jbrowse-plugin-graphgenomeviewer 7.3.1 → 7.4.0

package/dist/chunks/chunk-QASFRHPG.js

@@ -0,0 +1,2 @@
+import{l as o}from"./chunk-YBZA7LPQ.js";function u(a,r,e){return e?{...a,walkRowRuns:o(a,r)}:a}export{u as a};
+//# sourceMappingURL=chunk-QASFRHPG.js.map

package/dist/chunks/chunk-SI64QXFH.js

@@ -0,0 +1,4 @@
+import{a as I,b as L,f as S,h as w}from"./chunk-YBZA7LPQ.js";import{p as T}from"./chunk-4AAW5P6N.js";var O=62,Z=60,G=9,k=48,z=57,_=/^(?:LN:i|SN:Z|SO:i|SR:i):/,q=/^[PEOUFG]\t/,C=e=>e.endsWith("\r")?e.slice(0,-1):e;function P(){return{nodes:new T(new Int32Array(65536)),reversed:new T(new Uint8Array(65536))}}var R=class{constructor(){this.names=[],this.byName=new Map,this.byNumber=new Map}has(e){return this.byName.has(e)}add(e){let s=this.names.length;this.byName.set(e,s),this.names.push(e);let t=+e;return Number.isSafeInteger(t)&&String(t)===e&&this.byNumber.set(t,s),s}of(e){return this.byName.get(e)??this.add(e)}ofNumber(e){return this.byNumber.get(e)}};function U(e){let[,s,t="*",...r]=e.split("	");if(!s||/^\d+$/.test(t))return;let i=t==="*"?0:t.length,n,f,o;for(let c of r){if(!_.test(c))return;let a=c.slice(5),p=c.slice(0,2);p==="LN"?i=+a:p==="SN"?n=a:p==="SO"?f=+a:o=+a}return{name:s,length:i,stable:n!==void 0&&f!==void 0&&o!==void 0?{refName:n,start:f,rank:o}:void 0}}function $(e,s,t,r){let i=0,n=-1,f=0,o=!0,d=a=>{if(n>=0&&a>n){let p=o&&a-n<16&&(a-n===1||e.charCodeAt(n)!==k)?t.ofNumber(f):void 0;r.nodes.push(p??t.of(e.slice(n,a))),r.reversed.push(i)}},c=s;for(;c<e.length;c++){let a=e.charCodeAt(c);if(a===O||a===Z)d(c),i=a===Z?1:0,n=c+1,f=0,o=!0;else{if(a===G)break;o&&a>=k&&a<=z?f=f*10+a-k:o=!1}}return d(c),c}function x(e){let s=[],t=0;for(;s.length<6;){let d=e.indexOf("	",t);if(d===-1)return;s.push(e.slice(t,d)),t=d+1}let[,r,i,n,f,o]=s;return r&&i&&n&&f&&o&&t<e.length?{sample:r,haplotype:i,contig:n,start:f,end:o,body:t}:void 0}function K(e){let s=e.split(`
+`),t=new R,r=[],i=[],n=[],f=[],o=[],d=new Map;for(let u of s){if(q.test(u))return;if(u.startsWith("S	")){let l=U(C(u));if(!l||t.has(l.name))return;t.add(l.name),r.push(l.length);let h=-1;l.stable&&(h=d.get(l.stable.refName)??o.length,h===o.length&&(o.push(l.stable.refName),d.set(l.stable.refName,h))),i.push(h),n.push(l.stable?.start??0),f.push(l.stable?.rank??0)}}let c=[],a=[],p=[],v=[],E=[],W=[],y=[0],g=P(),A=new w,N=new w;for(let u of s)if(u.startsWith("L	")){let[,l,h,b,m]=C(u).split("	");l&&b&&m&&(c.push(t.of(l)),a.push(t.of(b)),p.push((h==="-"?1:0)|(m==="-"?2:0)))}else if(u.startsWith("W	")){let l=C(u),h=x(l);if(h){v.push(`${h.sample}#${h.haplotype}#${h.contig}`),E.push(h.start==="*"?0:+h.start),W.push(h.end==="*"?-1:+h.end);let b=$(l,h.body,t,g),m=F(l,b);if(m===void 0||(m.before&&A.push(m.before),m.after&&N.push(m.after),g.nodes.length===y.at(-1)))return;y.push(g.nodes.length)}}if(![A.kinds.length,N.kinds.length].some(u=>u>0&&u<v.length))return{nodes:{names:t.names,lengths:Int32Array.from(r),refs:Int32Array.from(i),starts:Float64Array.from(n),ranks:Int32Array.from(f),refNames:o},links:{from:Int32Array.from(c),to:Int32Array.from(a),strands:Uint8Array.from(p)},walks:{names:v,starts:Float64Array.from(E),ends:Float64Array.from(W),offsets:Int32Array.from(y),steps:g.nodes.data.slice(0,g.nodes.length),reversed:g.reversed.data.slice(0,g.reversed.length),...B(v.length,A,N)}}}function F(e,s){let t={};for(let r of s<e.length?e.slice(s+1).split("	"):[]){let i=r.slice(5);if(r.startsWith(`${I}:Z:`)){if(t.before=S(i),!t.before)return}else if(r.startsWith(`${L}:Z:`)&&(t.after=S(i),!t.after))return}return t}function B(e,s,t){return{...s.kinds.length===e&&e>0?