jbrowse-plugin-mafviewer 1.4.2 → 1.4.5

package/src/util/fastaUtils.ts

@@ -25,72 +25,44 @@ export function processFeaturesToFasta({
   const region = regions[0]!
   const sampleToRowMap = new Map(samples.map((s, i) => [s.id, i]))
   const rlen = region.end - region.start
-  const outputRows = samples.map(() => '-'.repeat(rlen))
+
+  // Use character arrays instead of strings for O(1) mutations
+  const outputRowsArrays = samples.map(() => new Array(rlen).fill('-'))
+
   for (const feature of features.values()) {
     const leftCoord = feature.get('start')
     const vals = feature.get('alignments') as Record<string, AlignmentRecord>
     const seq = feature.get('seq')
-    for (const [sample, val] of Object.entries(vals)) {
-      const origAlignment = val.seq
-      const alignment = origAlignment
 
+    for (const [sample, val] of Object.entries(vals)) {
+      const alignment = val.seq
       const row = sampleToRowMap.get(sample)
       if (row === undefined) {
         continue
       }
 
-      // gaps
-      for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
-        if (seq[i] !== '-') {
-          if (alignment[i] === '-') {
-            const l = leftCoord + o - region.start
-            if (l >= 0 && l < rlen) {
-              outputRows[row] =
-                outputRows[row]!.slice(0, l) +
-                '-' +
-                outputRows[row]!.slice(l + 1)
-            }
-          }
-          o++
-        }
-      }
+      const rowArray = outputRowsArrays[row]!
 
-      if (!showAllLetters) {
-        // matches
-        for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
-          if (seq[i] !== '-') {
-            const c = alignment[i]
-            const l = leftCoord + o - region.start
-            if (l >= 0 && l < rlen) {
-              if (seq[i] === c && c !== '-' && c !== ' ') {
-                outputRows[row] =
-                  outputRows[row]!.slice(0, l) +
-                  '.' +
-                  outputRows[row]!.slice(l + 1)
-              }
-            }
-            o++
-          }
-        }
-      }
-
-      // mismatches
+      // Single-pass processing: handle gaps, matches, and mismatches together
       for (let i = 0, o = 0, l = alignment.length; i < l; i++) {
-        const c = alignment[i]
         if (seq[i] !== '-') {
-          if (c !== '-') {
-            const l = leftCoord + o - region.start
-            if (l >= 0 && l < rlen) {
-              if (seq[i] !== c && c !== ' ') {
-                outputRows[row] =
-                  outputRows[row]!.slice(0, l) +
-                  c +
-                  outputRows[row]!.slice(l + 1)
-              } else if (showAllLetters) {
-                outputRows[row] =
-                  outputRows[row]!.slice(0, l) +
-                  c +
-                  outputRows[row]!.slice(l + 1)
+          const c = alignment[i]
+          const pos = leftCoord + o - region.start
+
+          if (pos >= 0 && pos < rlen) {
+            if (c === '-') {
+              // Gap
+              rowArray[pos] = '-'
+            } else if (c !== ' ') {
+              if (showAllLetters) {
+                // Show all letters mode: write character directly
+                rowArray[pos] = c
+              } else if (seq[i] === c) {
+                // Match: use dot notation
+                rowArray[pos] = '.'
+              } else {
+                // Mismatch: write character
+                rowArray[pos] = c
               }
             }
           }
@@ -99,5 +71,7 @@ export function processFeaturesToFasta({
       }
     }
   }
-  return outputRows
+
+  // Convert character arrays back to strings
+  return outputRowsArrays.map(arr => arr.join(''))
 }

package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.d.ts

@@ -1,30 +0,0 @@
-import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { Feature, Region } from '@jbrowse/core/util';
-import type { IndexData, OrganismRecord } from './types';
-export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
-    setupP?: Promise<IndexData>;
-    private cache;
-    getRefNames(): Promise<string[]>;
-    getChunk(buffer: Uint8Array, opts?: BaseOptions): Promise<{
-        uniqueId: string;
-        start: number;
-        end: number;
-        strand: number;
-        alignments: Record<string, OrganismRecord>;
-        seq: string;
-    } | undefined>;
-    setupPre(): Promise<IndexData>;
-    setup(opts?: BaseOptions): Promise<IndexData>;
-    readTaiFile(): Promise<IndexData>;
-    getFeatures(query: Region, opts?: BaseOptions): import("rxjs").Observable<Feature>;
-    getSamples(_query: Region): Promise<{
-        samples: {
-            id: string;
-            label?: string;
-            color?: string;
-        }[];
-        tree: Record<string, any> | undefined;
-    }>;
-    getLines(query: Region, byteRanges: IndexData): Promise<unknown>;
-    freeResources(): void;
-}

