jbrowse-plugin-graphgenomeviewer 7.1.0 → 7.1.2

package/dist/chunks/RgfaTabixAdapter-2OL5X3HF.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/RgfaTabixAdapter/rgfaBed.ts", "../../src/RgfaTabixAdapter/RgfaTabixAdapter.ts"],
-  "sourcesContent": ["// A segment as it appears in segs.bed.gz, and as it is repeated inside every\n// links.bed.gz row: `stableName start end segmentId rank [tags]`. The first\n// five are the SN/SO/SR tags rGFA already carries, projected to BED by\n// `gfatools gfa2bed -m`.\n//\n// `tags` is a space-separated list of GFA tags, written verbatim onto the\n// S-line formatSegment synthesizes, where the GFA parser reads them into\n// `GraphNode.tags` with no work here. It is the extension point for everything\n// the five columns cannot say: carriage on a path-derived graph (`SM:Z:`), the\n// collapse summary on a level-of-detail tier (`ct:Z:`, `cn:i:`, ...), a\n// precomputed layout position later. rGFA files have no sixth column at all,\n// so this is empty for them and nothing changes.\nexport interface RgfaSegment {\n  refName: string\n  start: number\n  end: number\n  id: string\n  rank: number\n  tags: string\n}\n\nexport interface RgfaLink {\n  source: string\n  sourceStrand: string\n  target: string\n  targetStrand: string\n  sourceSegment: RgfaSegment\n  targetSegment: RgfaSegment\n}\n\nexport function parseSegmentLine(line: string): RgfaSegment {\n  return parseSegmentRow(line).segment\n}\n\n// gfa-to-tabix's anchored layout files a segment under the reference interval\n// its bubble hangs from and states the segment's own coordinate after the rank:\n// `anchorName anchorStart anchorEnd segmentId rank stableName start end [tags]`.\n// One query over a region then returns every segment of every bubble under it,\n// and `anchored` tells a cut it has nothing left to follow.\nexport function parseSegmentRow(line: string) {\n  const cols = line.split('\\t')\n  const anchored = cols.length >= 8\n  const own = anchored ? 5 : 0\n  return {\n    anchored,\n    segment: {\n      refName: cols[own]!,\n      start: +cols[own + 1]!,\n      end: +cols[own + 2]!,\n      id: cols[3]!,\n      rank: +cols[4]!,\n      tags: cols[anchored ? 8 : 5] ?? '',\n    } satisfies RgfaSegment,\n  }\n}\n\n// Carriage as an ordinary feature attribute, for the linear track rather than\n// the graph. The tag column reaches the graph view through the synthesized\n// S-line (formatSegment below, then gfaConverter reads SM into\n// `GraphNode.samples`), and that route ends at the graph: `getFeatures` builds\n// its own features and had no way to say who carries a segment, so a lane\n// colored by carriage was not expressible.\n//\n// `SM:Z:` is its own grammar check here. build_pggb_tabix.sh wrote a bare\n// comma-separated list in this column before the tag column existed, and those\n// files are still hosted; a bare list has no prefix to match, so it is dropped\n// rather than read as one sample named `K12,Sakai,CFT073`.\n//\n// Undefined rather than [] when the tag is absent, matching gfaConverter: an\n// rGFA has no sixth column at all, so a segment that says nothing about\n// carriage stays distinguishable from one carried by nobody.\nexport function segmentSamples(segment: RgfaSegment) {\n  const tag = segment.tags.split(' ').find(t => t.startsWith('SM:Z:'))\n  if (tag === undefined) {\n    return undefined\n  }\n  const samples = tag\n    .slice('SM:Z:'.length)\n    .split(',')\n    .map(s => s.trim())\n    .filter(Boolean)\n  return samples.length > 0 ? samples : undefined\n}\n\n// `s322+` \u2014 the L-line's segment id with its orientation appended, mirroring\n// the GFA record it came from.\nfunction parseEndpoint(field: string) {\n  return { id: field.slice(0, -1), strand: field.slice(-1) }\n}\n\nexport function parseLinkLine(line: string): RgfaLink {\n  const cols = line.split('\\t')\n  const source = parseEndpoint(cols[3]!)\n  const target = parseEndpoint(cols[4]!)\n  return {\n    source: source.id,\n    sourceStrand: source.strand,\n    target: target.id,\n    targetStrand: target.strand,\n    sourceSegment: {\n      id: source.id,\n      refName: cols[5]!,\n      start: +cols[6]!,\n      end: +cols[7]!,\n      rank: +cols[8]!,\n      tags: cols[13] ?? '',\n    },\n    targetSegment: {\n      id: target.id,\n      refName: cols[9]!,\n      start: +cols[10]!,\n      end: +cols[11]!,\n      rank: +cols[12]!,\n      tags: cols[14] ?? '',\n    },\n  }\n}\n\nexport function linkKey(link: RgfaLink) {\n  return `${link.source}${link.sourceStrand}${link.target}${link.targetStrand}`\n}\n\n// The cut an anchored index gives: `under` is what the segment file returned\n// for the window, every segment of every bubble under it, and `found` is what\n// the link file returned. gfa-to-tabix files a link widely enough that `found`\n// holds every link touching a segment in `under` and every link between the\n// segments those lead to, plus links of neither kind, which are dropped here.\n// A backbone link that jumps the whole window, as a deletion or inversion\n// spanning it does, touches nothing in `under` and is kept by its own rule.\nexport function anchoredCut(\n  under: Map<string, RgfaSegment>,\n  found: RgfaLink[],\n  window: StableSpan,\n) {\n  const side = (segment: RgfaSegment) =>\n    segment.rank !== 0 || segment.refName !== window.refName\n      ? 0\n      : segment.end <= window.start\n        ? -1\n        : segment.start >= window.end\n          ? 1\n          : 0\n  const segments = new Map(under)\n  const links = new Map<string, RgfaLink>()\n  for (const link of found) {\n    if (\n      under.has(link.source) ||\n      under.has(link.target) ||\n      side(link.sourceSegment) * side(link.targetSegment) === -1\n    ) {\n      links.set(linkKey(link), link)\n      for (const segment of [link.sourceSegment, link.targetSegment]) {\n        if (!segments.has(segment.id)) {\n          segments.set(segment.id, segment)\n        }\n      }\n    }\n  }\n  for (const link of found) {\n    if (segments.has(link.source) && segments.has(link.target)) {\n      links.set(linkKey(link), link)\n    }\n  }\n  return { segments, links }\n}\n\n// Both endpoints of a link are written into every row, so the same link is\n// indexed under each endpoint's stable sequence and arrives twice for a region\n// covering both. Callers dedupe on linkKey.