{before:s.table()}:{},...t.kinds.length===e&&e>0?{after:t.table()}:{}}}var D=/([><])([^><]+)/g;function M(e){if(!e.startsWith(">")&&!e.startsWith("<"))return;let s=[];for(let[,t,r]of e.matchAll(D))s.push({name:r,strand:t===">"?"+":"-"});return s}function Q(e){let s=e.trimEnd(),t=s.split("	");if(t.length<12||s.startsWith("#"))return;let r=M(t[5]);if(!r)return;let i,n=!1;for(let f=12;f<t.length;f++){let o=t[f];o.startsWith("cs:Z:")?i=o.slice(5):o==="tp:A:S"&&(n=!0)}return{name:t[0],queryLength:+t[1],queryStart:+t[2],queryEnd:+t[3],strand:t[4]==="-"?"-":"+",path:r,pathLength:+t[6],pathStart:+t[7],pathEnd:+t[8],matches:+t[9],blockLength:+t[10],mappingQuality:+t[11],secondary:n,...i===void 0?{}:{cs:i}}}function Y(e){let s=[];for(let t of e.split(`
+`)){let r=Q(t);r&&s.push(r)}return s}var j=/:(\d+)|=([A-Za-z]+)|\*[a-zA-Z]([a-zA-Z])|\+([A-Za-z]+)|-([A-Za-z]+)|~[a-z]{2}(\d+)[a-z]{2}/g;function tt(e){let s=[];for(let t of e.matchAll(j))t[1]!==void 0?s.push({op:"match",length:+t[1]}):t[2]!==void 0?s.push({op:"match",length:t[2].length}):t[3]!==void 0?s.push({op:"substitution",seq:t[3].toUpperCase()}):t[4]!==void 0?s.push({op:"insertion",seq:t[4].toUpperCase()}):t[5]!==void 0?s.push({op:"deletion",length:t[5].length}):t[6]!==void 0&&s.push({op:"match",length:+t[6]});return s}export{K as a,Q as b,Y as c,tt as d};
+//# sourceMappingURL=chunk-SI64QXFH.js.map

package/dist/chunks/{chunk-VQ77X5QU.js.map → chunk-SI64QXFH.js.map}

@@ -1,7 +1,7 @@
 {
   "version": 3,
-  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-DZR37KXT.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.4.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-C44YRP5F.js"],
-  "sourcesContent": ["import {\n  END_STOP_TAG,\n  START_STOP_TAG,\n  StopColumns,\n  parseStopTag\n} from \"./chunk-EIY2SKD3.js\";\nimport {\n  Column\n} from \"./chunk-ZPZ7GNBT.js\";\n\n// src/gfa/gfaTables.ts\nvar GT = 62;\nvar LT = 60;\nvar TAB = 9;\nvar ZERO = 48;\nvar NINE = 57;\nvar TABLE_TAG = /^(?:LN:i|SN:Z|SO:i|SR:i):/;\nvar UNTABLED_RECORD = /^[PEOUFG]\\t/;\nvar trimCR = (line) => line.endsWith(\"\\r\") ? line.slice(0, -1) : line;\nfunction stepColumns() {\n  return {\n    nodes: new Column(new Int32Array(1 << 16)),\n    reversed: new Column(new Uint8Array(1 << 16))\n  };\n}\nvar SegmentIndex = class {\n  constructor() {\n    this.names = [];\n    this.byName = /* @__PURE__ */ new Map();\n    // ids that are plain decimal, so a walk step finds its segment without\n    // slicing a string out of the body\n    this.byNumber = /* @__PURE__ */ new Map();\n  }\n  has(name) {\n    return this.byName.has(name);\n  }\n  add(name) {\n    const i = this.names.length;\n    this.byName.set(name, i);\n    this.names.push(name);\n    const n = +name;\n    if (Number.isSafeInteger(n) && String(n) === name) {\n      this.byNumber.set(n, i);\n    }\n    return i;\n  }\n  of(name) {\n    return this.byName.get(name) ?? this.add(name);\n  }\n  ofNumber(n) {\n    return this.byNumber.get(n);\n  }\n};\nfunction readSegment(line) {\n  const [, name, sequence = \"*\", ...tags] = line.split(\"\t\");\n  if (!name || /^\\d+$/.test(sequence)) {\n    return void 0;\n  }\n  let length = sequence === \"*\" ? 