package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js

@@ -1,253 +0,0 @@
-import { unzip } from '@gmod/bgzf-filehandle';
-import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
-import { SimpleFeature, updateStatus, } from '@jbrowse/core/util';
-import QuickLRU from '@jbrowse/core/util/QuickLRU';
-import { openLocation } from '@jbrowse/core/util/io';
-import { ObservableCreate } from '@jbrowse/core/util/rxjs';
-import AbortablePromiseCache from 'abortable-promise-cache';
-import Long from 'long';
-import VirtualOffset from './virtualOffset';
-import parseNewick from '../parseNewick';
-import { normalize } from '../util';
-import { parseRowInstructions } from './rowInstructions';
-import { parseLineByLine } from './util';
-const toP = (s = 0) => +(+s).toFixed(1);
-export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
-    setupP;
-    cache = new AbortablePromiseCache({
-        cache: new QuickLRU({ maxSize: 50 }),
-        // @ts-expect-error
-        fill: async ({ nextEntry, firstEntry }, signal, statusCallback) => {
-            const file = openLocation(this.getConf('tafGzLocation'));
-            const response = await file.read(nextEntry.virtualOffset.blockPosition -
-                firstEntry.virtualOffset.blockPosition, firstEntry.virtualOffset.blockPosition);
-            const buffer = await unzip(response);
-            const slice = buffer.slice(firstEntry.virtualOffset.dataPosition);
-            return this.getChunk(slice, {
-                statusCallback: statusCallback,
-                signal,
-            });
-        },
-    });
-    async getRefNames() {
-        const data = await this.setup();
-        return Object.keys(data);
-    }
-    async getChunk(buffer, opts) {
-        const { statusCallback = () => { } } = opts || {};
-        const alignments = {};
-        const data = [];
-        let a0;
-        let j = 0;
-        let b = 0;
-        parseLineByLine(buffer, line => {
-            if (j++ % 100 === 0) {
-                statusCallback(`Processing ${toP(b / 1_000_000)}/${toP(buffer.length / 1_000_000)}Mb`);
-            }
-            b += line.length;
-            if (line) {
-                const [lineData, rowInstructions] = line.split(' ; ');
-                if (rowInstructions) {
-                    for (const ins of parseRowInstructions(rowInstructions)) {
-                        if (ins.type === 'i') {
-                            data.splice(ins.row, 0, ins);
-                            if (!alignments[ins.asm]) {
-                                alignments[ins.asm] = {
-                                    start: ins.start,
-                                    strand: ins.strand,
-                                    srcSize: ins.length,
-                                    chr: ins.ref,
-                                    data: '',
-                                };
-                            }
-                            const e = alignments[ins.asm];
-                            e.data += ' '.repeat(Math.max(0, j - e.data.length - 1)); // catch it up
-                        }
-                        else if (ins.type === 's') {
-                            if (!alignments[ins.asm]) {
-                                alignments[ins.asm] = {
-                                    start: ins.start,
-                                    strand: ins.strand,
-                                    srcSize: ins.length,
-                                    chr: ins.ref,
-                                    data: '',
-                                };
-                            }
-                            const e = alignments[ins.asm];
-                            e.data += ' '.repeat(Math.max(0, j - e.data.length - 1)); // catch it up
-                            data[ins.row] = ins;
-                        }
-                        else if (ins.type === 'd') {
-                            data.splice(ins.row, 1);
-                        }
-                        // no gaps for now(?)
-                        // else if (ins.type === 'g') {
-                        //   console.log('g??')
-                        // } else if (ins.type === 'G') {
-                        //   console.log('G??')
-                        // }
-                    }
-                    if (!a0) {
-                        a0 = data[0];
-                    }
-                }
-                const lineLen = lineData.length;
-                for (let i = 0; i < lineLen; i++) {
-                    const letter = lineData[i];
-                    const r = data[i];
-                    if (r) {
-                        alignments[r.asm].data += letter;
-                    }
-                    else {
-                        // not sure why but chr22_KI270731v1_random.taf.gz ends up here
-                    }
-                }
-            }
-        });
-        if (a0) {
-            const row0 = alignments[a0.asm];
-            // see
-            // https://github.com/ComparativeGenomicsToolkit/taffy/blob/f5a5354/docs/taffy_utilities.md#referenced-based-maftaf-and-indexing
-            // for the significance of row[0]:
-            //
-            // "An anchor line in TAF is a column from which all sequence
-            // coordinates can be deduced without scanning backwards to previous