\n\nexport interface StableSpan {\n  refName: string\n  start: number\n  end: number\n}\n\n// Where a cut reads links once more to close itself. A hop reads the links of\n// the segments the round before it reached, so a link between two segments of\n// the last round is never read and an allele reached from both ends draws as\n// two stubs. rGFA lays an allele out as one stretch of the stable sequence that\n// introduced it, so pieces of one sequence within the window's length of each\n// other merge into a span, and reading it brings the pieces between too.\n// Backbone reached past the window is unread for the same reason; its spans\n// join only abutting pieces, since the reference past the window is not the\n// cut's to fill. A span whose segments were all read and abut is skipped.\nexport function closingSpans(\n  held: RgfaSegment[],\n  unread: Set<string>,\n  window: StableSpan,\n) {\n  const outside = (segment: RgfaSegment) =>\n    segment.refName !== window.refName ||\n    segment.end <= window.start ||\n    segment.start >= window.end\n  return [\n    ...mergedSpans(\n      held.filter(segment => segment.rank > 0),\n      unread,\n      window.end - window.start,\n    ),\n    ...mergedSpans(\n      held.filter(segment => segment.rank === 0 && outside(segment)),\n      new Set(held.map(segment => segment.id)),\n      0,\n    ),\n  ]\n}\n\nfunction mergedSpans(\n  segments: RgfaSegment[],\n  unread: Set<string>,\n  maxGap: number,\n) {\n  const sorted = [...segments].sort(\n    (a, b) => compare(a.refName, b.refName) || a.start - b.start,\n  )\n  const spans: (StableSpan & { needed: boolean })[] = []\n  for (const segment of sorted) {\n    const span = spans.at(-1)\n    if (\n      span?.refName === segment.refName &&\n      segment.start - span.end <= maxGap\n    ) {\n      span.needed ||= segment.start > span.end || unread.has(segment.id)\n      span.end = Math.max(span.end, segment.end)\n    } else {\n      spans.push({\n        refName: segment.refName,\n        start: segment.start,\n        end: segment.end,\n        needed: unread.has(segment.id),\n      })\n    }\n  }\n  return spans\n    .filter(span => span.needed)\n    .map(({ refName, start, end }): StableSpan => ({ refName, start, end }))\n}\n\n// The links a closing read keeps: each end is a segment the cut holds or one\n// lying inside a span. Following anything else is what another hop is for.\nexport function closingLinks(\n  found: RgfaLink[],\n  held: Map<string, RgfaSegment>,\n  spans: StableSpan[],\n) {\n  const inside = (segment: RgfaSegment) =>\n    held.has(segment.id) ||\n    spans.some(\n      span =>\n        span.refName === segment.refName &&\n        segment.start >= span.start &&\n        segment.end <= span.end,\n    )\n  return found.filter(\n    link => inside(link.sourceSegment) && inside(link.targetSegment),\n  )\n}\n\n// Segments carry no sequence here \u2014 the BED records only their span \u2014 so every\n// S-line is written with `*` and an LN tag, which is what the GFA spec asks for\n// and what packages/graph-core's parser reads back as the node length.\n// `NM:i:0`, `SM:Z:HG002.1,HG002.2` \u2014 the GFA tag grammar, checked rather than\n// trusted. Files built before the tag column existed put a bare comma-separated\n// sample list here, and passing that through would put a field that is not a\n// tag on an S-line, which is a malformed GFA rather than a missing annotation.\n// Dropping it degrades to the pre-tag behaviour instead.\nconst GFA_TAG = /^[A-Za-z][A-Za-z0-9]:[AifZJHB]:/\n\nfunction formatSegment(segment: RgfaSegment) {\n  const { id, refName, start, end, rank, tags } = segment\n  const valid = tags.split(' ').filter(t => GFA_TAG.test(t))\n  const extra = valid.length === 0 ? '' : `\\t${valid.join('\\t')}`\n  return `S\\t${id}\\t*\\tLN:i:${end - start}\\tSN:Z:${refName}\\tSO:i:${start}\\tSR:i:${rank}${extra}`\n}\n\nfunction formatLink(link: RgfaLink) {\n  const { source, sourceStrand, target, targetStrand } = link\n  return `L\\t${source}\\t${sourceStrand}\\t${target}\\t${targetStrand}\\t0M`\n}\n\n// Codepoint order, not localeCompare: the byte-identical-output guarantee below\n// has to hold across locales.\nfunction compare(a: string, b: string) {\n  return a < b ? -1 : a > b ? 1 : 0\n}\n\n// Deterministic ordering: the same region always produces byte-identical GFA,\n// so a layout computed from it is reproducible.\nexport function formatSubgraph(\n  segments: Map<string, RgfaSegment>,\n  links: Map<string, RgfaLink>,\n) {\n  const sortedSegments = [...segments.values()].sort(\n    (a, b) =>\n      compare(a.refName, b.refName) || a.start - b.start || compare(a.id, b.id),\n  )\n  const sortedLinks = [...links.keys()].sort((a, b) => compare(a, b))\n  return [\n    'H\\tVN:Z:1.0',\n    ...sortedSegments.map(s => formatSegment(s)),\n    ...sortedLinks.map(k => formatLink(links.get(k)!)),\n  ].join('\\n')\n}\n", "import { resolvePanSNPrefix } from '@jbrowse/bandage-core/pansn'\nimport { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport { SimpleFeature, updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { WalkReader, referenceNodes } from '@jbrowse/graph-walks'\n\nimport { locationIsSet } from '../locationName.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { getLines } from '../tabixRange.ts'\nimport {\n  anchoredCut,\n  closingLinks,\n  closingSpans,\n  formatSubgraph,\n  linkKey,\n  parseLinkLine,\n  parseSegmentRow,\n  segmentSamples,\n} from './rgfaBed.ts'\nimport { walkSubgraph } from './walkReader.ts'\n\nimport type { RgfaTabixAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions, SubgraphTier } from '../GetSubgraph.ts'\nimport type { RgfaLink, RgfaSegment } from './rgfaBed.ts'\nimport type { WalkCut } from './walkRowRuns.ts'\nimport type { TabixIndexedFile } from '@gmod/tabix'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { FileLocation, Region } from '@jbrowse/core/util/types'\n\n// What a hop follows: alleles, never the backbone. A rank-0 segment reached\n// through a link is flanking backbone, usually outside the window, so querying\n// its links walks the reference away from the region, brings back more backbone,\n// and closes nothing. Every segment that closes a bubble is an allele interior,\n// and an allele interior is rank > 0 in both index formats (rGFA's SR tag, and\n// pggb's rank 0-or-1 against the anchor path). Reached backbone still becomes a\n// node and its edge still draws; it is only not walked through.