0 : sequence.length;\n  let refName;\n  let start;\n  let rank;\n  for (const tag of tags) {\n    if (!TABLE_TAG.test(tag)) {\n      return void 0;\n    }\n    const value = tag.slice(5);\n    const key = tag.slice(0, 2);\n    if (key === \"LN\") {\n      length = +value;\n    } else if (key === \"SN\") {\n      refName = value;\n    } else if (key === \"SO\") {\n      start = +value;\n    } else {\n      rank = +value;\n    }\n  }\n  const stable = refName !== void 0 && start !== void 0 && rank !== void 0 ? { refName, start, rank } : void 0;\n  return { name, length, stable };\n}\nfunction readWalkBody(line, from, segments, steps) {\n  let reversed = 0;\n  let start = -1;\n  let value = 0;\n  let decimal = true;\n  const finish = (end) => {\n    if (start >= 0 && end > start) {\n      const node = decimal && end - start < 16 && (end - start === 1 || line.charCodeAt(start) !== ZERO) ? segments.ofNumber(value) : void 0;\n      steps.nodes.push(node ?? segments.of(line.slice(start, end)));\n      steps.reversed.push(reversed);\n    }\n  };\n  let i = from;\n  for (; i < line.length; i++) {\n    const ch = line.charCodeAt(i);\n    if (ch === GT || ch === LT) {\n      finish(i);\n      reversed = ch === LT ? 1 : 0;\n      start = i + 1;\n      value = 0;\n      decimal = true;\n    } else if (ch === TAB) {\n      break;\n    } else if (decimal && ch >= ZERO && ch <= NINE) {\n      value = value * 10 + ch - ZERO;\n    } else {\n      decimal = false;\n    }\n  }\n  finish(i);\n  return i;\n}\nfunction walkFields(line) {\n  const fields = [];\n  let at = 0;\n  while (fields.length < 6) {\n    const tab = line.indexOf(\"\t\", at);\n    if (tab === -1) {\n      return void 0;\n    }\n    fields.push(line.slice(at, tab));\n    at = tab + 1;\n  }\n  const [, sample, haplotype, contig, start, end] = fields;\n  return sample && haplotype && contig && start && end && at < line.length ? { sample, haplotype, contig, start, end, body: at } : void 0;\n}\nfunction gfaTables(text) {\n  const lines = text.split(\"\\n\");\n  const segments = new SegmentIndex();\n  const lengths = [];\n  const refs = [];\n  const starts = [];\n  const ranks = [];\n  const refNames = [];\n  const refIndex = /* @__PURE__ */ new Map();\n  for (const raw of lines) {\n    if (UNTABLED_RECORD.test(raw)) {\n      return void 0;\n    }\n    if (raw.startsWith(\"S\t\")) {\n      const s = readSegment(trimCR(raw));\n      if (!s || segments.has(s.name)) {\n        return void 0;\n      }\n      segments.add(s.name);\n      lengths.push(s.length);\n      let ref = -1;\n      if (s.stable) {\n        ref = refIndex.get(s.stable.refName) ?? refNames.length;\n        if (ref === refNames.length) {\n          refNames.push(s.stable.refName);\n          refIndex.set(s.stable.refName, ref);\n        }\n      }\n      refs.push(ref);\n      starts.push(s.stable?.start ?? 0);\n      ranks.push(s.stable?.rank ?? 0);\n    }\n  }\n  const from = [];\n  const to = [];\n  const strands = [];\n  const names = [];\n  const walkStarts = [];\n  const walkEnds = [];\n  const offsets = [0];\n  const steps = stepColumns();\n  const before = new StopColumns();\n  const after = new StopColumns();\n  for (const raw of lines) {\n    if (raw.startsWith(\"L\t\")) {\n      const [, source, strand1, target, strand2] = trimCR(raw).split(\"\t\");\n      if (source && target && strand2) {\n        from.push(segments.of(source));\n        to.push(segments.of(target));\n        strands.push((strand1 === \"-\" ? 