-            // lines "
-            return {
-                uniqueId: `${row0.start}-${row0.data.length}`,
-                start: row0.start,
-                end: row0.start + row0.data.length,
-                strand: row0.strand,
-                alignments,
-                seq: row0.data,
-            };
-        }
-        return undefined;
-    }
-    setupPre() {
-        if (!this.setupP) {
-            this.setupP = this.readTaiFile().catch((e) => {
-                this.setupP = undefined;
-                throw e;
-            });
-        }
-        return this.setupP;
-    }
-    setup(opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return updateStatus('Downloading index', statusCallback, () => this.setupPre());
-    }
-    async readTaiFile() {
-        const text = await openLocation(this.getConf('taiLocation')).readFile('utf8');
-        const lines = text
-            .split('\n')
-            .map(f => f.trim())
-            .filter(line => !!line);
-        const entries = {};
-        let lastChr = '';
-        let lastChrStart = 0;
-        let lastRawVirtualOffset = 0;
-        for (const line of lines) {
-            const [chr, chrStart, virtualOffset] = line.split('\t');
-            const relativizedVirtualOffset = lastRawVirtualOffset + +virtualOffset;
-            const currChr = chr === '*' ? lastChr : chr.split('.').at(-1);
-            // bgzip TAF files store virtual offsets in plaintext in the TAI file
-            // these virtualoffsets are 64bit values, so the long library is needed
-            // to accurately do the bit manipulations needed
-            const x = Long.fromNumber(relativizedVirtualOffset);
-            const y = x.shiftRightUnsigned(16);
-            const z = x.and(0xffff);
-            const voff = new VirtualOffset(y.toNumber(), z.toNumber());
-            if (!entries[currChr]) {
-                entries[currChr] = [];
-                lastChr = '';
-                lastChrStart = 0;
-                lastRawVirtualOffset = 0;
-            }
-            const currStart = +chrStart + lastChrStart;
-            entries[currChr].push({
-                chrStart: currStart,
-                virtualOffset: voff,
-            });
-            lastChr = currChr;
-            lastChrStart = currStart;
-            lastRawVirtualOffset = relativizedVirtualOffset;
-        }
-        return entries;
-    }
-    getFeatures(query, opts) {
-        const { statusCallback = () => { } } = opts || {};
-        return ObservableCreate(async (observer) => {
-            try {
-                const byteRanges = await this.setup();
-                const feat = await updateStatus('Downloading alignments', statusCallback, () => this.getLines(query, byteRanges));
-                if (feat) {
-                    observer.next(
-                    // @ts-expect-error
-                    new SimpleFeature({
-                        ...feat,
-                        refName: query.refName,
-                    }));
-                }
-                else {
-                    console.error('no feature found');
-                }
-                statusCallback('');
-                observer.complete();
-            }
-            catch (e) {
-                observer.error(e);
-            }
-        });
-    }
-    async getSamples(_query) {
-        const nhLoc = this.getConf('nhLocation');
-        const nh = nhLoc.uri === '/path/to/my.nh'
-            ? undefined
-            : await openLocation(nhLoc).readFile('utf8');
-        // TODO: we may need to resolve the exact set of rows in the visible region
-        // here
-        return {
-            samples: normalize(this.getConf('samples')),
-            tree: nh ? parseNewick(nh) : undefined,
-        };
-    }
-    // TODO: cache processed large chunks
-    async getLines(query, byteRanges) {
-        const records = byteRanges[query.refName];
-        if (records) {
-            let firstEntry;
-            let nextEntry;
-            // two pass:
-            // first pass: find first block greater than query start, then -1 from
-            // that
-            for (let i = 0; i < records.length; i++) {
-                if (records[i].chrStart >= query.start) {
-                    firstEntry = records[Math.max(i - 1, 0)];
-                    break;
-                }
-            }
-            // second pass: find first block where query end less than record start,
-            // and +1 from that
-            for (let i = 0; i < records.length; i++) {
-                if (query.end <= records[i].chrStart) {
-                    nextEntry = records[i + 1];
-                    break;
-                }
-            }
-            nextEntry = nextEntry ?? records.at(-1);
-            // we NEED at least a firstEntry (validate behavior?) because othrwise it fetches whole
-            // file whn you request e.g. out of range region (e.g. taf in chr22:1-100
-            // and you are at chr22:200-300)
-            if (firstEntry && nextEntry) {
-                return this.cache.get(`${JSON.stringify(nextEntry)}_${JSON.stringify(firstEntry)}`, {
-                    nextEntry,
-                    firstEntry,
-                });
-            }
-        }
-        return undefined;
-    }
-    freeResources() { }
-}
-//# sourceMappingURL=BgzipTaffyAdapter.js.map

