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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,139 @@ | ||
| import {igvxhr} from "../../node_modules/igv-utils/src/index.js" | ||
| import {buildOptions} from "../util/igvUtils.js" | ||
| import BinaryParser from "../binary.js" | ||
|
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| /** | ||
| * A UCSC BigBed B+ tree, used to support searching the "extra indexes". | ||
| * | ||
| * Nodes are loaded on demand during search, avoiding the need to read the entire tree into | ||
| * memory. Tree nodes can be scattered across the file, making loading the entire tree unfeasible in reasonable time. | ||
| */ | ||
| export default class BPChromTree { | ||
|
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| static magic = 2026540177 | ||
| littleEndian = true | ||
| nodeCache = new Map() | ||
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| static async loadBpTree(path, startOffset) { | ||
| const bpTree = new BPChromTree(path, startOffset) | ||
| return bpTree.init() | ||
| } | ||
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| constructor(path, startOffset) { | ||
| this.path = path | ||
| this.startOffset = startOffset | ||
| this.littleEndian = littleEndian | ||
| } | ||
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| async init() { | ||
| const binaryParser = await this.#getParserFor(this.startOffset, 32) | ||
| let magic = binaryParser.getInt() | ||
| if(magic !== BPChromTree.magic) { | ||
| binaryParser.setPosition(0) | ||
| this.littleEndian = !this.littleEndian | ||
| binaryParser.littleEndian = this.littleEndian | ||
| magic = binaryParser.getInt() | ||
| if(magic !== BPChromTree.magic) { | ||
| throw Error(`Bad magic number ${magic}`) | ||
| } | ||
| } | ||
| const blockSize = binaryParser.getInt() | ||
| const keySize = binaryParser.getInt() | ||
| const valSize = binaryParser.getInt() | ||
| const itemCount = binaryParser.getLong() | ||
| const reserved = binaryParser.getLong() | ||
| const nodeOffset = this.startOffset + 32 | ||
| this.header = {magic, blockSize, keySize, valSize, itemCount, reserved, nodeOffset} | ||
| return this | ||
| } | ||
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| async search(term) { | ||
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| if(!this.header) { | ||
| await this.init(); | ||
| } | ||
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| const {keySize, valSize} = this.header | ||
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| if (valSize !== 8) { | ||
| throw Error(`Unexpected valSize ${valSize}`) | ||
| } | ||
|
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| const readTreeNode = async (offset) => { | ||
|
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| if (this.nodeCache.has(offset)) { | ||
| return this.nodeCache.get(offset) | ||
| } else { | ||
|
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| let binaryParser = await this.#getParserFor(offset, 4) | ||
| const type = binaryParser.getByte() | ||
| const reserved = binaryParser.getByte() | ||
| const count = binaryParser.getUShort() | ||
| const items = [] | ||
|
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| if (type === 1) { | ||
| // Leaf node -- we walk through all items, rather return on match, because nodes are cached | ||
| const size = count * (keySize + valSize) | ||
| binaryParser = await this.#getParserFor(offset + 4, size) | ||
| for (let i = 0; i < count; i++) { | ||
| const key = binaryParser.getFixedLengthString(keySize) | ||
| const chromId = binaryParser.getUInt(); | ||
| const chromSize = binaryParser.getUInt(); | ||
| items.push({key, chromId, chromSize}) | ||
| } | ||
| } else { | ||
| // Non leaf node | ||
| const size = count * (keySize + 8) | ||
| binaryParser = await this.#getParserFor(offset + 4, size) | ||
|
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| for (let i = 0; i < count; i++) { | ||
| const key = binaryParser.getFixedLengthString(keySize) | ||
| const offset = binaryParser.getLong() | ||
| items.push({key, offset}) | ||
| } | ||
| } | ||
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| const node = {type, count, items} | ||
| this.nodeCache.set(offset, node) | ||
| return node | ||
| } | ||
| } | ||
|
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| const walkTreeNode = async (offset) => { | ||
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| const node = await readTreeNode(offset) | ||
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| if (node.type === 1) { | ||
| // Leaf node | ||
| for (let item of node.items) { | ||
| if (term === item.key) { | ||
| return item | ||
| } | ||
| } | ||
| } else { | ||
| // Non leaf node | ||
| // Read and discard the first key. | ||
| let childOffset = node.items[0].offset | ||
|
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| for (let i = 1; i < node.items.length; i++) { | ||
| const key = node.items[i].key | ||
| if (term.localeCompare(key) < 0) { | ||
| break | ||
| } | ||
| childOffset = node.items[i].offset | ||
| } | ||
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| return walkTreeNode(childOffset) | ||
| } | ||
| } | ||
|
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| // Kick things off | ||
| return walkTreeNode(this.header.nodeOffset) | ||
| } | ||
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| async #getParserFor(start, size) { | ||
| const data = await igvxhr.loadArrayBuffer(this.path, {range: {start, size}}) | ||
| return new BinaryParser(new DataView(data), this.littleEndian) | ||
| } | ||
|
|
||
| } |
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