jbrowse-plugin-mafviewer 1.4.7 → 1.5.0

package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.d.ts

@@ -0,0 +1,55 @@
+import { BaseFeatureDataAdapter, BaseOptions } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { Feature, Region } from '@jbrowse/core/util';
+import type { RowInstruction } from './rowInstructions';
+import type { AlignmentRecord, IndexData } from './types';
+interface RowState {
+    sequenceName: string;
+    start: number;
+    strand: number;
+    sequenceLength: number;
+    bases: string;
+    length: number;
+}
+interface AlignmentBlock {
+    rows: RowState[];
+    columnNumber: number;
+}
+interface SetupData {
+    index: IndexData;
+    runLengthEncodeBases: boolean;
+}
+interface TafFeature {
+    uniqueId: string;
+    start: number;
+    end: number;
+    strand: number;
+    alignments: Record<string, AlignmentRecord>;
+    seq: string;
+}
+export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
+    setupP?: Promise<SetupData>;
+    getRefNames(): Promise<string[]>;
+    parseCoordinatesAndEstablishBlock(pBlock: AlignmentBlock | undefined, instructions: RowInstruction[]): AlignmentBlock;
+    parseBases(basesStr: string, runLengthEncodeBases: boolean): string;
+    parseTafBlocksStreaming(buffer: Uint8Array, runLengthEncodeBases: boolean): Generator<TafFeature>;
+    parseTafBlocks(buffer: Uint8Array, runLengthEncodeBases: boolean, _opts?: BaseOptions): TafFeature[];
+    private decoder;
+    finalizeBlock(block: AlignmentBlock, columns: string[]): void;
+    blockToFeature(block: AlignmentBlock): TafFeature | undefined;
+    setupPre(): Promise<SetupData>;
+    setup(opts?: BaseOptions): Promise<SetupData>;
+    doSetup(): Promise<SetupData>;
+    readHeader(): Promise<boolean>;
+    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;
+    }>;
+    freeResources(): void;
+}
+export {};