package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js.map

@@ -1 +0,0 @@
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package/dist/BgzipTaffyAdapter/configSchema.d.ts

@@ -1,44 +0,0 @@
-declare const configSchema: import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaType<{
-    /**
-     * #slot
-     */
-    samples: {
-        type: string;
-        description: string;
-        defaultValue: never[];
-    };
-    /**
-     * #slot
-     */
-    tafGzLocation: {
-        type: string;
-        description: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    /**
-     * #slot
-     */
-    taiLocation: {
-        type: string;
-        description: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-    /**
-     * #slot
-     */
-    nhLocation: {
-        type: string;
-        description: string;
-        defaultValue: {
-            uri: string;
-            locationType: string;
-        };
-    };
-}, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
-export default configSchema;

package/dist/BgzipTaffyAdapter/configSchema.js

@@ -1,53 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration';
-/**
- * #config BgzipTaffyAdapter
- * used to configure BgzipTaffy adapter
- */
-function x() { } // eslint-disable-line @typescript-eslint/no-unused-vars
-const configSchema = ConfigurationSchema('BgzipTaffyAdapter', {
-    /**
-     * #slot
-     */
-    samples: {
-        type: 'frozen',
-        description: 'string[] or {id:string,label:string,color?:string}[]',
-        defaultValue: [],
-    },
-    /**
-     * #slot
-     */
-    tafGzLocation: {
-        type: 'fileLocation',
-        description: 'bgzip taffy file',
-        defaultValue: {
-            uri: '/path/to/my.taf',
-            locationType: 'UriLocation',
-        },
-    },
-    /**
-     * #slot
-     */
-    taiLocation: {
-        type: 'fileLocation',
-        description: 'taffy index',
-        defaultValue: {
-            uri: '/path/to/my.taf.gz.tai',
-            locationType: 'UriLocation',
-        },
-    },
-    /**
-     * #slot
-     */
-    nhLocation: {
-        type: 'fileLocation',
-        description: 'newick tree',
-        defaultValue: {
-            uri: '/path/to/my.nh',
-            locationType: 'UriLocation',
-        },
-    },
-}, {
-    explicitlyTyped: true,
-});
-export default configSchema;
-//# sourceMappingURL=configSchema.js.map

package/dist/BgzipTaffyAdapter/configSchema.js.map

@@ -1 +0,0 @@
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package/dist/BgzipTaffyAdapter/index.d.ts

@@ -1,2 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager';
-export default function BgzipTaffyAdapterF(pluginManager: PluginManager): PluginManager;

package/dist/BgzipTaffyAdapter/index.js

@@ -1,11 +0,0 @@
-import { AdapterType } from '@jbrowse/core/pluggableElementTypes';
-import BgzipTaffyAdapter from './BgzipTaffyAdapter';
-import configSchema from './configSchema';
-export default function BgzipTaffyAdapterF(pluginManager) {
-    return pluginManager.addAdapterType(() => new AdapterType({
-        name: 'BgzipTaffyAdapter',
-        AdapterClass: BgzipTaffyAdapter,
-        configSchema,
-    }));
-}
-//# sourceMappingURL=index.js.map