\n//\n// This is gfabase's rule, arrived at from the other end. `gfabase sub` expands\n// from a seed either to the whole connected component (`--connected`, which its\n// own README calls overkill) or with `--cutpoints 1`, which takes the biconnected\n// component by *stopping at cutpoints*, the segments every end-to-end walk of\n// the chromosome must traverse. In a reference-anchored pangenome the cutpoints\n// are the backbone, and rank is what the index already states about it, so\n// `rank > 0` is that stopping rule without a connectivity index to build. The\n// third tool is the same shape again: `gfatools view -R` maps the region onto its\n// precomputed bubble decomposition and returns whole overlapping bubbles\n// (gfa_query_by_reg), which is complete for the same reason. Bandage's own\n// `--distance` is a node-step radius, but Bandage holds the entire graph in\n// memory, so its scope is a drawing filter rather than a fetch strategy.\n//\n// Measured with this rule: the E. coli paa window converges at one hop (17\n// segments at 1 and at 2), so the cut closes and stays closed. HPRC's amylase\n// window keeps growing (63 at 0, 78 at 1, 92 at 2) because its alleles have\n// alleles, and wall-clock is flat across all three, since a hop's queries go out\n// together and the remote index dominates.\n//\n// The exact version, when a graph ships a bubble index beside its segments:\n// gfatools' bubble rows carry the member segment ids of every bubble, so the\n// bubbles overlapping the region state which segments a complete cut must\n// contain. That turns the hop count into a termination condition rather than a\n// setting, and MinigraphBubbleAdapter already parses those rows.\nfunction offReference(segments: RgfaSegment[]) {\n  return segments.filter(segment => segment.rank > 0)\n}\n\ninterface GraphIndex {\n  segments: TabixIndexedFile\n  links: TabixIndexedFile\n  walks?: WalkReader\n  walkFile?: TabixIndexedFile\n  refNames: PanSNRefNames\n}\n\nexport default class RgfaTabixAdapter extends BaseFeatureDataAdapter<RgfaTabixAdapterConfig> {\n  public static capabilities = ['getFeatures', 'getRefNames']\n\n  private readonly fine\n  private coarse: GraphIndex | undefined\n\n  public constructor(\n    config: RgfaTabixAdapterConfig,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    this.fine = this.openIndex([])\n  }\n\n  // refNames off the SEGMENT index: it is the one that names every stable\n  // sequence the graph is anchored to, where the link index only names those a\n  // link touches. A walk-indexed graph's walk file names the same sequences,\n  // and it has no segment file.\n  private openIndex(under: string[]): GraphIndex {\n    const segments = openTabixSlot(\n      this,\n      [...under, 'segmentsLocation'],\n      [...under, 'segmentsIndex'],\n    )\n    const walksLocation: FileLocation = this.getConf('walksLocation')\n    const hasWalks = under.length === 0 && locationIsSet(walksLocation)\n    const links = openTabixSlot(\n      this,\n      [...under, 'linksLocation'],\n      [...under, 'linksIndex'],\n    )\n    const walkFile = hasWalks\n      ? openTabixSlot(this, ['walksLocation'], ['walksIndex'])\n      : undefined\n    return {\n      segments,\n      links,\n      walkFile,\n      walks: walkFile ? new WalkReader(walkFile) : undefined,\n      refNames: new PanSNRefNames(walkFile ?? segments, this),\n    }\n  }\n\n  /**\n   * The haplotypes a walk-indexed graph's header names, `sample#haplotype`\n   * in byte order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    const header = await this.fine.walks?.header(opts)\n    return header?.haplotypes.length ? header.haplotypes : undefined\n  }\n\n  private index(tier: SubgraphTier = 'fine') {\n    if (tier === 'fine') {\n      return this.fine\n    }\n    this.coarse ??= this.openIndex(['coarse'])\n    return this.coarse\n  }\n\n  async getRefNames(opts: BaseOptions = {}) {\n    return this.fine.refNames.assemblyRefNames(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.fine.refNames.resolve(query, opts)\n      if (tabixRefName !== undefined) {\n        // a walk-indexed node row names only its chunk's first base, and a\n        // node crossing in from a chunk before is filed there\n        const { walks, walkFile } = this.fine\n        const start = walks\n          ? await walks.queryStart(query.start, opts)\n          : query.start\n        if (walkFile && walks) {\n          // a walk-indexed graph's reference nodes are its ref rows' steps\n          await walks.header(opts)\n          const refRows: string[][] = []\n          await updateStatus('Downloading walks', statusCallback, () =>\n            getLines(walkFile, tabixRefName, start, query.end, {\n              signal,\n              lineCallback: line => {\n                const cols = line.split('\\t')\n                if (cols[3] === 'ref') {\n                  refRows.push(cols)\n                }\n              },\n            }),\n          )\n          // every node of the chunks read that ends past the window's start\n          const seen = new Set<number>()\n          for (const node of referenceNodes(refRows)) {\n            if (\n              node.refName === tabixRefName &&\n              node.end > query.start &&\n              !seen.has(node.id)\n            ) {\n              seen.add(node.id)\n              const id = String(node.id)\n              observer.next(\n                new SimpleFeature({\n                  uniqueId: id,\n                  refName: query.refName,\n                  start: node.start,\n                  end: node.end,\n                  name: id,\n                  type: 'segment',\n                  rank: 0,\n                  stableName: node.refName,\n                }),\n              )\n            }\n          }\n          observer.complete()\n          return\n        }\n        await updateStatus('Downloading segments', statusCallback, () =>\n          getLines(this.fine.segments, tabixRefName, start, query.end, {\n            signal,\n            lineCallback: line => {\n              const { segment, anchored } = parseSegmentRow(line)\n              // An anchored index also returns the alleles under the region,\n              // which lie on other stable sequences and have no place on this\n              // one; a lookback chunk returns nodes ending before it\n              if (\n                (anchored && segment.refName !