc).endsWith(SEGMENTS_SUFFIX)\n}\n\nfunction linksLocation(loc: FileLocation) {\n  if (!isSegmentsLocation(loc)) {\n    throw new Error(\n      `Expected a segments BED ending in ${SEGMENTS_SUFFIX}, got ${locationName(loc) || 'a blob'}`,\n    )\n  }\n  return renamed(\n    loc,\n    name => `${name.slice(0, -SEGMENTS_SUFFIX.length)}.links.bed.gz`,\n  )\n}\n\nfunction tabixIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  return indexLoc\n    ? {\n        location: indexLoc,\n        indexType: makeIndexType(locationName(indexLoc), 'CSI', 'TBI'),\n      }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\n// The links file's index is assumed beside it, of the kind the segments' is.\nfunction siblingIndex(loc: FileLocation, indexLoc: FileLocation | undefined) {\n  const csi = indexLoc !== undefined && locationName(indexLoc).endsWith('.csi')\n  return csi\n    ? { location: sibling(loc, '.csi'), indexType: 'CSI' }\n    : { location: sibling(loc, '.tbi'), indexType: 'TBI' }\n}\n\nfunction panSN(assembly: string, sample: string) {\n  const name = sample.trim()\n  return name ? { assemblyNameToPanSN: { [assembly]: name } } : {}\n}\n\nexport function buildAdapterConfig({\n  choice,\n  loc,\n  indexLoc,\n  assembly,\n  sample,\n}: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  assembly: string\n  sample: string\n}) {\n  if (choice === 'MinigraphBubbleAdapter') {\n    return {\n      type: 'MinigraphBubbleAdapter',\n      bubblesLocation: loc,\n      index: tabixIndex(loc, indexLoc),\n      ...panSN(assembly, sample),\n    }\n  }\n  const links = linksLocation(loc)\n  return {\n    type: 'RgfaTabixAdapter',\n    segmentsLocation: loc,\n    segmentsIndex: tabixIndex(loc, indexLoc),\n    linksLocation: links,\n    linksIndex: siblingIndex(links, indexLoc),\n    ...panSN(assembly, sample),\n  }\n}\n\nexport function buildTrackConfig(args: {\n  choice: GraphFileChoice\n  loc: FileLocation\n  indexLoc: FileLocation | undefined\n  assembly: string\n  sample: string\n  trackId: string\n  name: string\n}) {\n  const { choice, assembly, trackId, name } = args\n  return {\n    type: choice === 'RgfaTabixAdapter' ? 'GraphTrack' : 'FeatureTrack',\n    trackId,\n    name,\n    assemblyNames: [assembly],\n    adapter: buildAdapterConfig(args),\n    ...(choice === 'RgfaTabixAdapter'\n      ? { displayDefaults: { showLabels: 'none' } }\n      : {}),\n  }\n}\n"],