package/dist/BgzipTaffyAdapter/index.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/BgzipTaffyAdapter/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAA;AAEjE,OAAO,iBAAiB,MAAM,qBAAqB,CAAA;AACnD,OAAO,YAAY,MAAM,gBAAgB,CAAA;AAEzC,MAAM,CAAC,OAAO,UAAU,kBAAkB,CAAC,aAA4B;IACrE,OAAO,aAAa,CAAC,cAAc,CACjC,GAAG,EAAE,CACH,IAAI,WAAW,CAAC;QACd,IAAI,EAAE,mBAAmB;QACzB,YAAY,EAAE,iBAAiB;QAC/B,YAAY;KACb,CAAC,CACL,CAAA;AACH,CAAC"}

package/dist/BgzipTaffyAdapter/rowInstructions.d.ts

@@ -1,35 +0,0 @@
-interface RowInsert {
-    type: 'i';
-    row: number;
-    asm: string;
-    ref: string;
-    start: number;
-    strand: number;
-    length: number;
-}
-interface RowSubstitute {
-    type: 's';
-    row: number;
-    asm: string;
-    ref: string;
-    start: number;
-    strand: number;
-    length: number;
-}
-interface RowDelete {
-    type: 'd';
-    row: number;
-}
-interface RowGap {
-    type: 'g';
-    row: number;
-    gapLen: number;
-}
-interface RowGapSubstring {
-    type: 'G';
-    row: number;
-    gapSubstring: string;
-}
-type RowInstruction = RowInsert | RowDelete | RowGap | RowGapSubstring | RowSubstitute;
-export declare function parseRowInstructions(meta: string): RowInstruction[];
-export {};

package/dist/BgzipTaffyAdapter/rowInstructions.js

@@ -1,55 +0,0 @@
-export function parseRowInstructions(meta) {
-    const ret = meta.split(' ');
-    const rows = [];
-    for (let i = 0; i < ret.length;) {
-        const type = ret[i++];
-        if (type === 'i') {
-            const row = +ret[i++];
-            const [asm, ref] = ret[i++].split('.');
-            rows.push({
-                type,
-                row,
-                asm: asm,
-                ref: ref,
-                start: +ret[i++],
-                strand: ret[i++] === '-' ? -1 : 1,
-                length: +ret[i++],
-            });
-        }
-        if (type === 's') {
-            const row = +ret[i++];
-            const [asm, ref] = ret[i++].split('.');
-            rows.push({
-                type,
-                row,
-                asm: asm,
-                ref: ref,
-                start: +ret[i++],
-                strand: ret[i++] === '-' ? -1 : 1,
-                length: +ret[i++],
-            });
-        }
-        else if (type === 'd') {
-            rows.push({
-                type,
-                row: +ret[i++],
-            });
-        }
-        else if (type === 'g') {
-            rows.push({
-                type,
-                row: +ret[i++],
-                gapLen: +ret[i++],
-            });
-        }
-        else if (type === 'G') {
-            rows.push({
-                type,
-                row: +ret[i++],
-                gapSubstring: ret[i++],
-            });
-        }
-    }
-    return rows;
-}
-//# sourceMappingURL=rowInstructions.js.map

package/dist/BgzipTaffyAdapter/rowInstructions.js.map

@@ -1 +0,0 @@
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package/dist/BgzipTaffyAdapter/types.d.ts

@@ -1,13 +0,0 @@
-import VirtualOffset from './virtualOffset';
-export interface OrganismRecord {
-    chr: string;
-    start: number;
-    srcSize: number;
-    strand: number;
-    data: string;
-}
-export interface ByteRange {
-    chrStart: number;
-    virtualOffset: VirtualOffset;
-}
-export type IndexData = Record<string, ByteRange[]>;

package/dist/BgzipTaffyAdapter/types.js

@@ -1,2 +0,0 @@
-export {};
-//# sourceMappingURL=types.js.map

package/dist/BgzipTaffyAdapter/types.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/BgzipTaffyAdapter/types.ts"],"names":[],"mappings":""}

package/dist/BgzipTaffyAdapter/util.d.ts

@@ -1 +0,0 @@
-export declare function parseLineByLine<T>(buffer: Uint8Array, cb: (line: string) => T | undefined): T[];