1 : 0) | (strand2 === \"-\" ? 2 : 0));\n      }\n    } else if (raw.startsWith(\"W\t\")) {\n      const line = trimCR(raw);\n      const w = walkFields(line);\n      if (w) {\n        names.push(`${w.sample}#${w.haplotype}#${w.contig}`);\n        walkStarts.push(w.start === \"*\" ? 0 : +w.start);\n        walkEnds.push(w.end === \"*\" ? -1 : +w.end);\n        const end = readWalkBody(line, w.body, segments, steps);\n        const tags = walkTags(line, end);\n        if (tags === void 0) {\n          return void 0;\n        }\n        if (tags.before) {\n          before.push(tags.before);\n        }\n        if (tags.after) {\n          after.push(tags.after);\n        }\n        if (steps.nodes.length === offsets.at(-1)) {\n          return void 0;\n        }\n        offsets.push(steps.nodes.length);\n      }\n    }\n  }\n  if ([before.kinds.length, after.kinds.length].some(\n    (n) => n > 0 && n < names.length\n  )) {\n    return void 0;\n  }\n  return {\n    nodes: {\n      names: segments.names,\n      lengths: Int32Array.from(lengths),\n      refs: Int32Array.from(refs),\n      starts: Float64Array.from(starts),\n      ranks: Int32Array.from(ranks),\n      refNames\n    },\n    links: {\n      from: Int32Array.from(from),\n      to: Int32Array.from(to),\n      strands: Uint8Array.from(strands)\n    },\n    walks: {\n      names,\n      starts: Float64Array.from(walkStarts),\n      ends: Float64Array.from(walkEnds),\n      offsets: Int32Array.from(offsets),\n      steps: steps.nodes.data.slice(0, steps.nodes.length),\n      reversed: steps.reversed.data.slice(0, steps.reversed.length),\n      ...stopColumns(names.length, before, after)\n    }\n  };\n}\nfunction walkTags(line, from) {\n  const out = {};\n  for (const tag of from < line.length ? line.slice(from + 1).split(\"\t\") : []) {\n    const value = tag.slice(5);\n    if (tag.startsWith(`${START_STOP_TAG}:Z:`)) {\n      out.before = parseStopTag(value);\n      if (!out.before) {\n        return void 0;\n      }\n    } else if (tag.startsWith(`${END_STOP_TAG}:Z:`)) {\n      out.after = parseStopTag(value);\n      if (!out.after) {\n        return void 0;\n      }\n    }\n  }\n  return out;\n}\nfunction stopColumns(walks, before, after) {\n  return {\n    ...before.kinds.length === walks && walks > 0 ? { before: before.table() } : {},\n    ...after.kinds.length === walks && walks > 0 ? { after: after.table() } : {}\n  };\n}\n\nexport {\n  gfaTables\n};\n", "// src/gaf/parseGaf.ts\nvar STEP = /([><])([^><]+)/g;\nfunction parseGafPath(column) {\n  if (!column.startsWith(\">\") && !column.startsWith(\"<\")) {\n    return void 0;\n  }\n  const steps = [];\n  for (const [, arrow, name] of column.matchAll(STEP)) {\n    steps.push({ name, strand: arrow === \">\" ? \"+\" : \"-\" });\n  }\n  return steps;\n}\nfunction parseGafLine(line) {\n  const columns = line.split(\"\t\");\n  if (columns.length < 12 || line.startsWith(\"#\")) {\n    return void 0;\n  }\n  const path = parseGafPath(columns[5]);\n  if (!path) {\n    return void 0;\n  }\n  let cs;\n  let secondary = false;\n  for (let i = 12; i < columns.length; i++) {\n    const tag = columns[i];\n    if (tag.startsWith(\"cs:Z:\")) {\n      cs = tag.slice(5);\n    } else if (tag === \"tp:A:S\") {\n      secondary = true;\n    }\n  }\n  return {\n    name: columns[0],\n    queryLength: +columns[1],\n    queryStart: +columns[2],\n    queryEnd: +columns[3],\n    strand: columns[4] === \"-\" ? \"-\" : \"+\",\n    path,\n    pathLength: +columns[6],\n    pathStart: +columns[7],\n    pathEnd: +columns[8],\n    matches: +columns[9],\n    blockLength: +columns[10],\n    mappingQuality: +columns[11],\n    secondary,\n    ...cs === void 0 ? {} : { cs }\n  };\n}\nfunction parseGaf(text) {\n  const records = [];\n  for (const line of text.split(\"\\n\")) {\n    const record = parseGafLine(line.trimEnd());\n    if (record) {\n      records.push(record);\n    }\n  }\n  return records;\n}\nvar CS_OP = /:(\\d+)|=([A-Za-z]+)|\\*[a-zA-Z]([a-zA-Z])|\\+([A-Za-z]+)|-([A-Za-z]+)|~[a-z]{2}(\\d+)[a-z]{2}/g;\nfunction parseCs(cs) {\n  const ops = [];\n  for (const m of cs.matchAll(CS_OP)) {\n    if (m[1] !== void 0) {\n      ops.push({ op: \"match\", length: +m[1] });\n    } else if (m[2] !== void 0) {\n      ops.push({ op: \"match\", length: m[2].length });\n    } else if (m[3] !== void 0) {\n      ops.push({ op: \"substitution\", seq: m[3].toUpperCase() });\n    } else if (m[4] !== void 0) {\n      ops.push({ op: \"insertion\", seq: m[4].toUpperCase() });\n    } else if (m[5] !== void 0) {\n      ops.push({ op: \"deletion\", length: m[5].length });\n    } else if (m[6] !== void 0) {\n      ops.push({ op: \"match\", length: +m[6] });\n    }\n  }\n  return ops;\n}\n\nexport {\n  parseGafPath,\n  parseGafLine,\n  parseGaf,\n  parseCs\n};\n"],
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+  "sources": ["../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-VSSIYQYF.js", "../../node_modules/.pnpm/@jbrowse+bandage-core@11.7.0/node_modules/@jbrowse/bandage-core/dist/chunks/chunk-5OJZV6YT.js"],
+  "sourcesContent": ["import {\n  END_STOP_TAG,\n  START_STOP_TAG,\n  StopColumns,\n  parseStopTag\n} from \"./chunk-LG2UK4MB.js\";\nimport {\n  Column\n} from \"./chunk-ZPZ7GNBT.js\";\n\n// src/gfa/gfaTables.ts\nvar GT = 62;\nvar LT = 60;\nvar TAB = 9;\nvar ZERO = 48;\nvar NINE = 57;\nvar TABLE_TAG = /^(?:LN:i|SN:Z|SO:i|SR:i):/;\nvar UNTABLED_RECORD = /^[PEOUFG]\\t/;\nvar trimCR = (line) => line.endsWith(\"\\r\") ? line.slice(0, -1) : line;\nfunction stepColumns() {\n  return {\n    nodes: new Column(new Int32Array(1 << 16)),\n    reversed: new Column(new Uint8Array(1 << 16))\n  };\n}\nvar SegmentIndex = class {\n  constructor() {\n    this.names = [];\n    this.byName = /* @__PURE__ */ new Map();\n    // ids that are plain decimal, so a walk step finds its segment without\n    // slicing a string out of the body\n    this.byNumber = /* @__PURE__ */ new Map();\n  }\n  has(name) {\n    return this.byName.has(name);\n  }\n  add(name) {\n    const i = this.names.length;\n    this.byName.set(name, i);\n    this.names.push(name);\n    const n = +name;\n    if (Number.isSafeInteger(n) && String(n) === name) {\n      this.byNumber.set(n, i);\n    }\n    return i;\n  }\n  of(name) {\n    return this.byName.get(name) ?? 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 }

package/dist/chunks/{chunk-44CJ2N3N.js → chunk-UW7INEQF.js}

@@ -1,2 +1,2 @@
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