== tabixRefName) ||\n                segment.end <= query.start\n              ) {\n                return\n              }\n              // `samples` lists the haplotypes whose paths visit the segment and\n              // `sampleCount` counts them. A lane's color reads the count, and\n              // a count in jexl would otherwise rely on `.length` resolving\n              // through a member access on an array.\n              const samples = segmentSamples(segment)\n              observer.next(\n                new SimpleFeature({\n                  uniqueId: segment.id,\n                  refName: query.refName,\n                  start: segment.start,\n                  end: segment.end,\n                  name: segment.id,\n                  type: 'segment',\n                  rank: segment.rank,\n                  stableName: segment.refName,\n                  ...(samples && { samples, sampleCount: samples.length }),\n                }),\n              )\n            },\n          }),\n        )\n      }\n      observer.complete()\n    }, signal)\n  }\n\n  // Extract the graph around a region for GraphGenomeView: GFA text, or a\n  // walk-indexed graph's tables (walkSubgraph). The\n  // region's own segments come from segs.bed.gz; links.bed.gz supplies the edges\n  // incident to them *and* the coordinates of the segments on the other end,\n  // which typically sit on a different stable sequence (a rank>0 bubble) and so\n  // are not reachable by any coordinate query on this region.\n  //\n  // `hops` is extra rounds of link-following past the region's own segments\n  // and their immediate neighbours, each costing one tabix query per\n  // off-reference segment newly reached. After the last round, one more read\n  // per stretch of stable sequence the cut holds closes it (closingSpans), so\n  // an allele reached from both ends draws whole. The view asks for one hop; a\n  // hopless cut stays as cheap as it was. `signal` goes to every one of those\n  // queries, so a cut the view has replaced stops.\n  // `tier: 'coarse'` reads the `coarse` pair instead, the same way.\n  async getSubgraph(\n    region: Region,\n    opts: SubgraphAdapterOptions = {},\n  ): Promise<string | WalkCut> {\n    const { hops = 0, signal, tier } = opts\n    const index = this.index(tier)\n    const segments = new Map<string, RgfaSegment>()\n    const links = new Map<string, RgfaLink>()\n    const tabixRefName = await index.refNames.resolve(region, { signal })\n\n    const addLinksOver = async (\n      refName: string,\n      start: number,\n      end: number,\n    ) => {\n      const reached: RgfaSegment[] = []\n      await getLines(index.links, refName, start, end, {\n        signal,\n        lineCallback: line => {\n          const link = parseLinkLine(line)\n          links.set(linkKey(link), link)\n          for (const segment of [link.sourceSegment, link.targetSegment]) {\n            if (!segments.has(segment.id)) {\n              segments.set(segment.id, segment)\n              reached.push(segment)\n            }\n          }\n        },\n      })\n      return reached\n    }\n\n    if (tabixRefName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; a graph with PanSN names (GRCh38#0#chr1) needs ${region.assemblyName} mapped to its prefix in assemblyNameToPanSN`,\n      )\n    }\n    if (index.walks) {\n      return walkSubgraph(index.walks, tabixRefName, region, {\n        signal,\n        prefixes: opts.haplotypes?.map(lane => resolvePanSNPrefix(this, lane)),\n        walkRows: opts.walkRows,\n        stepBudget: this.getConf('walkStepBudget'),\n        byteBudget: this.getConf('walkByteBudget'),\n      })\n    }\n    const layout = { anchored: false }\n    await getLines(index.segments, tabixRefName, region.start, region.end, {\n      signal,\n      lineCallback: line => {\n        const row = parseSegmentRow(line)\n        layout.anchored ||= row.anchored\n        segments.set(row.segment.id, row.segment)\n      },\n    })\n    // An anchored index files every allele and every link under the reference\n    // interval its bubble hangs from, so one read of each file holds the whole\n    // graph under the region and there is nothing to hop to or close.\n    if (layout.anchored) {\n      const found: RgfaLink[] = []\n      await getLines(index.links, tabixRefName, region.start, region.end, {\n        signal,\n        lineCallback: line => {\n          found.push(parseLinkLine(line))\n        },\n      })\n      const cut = anchoredCut(segments, found, {\n        refName: tabixRefName,\n        start: region.start,\n        end: region.end,\n      })\n      return formatSubgraph(cut.segments, cut.links)\n    }\n    let frontier = offReference(\n      await addLinksOver(tabixRefName, region.start, region.end),\n    )\n    for (let hop = 0; hop < hops; hop++) {\n      // One hop's queries are independent of each other, so they go out\n      // together rather than one round-trip at a time. Their callbacks share\n      // the segment and link maps, which is safe because only one of them runs\n      // at a time, and the output is sorted at the end regardless of the order\n      // they arrive in.\n      const reached = await Promise.all(\n        frontier.map(segment =>\n          addLinksOver(segment.refName, segment.start, segment.end),\n        ),\n      )\n      frontier = offReference(reached.flat())\n    }\n    if (hops > 0) {\n      const spans = closingSpans(\n        [...segments.values()],\n        new Set(frontier.map(segment => segment.id)),\n        { refName: tabixRefName, start: region.start, end: region.end },\n      )\n      const found: RgfaLink[] = []\n      await Promise.all(\n        spans.map(span =>\n          getLines(index.links, span.refName, span.start, span.end, {\n            signal,\n            lineCallback: line => {\n              found.push(parseLinkLine(line))\n            },\n          }),\n        ),\n      )\n      for (const link of closingLinks(found, segments, spans)) {\n        links.set(linkKey(link), link)\n        for (const segment of [link.sourceSegment, link.targetSegment]) {\n          if (!segments.has(segment.id)) {\n            segments.set(segment.id, segment)\n          }\n        }\n      }\n    }\n\n    return formatSubgraph(segments, links)\n  }\n}\n"],
