@gmod/bam
Version:
Parser for BAM and BAM index (bai) files
130 lines • 5.49 kB
JavaScript
;
var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
if (k2 === undefined) k2 = k;
var desc = Object.getOwnPropertyDescriptor(m, k);
if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
desc = { enumerable: true, get: function() { return m[k]; } };
}
Object.defineProperty(o, k2, desc);
}) : (function(o, m, k, k2) {
if (k2 === undefined) k2 = k;
o[k2] = m[k];
}));
var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
Object.defineProperty(o, "default", { enumerable: true, value: v });
}) : function(o, v) {
o["default"] = v;
});
var __importStar = (this && this.__importStar) || (function () {
var ownKeys = function(o) {
ownKeys = Object.getOwnPropertyNames || function (o) {
var ar = [];
for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
return ar;
};
return ownKeys(o);
};
return function (mod) {
if (mod && mod.__esModule) return mod;
var result = {};
if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
__setModuleDefault(result, mod);
return result;
};
})();
var __importDefault = (this && this.__importDefault) || function (mod) {
return (mod && mod.__esModule) ? mod : { "default": mod };
};
Object.defineProperty(exports, "__esModule", { value: true });
const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
const bamFile_ts_1 = __importStar(require("./bamFile.js"));
const chunk_ts_1 = __importDefault(require("./chunk.js"));
const sam_ts_1 = require("./sam.js");
const util_ts_1 = require("./util.js");
const virtualOffset_ts_1 = require("./virtualOffset.js");
async function fetchOk(url, opts) {
const res = await fetch(url, opts);
if (!res.ok) {
throw new Error(`HTTP ${res.status} fetching ${url}: ${await res.text()}`);
}
return res;
}
async function fetchChunk({ url, headers }, opts) {
// pass base64 data URLs straight to fetch; otherwise apply headers (minus
// referer, which isn't a permitted client-set header).
// https://stackoverflow.com/a/54123275/2129219
const { referer: _referer, ...rest } = headers ?? {};
const res = url.startsWith('data:')
? await fetchOk(url)
: await fetchOk(url, { ...opts, headers: rest });
return new Uint8Array(await res.arrayBuffer());
}
async function fetchAndConcat(arr, opts) {
// Pipeline unzip after each fetch so decompression overlaps later fetches.
return (0, util_ts_1.concatUint8Array)(await Promise.all(arr.map(async (c) => (0, bgzf_filehandle_1.unzip)(await fetchChunk(c, opts)))));
}
class HtsgetFile extends bamFile_ts_1.default {
baseUrl;
trackId;
constructor(args) {
super({ htsget: true, recordClass: args.recordClass });
this.baseUrl = args.baseUrl;
this.trackId = args.trackId;
}
async getRecordsForRange(chr, min, max, opts) {
const base = `${this.baseUrl}/${this.trackId}`;
const url = `${base}?referenceName=${chr}&start=${min}&end=${max}&format=BAM`;
const chrId = this.chrToIndex?.[chr];
if (chrId === undefined) {
return [];
}
const result = await fetchOk(url, opts);
const data = await result.json();
const uncba = await fetchAndConcat(data.htsget.urls.slice(1), {
signal: opts?.signal,
});
const zero = new virtualOffset_ts_1.VirtualOffset(0, 0);
const allRecords = await this.readBamFeatures(uncba, [], [], new chunk_ts_1.default(zero, zero, 0));
return (0, util_ts_1.appendInRange)(allRecords, chrId, min, max);
}
async getHeaderPre(opts = {}) {
const url = `${this.baseUrl}/${this.trackId}?referenceName=na&class=header`;
const result = await fetchOk(url, opts);
const data = await result.json();
const uncba = await fetchAndConcat(data.htsget.urls, {
signal: opts.signal,
});
const dataView = new DataView(uncba.buffer);
if (dataView.getInt32(0, true) !== bamFile_ts_1.BAM_MAGIC) {
throw new Error('Not a BAM file');
}
const headLen = dataView.getInt32(4, true);
const decoder = new TextDecoder();
const headerText = decoder.decode(uncba.subarray(8, 8 + headLen));
const samHeader = (0, sam_ts_1.parseHeaderText)(headerText);
// use the @SQ lines in the header to figure out the
// mapping between ref ref ID numbers and names
const idToName = [];
const nameToId = {};
const sqLines = samHeader.filter(l => l.tag === 'SQ');
for (const [refId, sqLine] of sqLines.entries()) {
let refName = '';
let length = 0;
for (const item of sqLine.data) {
if (item.tag === 'SN') {
refName = item.value;
}
else if (item.tag === 'LN') {
length = +item.value;
}
}
nameToId[refName] = refId;
idToName[refId] = { refName, length };
}
this.chrToIndex = nameToId;
this.indexToChr = idToName;
return samHeader;
}
}
exports.default = HtsgetFile;
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