package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js

@@ -0,0 +1,364 @@
+import { unzip } from '@gmod/bgzf-filehandle';
+import { BaseFeatureDataAdapter, } from '@jbrowse/core/data_adapters/BaseAdapter';
+import { updateStatus } from '@jbrowse/core/util';
+import { openLocation } from '@jbrowse/core/util/io';
+import { ObservableCreate } from '@jbrowse/core/util/rxjs';
+import VirtualOffset from './virtualOffset';
+import parseNewick from '../parseNewick';
+import { normalize } from '../util';
+import { filterFirstLineInstructions, parseRowInstructions, } from './rowInstructions';
+import MafFeature from '../MafFeature';
+import { parseAssemblyAndChrSimple } from '../util/parseAssemblyName';
+// Binary search to find the index of the first element >= target
+function lowerBound(arr, target, getKey) {
+    let lo = 0;
+    let hi = arr.length;
+    while (lo < hi) {
+        const mid = (lo + hi) >>> 1;
+        if (getKey(arr[mid]) < target) {
+            lo = mid + 1;
+        }
+        else {
+            hi = mid;
+        }
+    }
+    return lo;
+}
+export default class BgzipTaffyAdapter extends BaseFeatureDataAdapter {
+    setupP;
+    async getRefNames() {
+        const { index } = await this.setup();
+        return Object.keys(index);
+    }
+    // Faithful translation of parse_coordinates_and_establish_block from taf.c
+    parseCoordinatesAndEstablishBlock(pBlock, instructions) {
+        const block = {
+            rows: [],
+            columnNumber: 0,
+        };
+        // Copy rows from previous block
+        if (pBlock) {
+            for (const pRow of pBlock.rows) {
+                block.rows.push({
+                    sequenceName: pRow.sequenceName,
+                    start: pRow.start + pRow.length,
+                    strand: pRow.strand,
+                    sequenceLength: pRow.sequenceLength,
+                    bases: '',
+                    length: 0,
+                });
+            }
+        }
+        // Apply coordinate instructions
+        for (const ins of instructions) {
+            if (ins.type === 'i') {
+                block.rows.splice(ins.row, 0, {
+                    sequenceName: ins.sequenceName,
+                    start: ins.start,
+                    strand: ins.strand,
+                    sequenceLength: ins.sequenceLength,
+                    bases: '',
+                    length: 0,
+                });
+            }
+            else if (ins.type === 's') {
+                const row = block.rows[ins.row];
+                if (row) {
+                    row.sequenceName = ins.sequenceName;
+                    row.start = ins.start;
+                    row.strand = ins.strand;
+                    row.sequenceLength = ins.sequenceLength;
+                }
+            }
+            else if (ins.type === 'd') {
+                if (block.rows[ins.row]) {
+                    block.rows.splice(ins.row, 1);
+                }
+            }
+            else if (ins.type === 'g') {
+                const row = block.rows[ins.row];
+                if (row) {
+                    row.start += ins.gapLength;
+                }
+            }
+            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
+            else if (ins.type === 'G') {
+                const row = block.rows[ins.row];
+                if (row) {
+                    row.start += ins.gapSubstring.length;
+                }
+            }
+        }
+        return block;
+    }
+    parseBases(basesStr, runLengthEncodeBases) {
+        if (runLengthEncodeBases) {
+            const tokens = basesStr.split(' ');
+            let result = '';
+            for (let i = 0; i < tokens.length; i += 2) {
+                const base = tokens[i];
+                const count = parseInt(tokens[i + 1], 10);
+                if (!isNaN(count) && base.length === 1) {
+                    result += base.repeat(count);
+                }
+            }
+            return result;
+        }
+        return basesStr;
+    }
+    // Streaming generator version of parseTafBlocks
+    // Yields features one at a time instead of collecting into array
+    *parseTafBlocksStreaming(buffer, runLengthEncodeBases) {
+        let pBlock;
+        let currentBlock;
+        let columns = [];
+        let isFirstCoordLine = true;
+        const decoder = new TextDecoder('ascii');
+        const text = decoder.decode(buffer);
+        const lines = text.split('\n');
+        for (const line of lines) {
+            const trimmedLine = line.trim();
+            if (!trimmedLine || trimmedLine.startsWith('#')) {
+                continue;
+            }
+            const semicolonIndex = trimmedLine.indexOf(' ; ');
+            const hasCoordinates = semicolonIndex !== -1;
+            if (hasCoordinates) {
+                // If we have a current block with columns, finalize and yield it
+                if (currentBlock && columns.length > 0) {
+                    this.finalizeBlock(currentBlock, columns);
+                    const feature = this.blockToFeature(currentBlock);
+                    if (feature) {
+                        yield feature;
+                    }
+                    pBlock = currentBlock;
+                }
+                // Parse the coordinate instructions
+                const basesAndTags = trimmedLine.slice(0, semicolonIndex);
+                let rowInstructions = trimmedLine.slice(semicolonIndex + 3);
+                const atIndex = rowInstructions.indexOf(' @');
+                if (atIndex !== -1) {
+                    rowInstructions = rowInstructions.slice(0, atIndex);
+                }
+                let instructions = parseRowInstructions(rowInstructions);
+                if (isFirstCoordLine) {
+                    instructions = filterFirstLineInstructions(instructions);
+                    isFirstCoordLine = false;
+                }
+                currentBlock = this.parseCoordinatesAndEstablishBlock(pBlock, instructions);
+                columns = [];
+                const basesAtIndex = basesAndTags.indexOf(' @');
+                const basesOnly = basesAtIndex !== -1
+                    ? basesAndTags.slice(0, basesAtIndex)
+                    : basesAndTags;
+                const bases = this.parseBases(basesOnly.trim(), runLengthEncodeBases);
+                if (bases.length > 0) {
+                    columns.push(bases);
+                }
+            }
+            else if (currentBlock) {
+                const basesAtIndex = trimmedLine.indexOf(' @');
+                const basesOnly = basesAtIndex !== -1 ? trimmedLine.slice(0, basesAtIndex) : trimmedLine;
+                const bases = this.parseBases(basesOnly.trim(), runLengthEncodeBases);
+                if (bases.length > 0) {
+                    columns.push(bases);
+                }
+            }
+        }
+        // Finalize and yield last block
+        if (currentBlock && columns.length > 0) {
+            this.finalizeBlock(currentBlock, columns);
+            const feature = this.blockToFeature(currentBlock);
+            if (feature) {
+                yield feature;
+            }
+        }
+    }
+    // Non-streaming version for backward compatibility (used in tests)