-  "mappings": 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-  "names": ["parseSegmentRow", "line", "cols", "anchored", "own", "segmentSamples", "segment", "tag", "t", "samples", "parseEndpoint", "field", "parseLinkLine", "source", "target", "linkKey", "link", "anchoredCut", "under", "found", "window", "side", "segments", "links", "closingSpans", "held", "unread", "outside", "mergedSpans", "maxGap", "sorted", "a", "b", "compare", "spans", "span", "refName", "start", "end", "closingLinks", "inside", "GFA_TAG", "formatSegment", "id", "rank", "tags", "valid", "extra", "formatLink", "sourceStrand", "targetStrand", "formatSubgraph", "sortedSegments", "sortedLinks", "s", "k", "offReference", "segments", "segment", "RgfaTabixAdapter", "BaseFeatureDataAdapter", "config", "getSubAdapter", "pluginManager", "under", "openTabixSlot", "walksLocation", "hasWalks", "locationIsSet", "links", "walkFile", "WalkReader", "PanSNRefNames", "opts", "header", "tier", "query", "signal", "statusCallback", "ObservableCreate", "observer", "tabixRefName", "walks", "start", "refRows", "updateStatus", "getLines", "line", "cols", "seen", "node", "referenceNodes", "id", "SimpleFeature", "anchored", "parseSegmentRow", "samples", "segmentSamples", "region", "hops", "index", "addLinksOver", "refName", "end", "reached", "link", "parseLinkLine", "linkKey", "walkSubgraph", "lane", "resolvePanSNPrefix", "layout", "row", "found", "cut", "anchoredCut", "formatSubgraph", "frontier", "hop", "spans", "closingSpans", "span", "closingLinks"]
-}

package/dist/chunks/WalkTabixSyntenyAdapter-UKFHCFOF.js

@@ -1,2 +0,0 @@
-import{b as q,c as D,d as H,e as G}from"./chunk-WX26KTZM.js";import{a as _}from"./chunk-LUTMKRXY.js";import{a as T,b as I,d as j,e as B}from"./chunk-SAMJE6GH.js";import{a as R}from"./chunk-KOB7YIMR.js";import{p as W,q as L}from"./chunk-IXQK7JAW.js";import"./chunk-TXI43PEN.js";import{f as $,g as v}from"./chunk-AMFIBQVR.js";import"./chunk-YBLNN5FU.js";import"./chunk-MVVXRZXV.js";import{a as P,c as F,d as A,e as k,f as N,g as x}from"./chunk-446RWIA3.js";import"./chunk-E7J6SB5P.js";import"./chunk-7WIBGKBU.js";import"./chunk-OGQ6OQDN.js";import"./chunk-NDRLCGPC.js";import{o as C}from"./chunk-TENPGIPX.js";var Z=50;function ee(m){let e=[];for(let t=0;t<m.length;t++){let[r,s]=m[t],[n,a]=m[t+1]??[];s===a&&s<=Z&&(r==="I"&&n==="D"||r==="D"&&n==="I")?(e.push(["X",s]),t++):e.push([r,s])}return e}function te(m){return m.map(([e,t])=>`${t}${e}`).join("")}function U(m){let e=new Map,t=n=>{let a=m.get(n),i=a===void 0?0:a.end-a.start,p=e.get(i);return p===void 0&&(p="N".repeat(i),e.set(i,p)),p},r=new Map,s=n=>{let a=r.get(n);return a===void 0&&(a=Array.from(n.ids,(i,p)=>2*i+n.rev[p]),r.set(n,a)),a};return(n,a)=>L({query:s(n),target:s(a),sequenceOf:t,bases:!1})}var ae=100;function E(m,e,t){let r=m.at(-1);t>0&&(r?.[0]===e?r[1]+=t:m.push([e,t]))}function X(m){let e=s=>{let n=m.get(s>>1);return n===void 0?0:n.end-n.start},t=s=>{let n=new Float64Array(s.length+1);return s.forEach((a,i)=>{n[i+1]=n[i]+e(a)}),n},r=s=>Array.from(s.ids,(n,a)=>2*n+s.rev[a]);return(s,n)=>{let a=r(n),i=r(s),[p,y]=W(i,a,e),[h,l]=W(i.map(b=>b^1).reverse(),a,e),d=l>y,c=d?h:p,f=Math.max(y,l);if(f<ae)return[];let u=t(a),o=t(i),g=b=>d?i.length-1-c[b][0]:c[b][0],w=[];c.forEach(([,b],S)=>{if(S>0){let[K,Q]=[g(S-1),g(S)].sort((V,Y)=>V-Y);E(w,"I",o[Q]-o[K+1]),E(w,"D",u[b]-u[c[S-1][1]+1])}E(w,"=",e(a[b]))});let[z,J]=[g(0),g(c.length-1)].sort((b,S)=>b-S);return[{queryStart:o[z],queryEnd:o[J+1],targetStart:u[c[0][1]],targetEnd:u[c.at(-1)[1]+1],strand:d?"-":"+",edits:w,sharedBases:f}]}}function O({chain:m,target:e,query:t,assemblyName:r,refName:s,mateAssemblyName:n}){let a=e.hapStart+m.targetStart,i=e.hapStart+m.targetEnd,p=t.hapStart+m.queryStart,y=t.hapStart+m.queryEnd,h=ee(m.edits),l=h.reduce((f,[u,o])=>f+(u==="="?o:0),0),d=h.reduce((f,[,u])=>f+u,0),c=`${e.name}:${a}-${i}|${t.name}:${p}-${y}`;return new T({uniqueId:c,assemblyName:r,refName:s,start:a,end:i,type:"match",strand:m.strand==="-"?-1:1,CIGAR:te(h),syntenyId:c,identity:l/Math.max(d,1),numMatches:l,blockLen:d,mate:{refName:A(t.name),start:p,end:y,assemblyName:n}})}var ne=m=>F(m.name)??m.name,M=class extends I{constructor(e,t,r){super(e,t,r);let s=$(this,["walksLocation"],["walksIndex"]);this.reader=new D(s),this.refNames=new v(s,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={}){let{haplotypes:t}=await this.reader.header(e);return t.length>0?t:void 0}async getHeader(e={}){let{haplotypes:t,references:r}=await this.reader.header(e),{anchor:s}=this,n=N(this,s),a=x(this);return{hasCoarseTier:!1,anchorAssemblyName:s,referenceSamples:r,lanes:t.filter(i=>i!==n&&P(i)!==n).map(i=>({name:B(a,i),label:i,group:P(i)}))}}async getRefNames(e={}){let{assemblyName:t}=e;return t===void 0||t===this.anchor?this.refNames.assemblyRefNames({...e,assemblyName:this.anchor}):[]}budgets(){return{stepBudget:this.getConf("walkStepBudget"),byteBudget:this.getConf("walkByteBudget"),budgetNames:H}}async getSubgraph(e,t={}){let{signal:r,haplotypes:s,walkRows:n}=t,a=await this.refNames.resolve(e,{signal:r});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 G(this.reader,a,e,{...this.budgets(),signal:r,prefixes:s?.map(i=>N(this,i)),walkRows:n})}async laneWalks(e,t,r,s,n){return C(n,s.statusCallback,()=>this.reader.cut(e,t,{...this.budgets(),signal:s.signal,keep:q(r,F(e)),links:!1}).catch(a=>{throw _(a)&&a instanceof Error&&(a.message=a.message.replace("to see the graph","to see lanes")),a}))}async anchorFeatures(e,t,r){let s=r.haplotypes?.length?r.haplotypes.map(o=>N(this,o)):void 0,n=N(this,r.targetAssemblyName),a=n===void 0?s:s===void 0||s.some(o=>k(n,o)||k(o,n))?[n]:[];if(a?.length===0)return[];let{start:i,end:p}=t,{graph:y,fragments:h}=await this.laneWalks(e,t,a,r,`Reading walks ${t.refName}:${i.toLocaleString()}-${p.toLocaleString()}`),l=X(y.nodes),d=x(this),c=h.filter(o=>o.name===e),f=o=>a===void 0?0:a.findIndex(g=>k(o.name,g));return h.filter(o=>o.name!==e&&f(o)>=0).sort((o,g)=>f(o)-f(g)).flatMap(o=>c.flatMap(g=>l(o,g).map(w=>O({chain:w,target:g,query:o,assemblyName:t.assemblyName,refName:t.refName,mateAssemblyName:B(d,ne(o))}))))}async pairFeatures(e,t,r,s){let[n]=r,a=r.map(l=>({pair:l,featurePrefix:N(this,l.queryAssemblyName),matePrefix:N(this,l.targetAssemblyName)})),{graph:i,fragments:p}=await this.laneWalks(e,t,a.flatMap(l=>[l.featurePrefix,l.matePrefix]),s,r.length===1&&n?`Reading ${n.queryAssemblyName} against ${n.targetAssemblyName}`:`Reading ${r.length} lane pairs`),y=U(i.nodes),h=l=>p.filter(d=>k(d.name,l));return a.flatMap(({pair:l,featurePrefix:d,matePrefix:c})=>h(d).flatMap(f=>h(c).flatMap(u=>y(u,f).map(o=>O({chain:o,target:f,query:u,assemblyName:l.queryAssemblyName,refName:A(f.name),mateAssemblyName:l.targetAssemblyName})))))}getFeatures(e,t={}){return R(async r=>{let s=e.assemblyName===this.anchor?await this.refNames.resolve(e,t):void 0;if(s!==void 0){let n=j(t),a=n.length>0?await this.pairFeatures(s,e,n,t):await this.anchorFeatures(s,e,t);for(let i of a)r.next(i)}r.complete()},t.signal)}};export{M as default};