-  "mappings": "+CAAA,IAAAA,EAAAC,EAAA,CAAAC,EAAAC,IAAA,CAAAA,EAAO,QAAU,eAAe,2BAA2B,ICA3D,IAAAC,EAA8B,SAMjBC,EAAqD,CAChE,iBAAkB,iCAClB,uBAAwB,+BAC1B,EAEaC,EAAqD,CAChE,iBACE,sHACF,uBACE,mFACJ,EAEMC,EAAkB,eAGjB,SAASC,EAASC,EAAa,CACpC,IAAMC,EAAMD,EAAI,OAAO,MAAM,EAC7B,OAAOC,IAAQ,GACX,CAAE,KAAMD,EAAK,MAAO,EAAG,EACvB,CAAE,KAAMA,EAAI,MAAM,EAAGC,CAAG,EAAG,MAAOD,EAAI,MAAMC,CAAG,CAAE,CACvD,CAEO,SAASC,EAAaC,EAAmB,CAC9C,MAAO,QAASA,EACZJ,EAASI,EAAI,GAAG,EAAE,KAClB,cAAeA,EACbA,EAAI,UACJ,EACR,CAEO,SAASC,EAAQD,EAAmBE,EAAkC,CAC3E,GAAI,QAASF,EAAK,CAChB,GAAM,CAAE,KAAAG,EAAM,MAAAC,CAAM,EAAIR,EAASI,EAAI,GAAG,EACxC,MAAO,CAAE,GAAGA,EAAK,IAAKE,EAAOC,CAAI,EAAIC,CAAM,CAC7C,CACA,MAAO,cAAeJ,EAAM,CAAE,GAAGA,EAAK,UAAWE,EAAOF,EAAI,SAAS,CAAE,EAAIA,CAC7E,CAEA,SAASK,EAAQL,EAAmBM,EAAgB,CAClD,OAAOL,EAAQD,EAAKG,GAAQA,EAAOG,CAAM,CAC3C,CAEO,SAASC,EAAmBP,EAAmB,CACpD,OAAOD,EAAaC,CAAG,EAAE,SAASL,CAAe,CACnD,CAEA,SAASa,EAAcR,EAAmB,CACxC,GAAI,CAACO,EAAmBP,CAAG,EACzB,MAAM,IAAI,MACR,qCAAqCL,CAAe,SAASI,EAAaC,CAAG,GAAK,QAAQ,EAC5F,EAEF,OAAOC,EACLD,EACAG,GAAQ,GAAGA,EAAK,MAAM,EAAG,CAACR,EAAgB,MAAM,CAAC,eACnD,CACF,CAEA,SAASc,EAAWT,EAAmBU,EAAoC,CACzE,OAAOA,EACH,CACE,SAAUA,EACV,aAAW,iBAAcX,EAAaW,CAAQ,EAAG,MAAO,KAAK,CAC/D,EACA,CAAE,SAAUL,EAAQL,EAAK,MAAM,EAAG,UAAW,KAAM,CACzD,CAGA,SAASW,EAAaX,EAAmBU,EAAoC,CAE3E,OADYA,IAAa,QAAaX,EAAaW,CAAQ,EAAE,SAAS,MAAM,EAExE,CAAE,SAAUL,EAAQL,EAAK,MAAM,EAAG,UAAW,KAAM,EACnD,CAAE,SAAUK,EAAQL,EAAK,MAAM,EAAG,UAAW,KAAM,CACzD,CAEA,SAASY,EAAMC,EAAkBC,EAAgB,CAC/C,IAAMX,EAAOW,EAAO,KAAK,EACzB,OAAOX,EAAO,CAAE,oBAAqB,CAAE,CAACU,CAAQ,EAAGV,CAAK,CAAE,EAAI,CAAC,CACjE,CAEO,SAASY,EAAmB,CACjC,OAAAC,EACA,IAAAhB,EACA,SAAAU,EACA,SAAAG,EACA,OAAAC,CACF,EAMG,CACD,GAAIE,IAAW,yBACb,MAAO,CACL,KAAM,yBACN,gBAAiBhB,EACjB,MAAOS,EAAWT,EAAKU,CAAQ,EAC/B,GAAGE,EAAMC,EAAUC,CAAM,CAC3B,EAEF,IAAMG,EAAQT,EAAcR,CAAG,EAC/B,MAAO,CACL,KAAM,mBACN,iBAAkBA,EAClB,cAAeS,EAAWT,EAAKU,CAAQ,EACvC,cAAeO,EACf,WAAYN,EAAaM,EAAOP,CAAQ,EACxC,GAAGE,EAAMC,EAAUC,CAAM,CAC3B,CACF,CAEO,SAASI,EAAiBC,EAQ9B,CACD,GAAM,CAAE,OAAAH,EAAQ,SAAAH,EAAU,QAAAO,EAAS,KAAAjB,CAAK,EAAIgB,EAC5C,MAAO,CACL,KAAMH,IAAW,mBAAqB,aAAe,eACrD,QAAAI,EACA,KAAAjB,EACA,cAAe,CAACU,CAAQ,EACxB,QAASE,EAAmBI,CAAI,EAChC,GAAIH,IAAW,mBACX,CAAE,gBAAiB,CAAE,WAAY,MAAO,CAAE,EAC1C,CAAC,CACP,CACF",
-  "names": ["require_tracks", "__commonJSMin", "exports", "module", "import_tracks", "GRAPH_FILE_LABELS", "GRAPH_FILE_FIELDS", "SEGMENTS_SUFFIX", "splitUri", "uri", "end", "locationName", "loc", "renamed", "rename", "name", "query", "sibling", "suffix", "isSegmentsLocation", "linksLocation", "tabixIndex", "indexLoc", "siblingIndex", "panSN", "assembly", "sample", "buildAdapterConfig", "choice", "links", "buildTrackConfig", "args", "trackId"]
-}