+    parseTafBlocks(buffer, runLengthEncodeBases, _opts) {
+        return [...this.parseTafBlocksStreaming(buffer, runLengthEncodeBases)];
+    }
+    // TextDecoder for efficient string building from typed array
+    decoder = new TextDecoder('ascii');
+    finalizeBlock(block, columns) {
+        const numCols = columns.length;
+        block.columnNumber = numCols;
+        // Pre-allocate buffer for bases (reused across rows)
+        const buffer = new Uint8Array(numCols);
+        const DASH = 45; // '-'.charCodeAt(0)
+        for (let j = 0; j < block.rows.length; j++) {
+            const row = block.rows[j];
+            let length = 0;
+            for (let i = 0; i < numCols; i++) {
+                const col = columns[i];
+                const charCode = col.charCodeAt(j);
+                // Use dash if character doesn't exist (NaN from charCodeAt)
+                buffer[i] = isNaN(charCode) ? DASH : charCode;
+                if (buffer[i] !== DASH) {
+                    length++;
+                }
+            }
+            row.bases = this.decoder.decode(buffer);
+            row.length = length;
+        }
+    }
+    blockToFeature(block) {
+        if (block.rows.length === 0 || block.columnNumber === 0) {
+            return undefined;
+        }
+        const row0 = block.rows[0];
+        const alignments = {};
+        for (const row of block.rows) {
+            const { assemblyName, chr } = parseAssemblyAndChrSimple(row.sequenceName);
+            alignments[assemblyName] = {
+                chr,
+                start: row.start,
+                srcSize: row.sequenceLength,
+                strand: row.strand,
+                seq: row.bases,
+            };
+        }
+        return {
+            uniqueId: `${row0.start}-${row0.length}`,
+            start: row0.start,
+            end: row0.start + row0.length,
+            strand: row0.strand,
+            alignments,
+            seq: row0.bases,
+        };
+    }
+    setupPre() {
+        if (!this.setupP) {
+            this.setupP = this.doSetup().catch((e) => {
+                this.setupP = undefined;
+                throw e;
+            });
+        }
+        return this.setupP;
+    }
+    setup(opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return updateStatus('Downloading index', statusCallback, () => this.setupPre());
+    }
+    async doSetup() {
+        const [index, runLengthEncodeBases] = await Promise.all([
+            this.readTaiFile(),
+            this.readHeader(),
+        ]);
+        return { index, runLengthEncodeBases };
+    }
+    async readHeader() {
+        try {
+            const file = openLocation(this.getConf('tafGzLocation'));
+            const response = await file.read(65536, 0);
+            const buffer = await unzip(response);
+            const decoder = new TextDecoder('ascii');
+            const text = decoder.decode(buffer.slice(0, 1000));
+            const firstLine = text.split('\n')[0] || '';
+            if (firstLine.startsWith('#taf')) {
+                return firstLine.includes('run_length_encode_bases:1');
+            }
+        }
+        catch {
+            // If we can't read the header, assume non-RLE
+        }
+        return false;
+    }
+    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 isRelative = chr === '*';
+            const currChr = isRelative ? lastChr : chr.split('.').at(-1);
+            const absVirtualOffset = isRelative
+                ? lastRawVirtualOffset + +virtualOffset
+                : +virtualOffset;
+            const absChrStart = isRelative ? lastChrStart + +chrStart : +chrStart;
+            const blockPosition = Math.floor(absVirtualOffset / 65536);
+            const dataPosition = absVirtualOffset % 65536;
+            const voff = new VirtualOffset(blockPosition, dataPosition);
+            if (!entries[currChr]) {
+                entries[currChr] = [];
+            }
+            entries[currChr].push({
+                chrStart: absChrStart,
+                virtualOffset: voff,
+            });
+            lastChr = currChr;
+            lastChrStart = absChrStart;
+            lastRawVirtualOffset = absVirtualOffset;
+        }
+        return entries;
+    }
+    getFeatures(query, opts) {
+        const { statusCallback = () => { } } = opts || {};
+        return ObservableCreate(async (observer) => {
+            try {
+                const { index, runLengthEncodeBases } = await this.setup(opts);
+                // Get byte range for this query
+                const records = index[query.refName];
+                if (!records || records.length === 0) {
+                    observer.complete();
+                    return;
+                }
+                const getKey = (r) => r.chrStart;
+                const startIdx = lowerBound(records, query.start, getKey);
+                const firstEntry = records[Math.max(startIdx - 1, 0)];
+                const endIdx = lowerBound(records, query.end, getKey);
+                const nextEntry = records[endIdx + 1] ?? records.at(-1);
+                if (!firstEntry || !nextEntry) {
+                    observer.complete();
+                    return;
+                }
+                // Read and decompress the data
+                const file = openLocation(this.getConf('tafGzLocation'));
+                const startBlock = firstEntry.virtualOffset.blockPosition;
+                const endBlock = nextEntry.virtualOffset.blockPosition;
+                const MIN_BLOCK_SIZE = 65536;
+                const readLength = endBlock > startBlock
+                    ? endBlock - startBlock + MIN_BLOCK_SIZE
+                    : MIN_BLOCK_SIZE;
+                const response = await updateStatus('Downloading alignments', statusCallback, () => file.read(readLength, startBlock));
+                const buffer = await unzip(response);
+                const startOffset = firstEntry.virtualOffset.dataPosition;
+                const nextOffset = nextEntry.virtualOffset.dataPosition;
+                const endOffset = endBlock === startBlock && nextOffset > startOffset
+                    ? nextOffset
+                    : buffer.length;
+                const slice = buffer.slice(startOffset, endOffset);
+                // Stream features using generator - no caching, immediate GC eligible
+                for (const feat of this.parseTafBlocksStreaming(slice, runLengthEncodeBases)) {
+                    // Filter features that overlap with query region
+                    if (feat.end > query.start && feat.start < query.end) {
+                        observer.next(new MafFeature(feat.uniqueId, feat.start, feat.end, query.refName, feat.strand, feat.alignments, feat.seq));
+                    }
+                }
+                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');
+        return {
+            samples: normalize(this.getConf('samples')),
+            tree: nh ? parseNewick(nh) : undefined,
+        };
+    }
+    freeResources() { }
+}
+//# sourceMappingURL=BgzipTaffyAdapter.js.map

package/dist/BgzipTaffyAdapter/BgzipTaffyAdapter.js.map

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

@@ -0,0 +1 @@
+export {};