-//# sourceMappingURL=WalkTabixSyntenyAdapter-UKFHCFOF.js.map

package/dist/chunks/WalkTabixSyntenyAdapter-UKFHCFOF.js.map

@@ -1,7 +0,0 @@
-{
-  "version": 3,
-  "sources": ["../../src/WalkTabixSyntenyAdapter/walkLanes.ts", "../../src/WalkTabixSyntenyAdapter/WalkTabixSyntenyAdapter.ts"],
-  "sourcesContent": ["import { weightedLcs } from '@gmod/gbz-base/lcs'\nimport { pairAlignments } from '@gmod/gbz-base/pairAlignment'\nimport { panSNContig } from '@jbrowse/bandage-core/pansn'\n\nimport SyntenyFeature from '../synteny/SyntenyFeature.ts'\n\nimport type { PairChain, PairEdit } from '@gmod/gbz-base/pairAlignment'\nimport type { WalkFragment, WalkNode } from '@jbrowse/graph-walks'\n\n// The longest bubble with equal bases on both sides that is written as\n// mismatches; a longer one stays an insertion and a deletion\nconst BALANCED_BUBBLE_MAX_BP = 50\n\n/**\n * A chain's edits with each short balanced bubble as `X`. The walks carry no\n * bases, so two walks differ wherever they leave a shared node, and a SNP is\n * one base inserted and one deleted until it is read as the mismatch it is.\n */\nexport function bubblesAsMismatches(edits: PairEdit[]) {\n  const out: PairEdit[] = []\n  for (let i = 0; i < edits.length; i++) {\n    const [op, len] = edits[i]!\n    const [nextOp, nextLen] = edits[i + 1] ?? []\n    if (\n      len === nextLen &&\n      len <= BALANCED_BUBBLE_MAX_BP &&\n      ((op === 'I' && nextOp === 'D') || (op === 'D' && nextOp === 'I'))\n    ) {\n      out.push(['X', len])\n      i++\n    } else {\n      out.push([op, len])\n    }\n  }\n  return out\n}\n\nfunction cigarOf(edits: PairEdit[]) {\n  return edits.map(([op, len]) => `${len}${op}`).join('')\n}\n\n/**\n * Aligns one walk fragment to another on the nodes both visit, from node\n * lengths alone: the fragments' steps as the handles gbz-base's chainer reads,\n * and a stand-in sequence of each node's length.\n */\nexport function walkAligner(nodes: Map<number, WalkNode>) {\n  const standIn = new Map<number, string>()\n  const sequenceOf = (id: number) => {\n    const node = nodes.get(id)\n    const length = node === undefined ? 0 : node.end - node.start\n    let sequence = standIn.get(length)\n    if (sequence === undefined) {\n      sequence = 'N'.repeat(length)\n      standIn.set(length, sequence)\n    }\n    return sequence\n  }\n  const handles = new Map<WalkFragment, number[]>()\n  const handlesOf = (fragment: WalkFragment) => {\n    let steps = handles.get(fragment)\n    if (steps === undefined) {\n      steps = Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n      handles.set(fragment, steps)\n    }\n    return steps\n  }\n  return (query: WalkFragment, target: WalkFragment) =>\n    pairAlignments({\n      query: handlesOf(query),\n      target: handlesOf(target),\n      sequenceOf,\n      bases: false,\n    })\n}\n\n// The fewest bases on shared nodes a record against the reference keeps,\n// gbz-base's floor for a pair record\nconst MIN_MATCH_BP = 100\n\nfunction appendEdit(edits: PairEdit[], op: PairEdit[0], len: number) {\n  const last = edits.at(-1)\n  if (len > 0) {\n    if (last?.[0] === op) {\n      last[1] += len\n    } else {\n      edits.push([op, len])\n    }\n  }\n}\n\n/**\n * Aligns a haplotype's walk fragment to the reference's as gbz-base aligns a\n * walk to its reference path: the heaviest common subsequence of their steps,\n * each node weighing its length, read in whichever direction shares more. A\n * pair chain leaves out every node either walk passes twice, which is the\n * whole of a collapsed copy-number array (amylase, KIV-2); the subsequence\n * matches one pass over it, and the other copies are insertions.\n */\nexport function referenceAligner(nodes: Map<number, WalkNode>) {\n  const lengthOf = (handle: number) => {\n    const node = nodes.get(handle >> 1)\n    return node === undefined ? 0 : node.end - node.start\n  }\n  const offsets = (handles: number[]) => {\n    const out = new Float64Array(handles.length + 1)\n    handles.forEach((handle, i) => {\n      out[i + 1] = out[i]! + lengthOf(handle)\n    })\n    return out\n  }\n  const handlesOf = (fragment: WalkFragment) =>\n    Array.from(fragment.ids, (id, i) => 2 * id + fragment.rev[i]!)\n\n  return (query: WalkFragment, target: WalkFragment): PairChain[] => {\n    const ref = handlesOf(target)\n    const hap = handlesOf(query)\n    const [same, sameWeight] = weightedLcs(hap, ref, lengthOf)\n    const [turned, turnedWeight] = weightedLcs(\n      hap.map(handle => handle ^ 1).reverse(),\n      ref,\n      lengthOf,\n    )\n    const reverse = turnedWeight > sameWeight\n    const pairs = reverse ? turned : same\n    const sharedBases = Math.max(sameWeight, turnedWeight)\n    if (sharedBases < MIN_MATCH_BP) {\n      return []\n    }\n    const refAt = offsets(ref)\n    const hapAt = offsets(hap)\n    // a pair's haplotype step, counted along the haplotype\n    const stepOf = (k: number) =>\n      reverse ? hap.length - 1 - pairs[k]![0] : pairs[k]![0]\n    const edits: PairEdit[] = []\n    pairs.forEach(([, r], k) => {\n      if (k > 0) {\n        const [lo, hi] = [stepOf(k - 1), stepOf(k)].sort((x, y) => x - y)\n        appendEdit(edits, 'I', hapAt[hi!]! - hapAt[lo! + 1]!)\n        appendEdit(edits, 'D', refAt[r]! - refAt[pairs[k - 1]![1] + 1]!)\n      }\n      appendEdit(edits, '=', lengthOf(ref[r]!))\n    })\n    const [lo, hi] = [stepOf(0), stepOf(pairs.length - 1)].sort((x, y) => x - y)\n    return [\n      {\n        queryStart: hapAt[lo!]!,\n        queryEnd: hapAt[hi! + 1]!,\n        targetStart: refAt[pairs[0]![1]]!,\n        targetEnd: refAt[pairs.at(-1)![1] + 1]!,\n        strand: reverse ? '-' : '+',\n        edits,\n        sharedBases,\n      },\n    ]\n  }\n}\n\n/**\n * One record of a walk aligned to another: on the target walk's contig, with\n * the query walk as its mate and the CIGAR read along the target, a `D` being\n * target bases the query lacks.\n */\nexport function chainFeature({\n  chain,\n  target,\n  query,\n  assemblyName,\n  refName,\n  mateAssemblyName,\n}: {\n  chain: PairChain\n  target: WalkFragment\n  query: WalkFragment\n  assemblyName: string\n  refName: string\n  mateAssemblyName: string\n}) {\n  const start = target.hapStart + chain.targetStart\n  const end = target.hapStart + chain.targetEnd\n  const mateStart = query.hapStart + chain.queryStart\n  const mateEnd = query.hapStart + chain.queryEnd\n  const edits = bubblesAsMismatches(chain.edits)\n  const matches = edits.reduce((sum, [op, n]) => sum + (op === '=' ? n : 0), 0)\n  const columns = edits.reduce((sum, [, n]) => sum + n, 0)\n  const id = `${target.name}:${start}-${end}|${query.name}:${mateStart}-${mateEnd}`\n  return new SyntenyFeature({\n    uniqueId: id,\n    assemblyName,\n    refName,\n    start,\n    end,\n    type: 'match',\n    strand: chain.strand === '-' ? -1 : 1,\n    CIGAR: cigarOf(edits),\n    syntenyId: id,\n    identity: matches / Math.max(columns, 1),\n    numMatches: matches,\n    blockLen: columns,\n    mate: {\n      refName: panSNContig(query.name),\n      start: mateStart,\n      end: mateEnd,\n      assemblyName: mateAssemblyName,\n    },\n  })\n}\n", "import {\n  assemblyByPanSNPrefix,\n  panSNContig,\n  panSNHaplotype,\n  panSNMatchesPrefix,\n  panSNSample,\n  resolvePanSNPrefix,\n} from '@jbrowse/bandage-core/pansn'\nimport { updateStatus } from '@jbrowse/core/util'\nimport { ObservableCreate } from '@jbrowse/core/util/rxjs'\nimport { WalkReader, walkNameFilter } from '@jbrowse/graph-walks'\n\nimport { chainFeature, referenceAligner, walkAligner } from './walkLanes.ts'\nimport { isNodeLimitError } from '../LinearGraphDisplay/denseWindow.ts'\nimport { BUDGET_SLOTS, walkSubgraph } from '../RgfaTabixAdapter/walkReader.ts'\nimport { PanSNRefNames, openTabixSlot } from '../panSNTabix.ts'\nimport { ComparativeAdapterBase } from '../synteny/ComparativeAdapterBase.ts'\nimport { laneAssemblyName, requestedPairs } from '../synteny/lanePairs.ts'\n\nimport type { WalkTabixSyntenyAdapterConfig } from './configSchema.ts'\nimport type { SubgraphAdapterOptions } from '../GetSubgraph.ts'\nimport type { LaneFeatureOptions, LanePair } from '../synteny/lanePairs.ts'\nimport type PluginManager from '@jbrowse/core/PluginManager'\nimport type { BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter'\nimport type { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'\nimport type { Feature } from '@jbrowse/core/util'\nimport type { Region } from '@jbrowse/core/util/types'\nimport type { WalkFragment } from '@jbrowse/graph-walks'\n\nconst haplotypeOf = (fragment: WalkFragment) =>\n  panSNHaplotype(fragment.name) ?? fragment.name\n\nexport default class WalkTabixSyntenyAdapter extends ComparativeAdapterBase<WalkTabixSyntenyAdapterConfig> {\n  private readonly reader\n  private readonly refNames\n\n  public constructor(\n    config: WalkTabixSyntenyAdapterConfig,\n    getSubAdapter?: getSubAdapterType,\n    pluginManager?: PluginManager,\n  ) {\n    super(config, getSubAdapter, pluginManager)\n    const walks = openTabixSlot(this, ['walksLocation'], ['walksIndex'])\n    this.reader = new WalkReader(walks)\n    this.refNames = new PanSNRefNames(walks, this)\n  }\n\n  private get anchor() {\n    const anchor = this.getConf('assemblyNames')[0]\n    if (anchor === undefined) {\n      throw new Error(\n        'WalkTabixSyntenyAdapter needs assemblyNames: its first entry is the assembly the reference sample is loaded as',\n      )\n    }\n    return anchor\n  }\n\n  /**\n   * The haplotypes the walk file's header names, `sample#haplotype` in byte\n   * order, or undefined when it names none\n   */\n  async getHaplotypeNames(opts: BaseOptions = {}) {\n    const { haplotypes } = await this.reader.header(opts)\n    return haplotypes.length > 0 ? haplotypes : undefined\n  }\n\n  /**\n   * `lanes` is every haplotype the header names but the anchor's own,\n   * declared up front so the display can offer the whole graph's haplotypes\n   * before a fetch has placed any of them\n   */\n  async getHeader(opts: BaseOptions = {}) {\n    const { haplotypes, references } = await this.reader.header(opts)\n    const { anchor } = this\n    const anchorPrefix = resolvePanSNPrefix(this, anchor)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    return {\n      hasCoarseTier: false,\n      anchorAssemblyName: anchor,\n      referenceSamples: references,\n      lanes: haplotypes\n        .filter(\n          prefix =>\n            prefix !== anchorPrefix && panSNSample(prefix) !== anchorPrefix,\n        )\n        .map(prefix => ({\n          name: laneAssemblyName(asmByPrefix, prefix),\n          label: prefix,\n          group: panSNSample(prefix),\n        })),\n    }\n  }\n\n  // A lane's contigs are named only in its walk rows, so only the anchor's\n  // are listed\n  async getRefNames(opts: BaseOptions = {}) {\n    const { assemblyName } = opts\n    return assemblyName === undefined || assemblyName === this.anchor\n      ? this.refNames.assemblyRefNames({ ...opts, assemblyName: this.anchor })\n      : []\n  }\n\n  private budgets() {\n    return {\n      stepBudget: this.getConf('walkStepBudget'),\n      byteBudget: this.getConf('walkByteBudget'),\n      budgetNames: BUDGET_SLOTS,\n    }\n  }\n\n  /**\n   * The graph display's cut of the window, as RgfaTabixAdapter cuts a\n   * walk-indexed graph: the reference walk first, then the walks `haplotypes`\n   * asks for, and the nodes and links they visit\n   */\n  async getSubgraph(region: Region, opts: SubgraphAdapterOptions = {}) {\n    const { signal, haplotypes, walkRows } = opts\n    const refName = await this.refNames.resolve(region, { signal })\n    if (refName === undefined) {\n      throw new Error(\n        `${region.assemblyName} ${region.refName} is not in this graph's index; the graph is cut on ${this.anchor}, mapped to its PanSN prefix in assemblyNameToPanSN`,\n      )\n    }\n    return walkSubgraph(this.reader, refName, region, {\n      ...this.budgets(),\n      signal,\n      prefixes: haplotypes?.map(lane => resolvePanSNPrefix(this, lane)),\n      walkRows,\n    })\n  }\n\n  // The window's walks for the haplotypes named and the reference, with no\n  // link read; a window past a budget fails as a zoom-in notice for lanes\n  private async laneWalks(\n    refName: string,\n    region: Region,\n    prefixes: string[] | undefined,\n    opts: LaneFeatureOptions,\n    status: string,\n  ) {\n    return updateStatus(status, opts.statusCallback, () =>\n      this.reader\n        .cut(refName, region, {\n          ...this.budgets(),\n          signal: opts.signal,\n          keep: walkNameFilter(prefixes, panSNHaplotype(refName)),\n          links: false,\n        })\n        .catch((error: unknown) => {\n          if (isNodeLimitError(error) && error instanceof Error) {\n            error.message = error.message.replace(\n              'to see the graph',\n              'to see lanes',\n            )\n          }\n          throw error\n        }),\n    )\n  }\n\n  /**\n   * One record per stretch a haplotype's walk shares with the reference's,\n   * on the reference with the haplotype as its mate\n   */\n  private async anchorFeatures(\n    refName: string,\n    region: Region,\n    opts: LaneFeatureOptions,\n  ) {\n    const wanted = opts.haplotypes?.length\n      ? opts.haplotypes.map(lane => resolvePanSNPrefix(this, lane))\n      : undefined\n    const target = resolvePanSNPrefix(this, opts.targetAssemblyName)\n    const prefixes =\n      target === undefined\n        ? wanted\n        : wanted === undefined ||\n            wanted.some(\n              prefix =>\n                panSNMatchesPrefix(target, prefix) ||\n                panSNMatchesPrefix(prefix, target),\n            )\n          ? [target]\n          : []\n    if (prefixes?.length === 0) {\n      return []\n    }\n    const { start, end } = region\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      prefixes,\n      opts,\n      `Reading walks ${region.refName}:${start.toLocaleString()}-${end.toLocaleString()}`,\n    )\n    const align = referenceAligner(graph.nodes)\n    const asmByPrefix = assemblyByPanSNPrefix(this)\n    const references = fragments.filter(f => f.name === refName)\n    // lanes come back in the order the fetch names them, which is the order\n    // the display stacks lanes of equal weight in\n    const rank = (fragment: WalkFragment) =>\n      prefixes === undefined\n        ? 0\n        : prefixes.findIndex(prefix =>\n            panSNMatchesPrefix(fragment.name, prefix),\n          )\n    const shown = fragments\n      .filter(fragment => fragment.name !== refName && rank(fragment) >= 0)\n      .sort((a, b) => rank(a) - rank(b))\n    return shown.flatMap(query =>\n      references.flatMap(reference =>\n        align(query, reference).map(chain =>\n          chainFeature({\n            chain,\n            target: reference,\n            query,\n            assemblyName: region.assemblyName,\n            refName: region.refName,\n            mateAssemblyName: laneAssemblyName(asmByPrefix, haplotypeOf(query)),\n          }),\n        ),\n      ),\n    )\n  }\n\n  /**\n   * Each pair's two lanes read out of the anchor window, all pairs in one\n   * read, and each walk of a pair's query lane aligned to each walk of its\n   * target lane. A pair's records sit on its query lane's contigs, the lane\n   * the display draws on top.\n   */\n  private async pairFeatures(\n    refName: string,\n    region: Region,\n    pairs: LanePair[],\n    opts: LaneFeatureOptions,\n  ) {\n    const [first] = pairs\n    const sides = pairs.map(pair => ({\n      pair,\n      featurePrefix: resolvePanSNPrefix(this, pair.queryAssemblyName),\n      matePrefix: resolvePanSNPrefix(this, pair.targetAssemblyName),\n    }))\n    const { graph, fragments } = await this.laneWalks(\n      refName,\n      region,\n      sides.flatMap(side => [side.featurePrefix, side.matePrefix]),\n      opts,\n      pairs.length === 1 && first\n        ? `Reading ${first.queryAssemblyName} against ${first.targetAssemblyName}`\n        : `Reading ${pairs.length} lane pairs`,\n    )\n    const align = walkAligner(graph.nodes)\n    const walksOf = (prefix: string) =>\n      fragments.filter(f => panSNMatchesPrefix(f.name, prefix))\n    return sides.flatMap(({ pair, featurePrefix, matePrefix }) =>\n      walksOf(featurePrefix).flatMap(target =>\n        walksOf(matePrefix).flatMap(query =>\n          align(query, target).map(chain =>\n            chainFeature({\n              chain,\n              target,\n              query,\n              assemblyName: pair.queryAssemblyName,\n              refName: panSNContig(target.name),\n              mateAssemblyName: pair.targetAssemblyName,\n            }),\n          ),\n        ),\n      ),\n    )\n  }\n\n  // The files are filed under the reference alone, so a window on a\n  // haplotype lane has no answer: a lane pair is read inside the anchor's\n  getFeatures(region: Region, opts: LaneFeatureOptions = {}) {\n    return ObservableCreate<Feature>(async observer => {\n      const refName =\n        region.assemblyName === this.anchor\n          ? await this.refNames.resolve(region, opts)\n          : undefined\n      if (refName !== undefined) {\n        const pairs = requestedPairs(opts)\n        const features =\n          pairs.length > 0\n            ? await this.pairFeatures(refName, region, pairs, opts)\n            : await this.anchorFeatures(refName, 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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-  "names": ["BALANCED_BUBBLE_MAX_BP", "bubblesAsMismatches", "edits", "out", "i", "op", "len", "nextOp", "nextLen", "cigarOf", "walkAligner", "nodes", "standIn", "sequenceOf", "id", "node", "length", "sequence", "handles", "handlesOf", "fragment", "steps", "query", "target", "pairAlignments", "MIN_MATCH_BP", "appendEdit", "last", "referenceAligner", "lengthOf", "handle", "offsets", "ref", "hap", "same", "sameWeight", "weightedLcs", "turned", "turnedWeight", "reverse", "pairs", "sharedBases", "refAt", "hapAt", "stepOf", "k", "r", "lo", "hi", "x", "y", "chainFeature", "chain", "assemblyName", "refName", "mateAssemblyName", "start", "end", "mateStart", "mateEnd", "matches", "sum", "n", "columns", "SyntenyFeature", "panSNContig", "haplotypeOf", "fragment", "panSNHaplotype", "WalkTabixSyntenyAdapter", "ComparativeAdapterBase", "config", "getSubAdapter", "pluginManager", "walks", "openTabixSlot", "WalkReader", "PanSNRefNames", "anchor", "opts", "haplotypes", "references", "anchorPrefix", "resolvePanSNPrefix", "asmByPrefix", "assemblyByPanSNPrefix", "prefix", "panSNSample", "laneAssemblyName", "assemblyName", "BUDGET_SLOTS", "region", "signal", "walkRows", "refName", "walkSubgraph", "lane", "prefixes", "status", "updateStatus", "walkNameFilter", "error", "isNodeLimitError", "wanted", "target", "panSNMatchesPrefix", "start", "end", "graph", "fragments", "align", "referenceAligner", "f", "rank", "a", "b", "query", "reference", "chain", "chainFeature", "pairs", "first", "sides", "pair", "side", "walkAligner", "walksOf", "featurePrefix", "matePrefix", "panSNContig", "ObservableCreate", "observer", "requestedPairs", "features", "feature"]
-}

package/dist/chunks/chunk-5SFGHDQA.js

@@ -1,2 +0,0 @@
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