@gmod/tabix 3.5.1 → 3.5.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +46 -19
- package/dist/csi.js +1 -1
- package/dist/csi.js.map +1 -1
- package/dist/tabix-bundle.js +1 -1
- package/dist/tabixIndexedFile.d.ts +17 -0
- package/dist/tabixIndexedFile.js +107 -3
- package/dist/tabixIndexedFile.js.map +1 -1
- package/dist/tbi.js +12 -15
- package/dist/tbi.js.map +1 -1
- package/dist/util.d.ts +11 -2
- package/dist/util.js +31 -5
- package/dist/util.js.map +1 -1
- package/esm/csi.js +2 -2
- package/esm/csi.js.map +1 -1
- package/esm/tabixIndexedFile.d.ts +17 -0
- package/esm/tabixIndexedFile.js +107 -3
- package/esm/tabixIndexedFile.js.map +1 -1
- package/esm/tbi.js +13 -16
- package/esm/tbi.js.map +1 -1
- package/esm/util.d.ts +11 -2
- package/esm/util.js +30 -4
- package/esm/util.js.map +1 -1
- package/package.json +4 -7
- package/src/csi.ts +2 -2
- package/src/tabixIndexedFile.ts +146 -3
- package/src/tbi.ts +13 -14
- package/src/util.ts +35 -8
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@@ -31,6 +31,7 @@ export default class TabixIndexedFile {
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csiPath?: string;
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csiUrl?: string;
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csiFilehandle?: GenericFilehandle;
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/** budget for the decompressed chunk cache, in bytes */
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chunkCacheSize?: number;
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});
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/**
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@@ -73,6 +74,22 @@ export default class TabixIndexedFile {
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depth?: number;
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}>;
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getHeaderBuffer(opts?: Options): Promise<Uint8Array<ArrayBufferLike>>;
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/**
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* The leading lines the index says to skip — `tabix -S N` — which is where a
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* file whose header row is not commented keeps it. Empty when the index
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* records no skipped lines.
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*
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* Deliberately not part of `getHeader`. htslib draws the same distinction:
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* its indexer treats a line as non-data when `lineno <= line_skip` OR it
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* begins with the meta character (tbx.c), while `tabix -H` prints only the
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* leading meta-character lines and never consults line_skip (tabix.c).
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* `getHeader` mirrors `-H`, so a bare header row is absent from it, and
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* callers that need one were left re-reading the file themselves — guessing
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* at a read size, and unable to tell a headerless file from an uncommented
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* one. PLINK `.ld`, bedGraph and BED deflines are all routinely written this
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* way.
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*/
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getSkippedLines(opts?: Options): Promise<string[]>;
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getHeader(opts?: Options): Promise<string>;
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getReferenceSequenceNames(opts?: Options): Promise<string[]>;
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/** @param refName reference sequence name */
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package/dist/tabixIndexedFile.js
CHANGED
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@@ -5,7 +5,6 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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Object.defineProperty(exports, "__esModule", { value: true });
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const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
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const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
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const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
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const generic_filehandle2_1 = require("generic-filehandle2");
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const csi_ts_1 = __importDefault(require("./csi.js"));
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const tbi_ts_1 = __importDefault(require("./tbi.js"));
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@@ -18,6 +17,85 @@ const SEMICOLON = 59;
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// is parsing. Six is the HTTP/1.1 per-host connection cap browsers enforce, so
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// going much above it buys nothing on the transport that matters.
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const MAX_READ_AHEAD_CHUNKS = 6;
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// SYNC: ~/src/gmod/bam-js/src/bamFile.ts DEFAULT_MAX_CACHE_BYTES
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//
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// We fetch compressed and cache decompressed, and an entry is a whole chunk, so
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// entry count says nothing about memory. How little is easy to underestimate:
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// a dense VCF (test/data/1kg.chr1.subset.vcf.gz — 213MB over 600kb of chr1)
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// has single index bins of 17MB compressed, 120MB decompressed. Panning it
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// under the old 80-entry cache peaked at 2GB RSS.
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const DEFAULT_CHUNK_CACHE_BYTES = 100 * 2 ** 20;
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/**
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* Backing store for the chunk cache, bounded by the decompressed size of the
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* chunks it holds rather than by entry count.
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*
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* A chunk's size is only known once its read settles, so `set` records the
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* entry immediately and charges it to the budget later. Unsettled entries are
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* therefore free, which is what we want: they are reads a query is waiting on.
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*/
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class ByteBoundedChunkCache {
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entries = new Map();
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bytes = 0;
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maxBytes;
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constructor(maxBytes) {
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this.maxBytes = maxBytes;
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}
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get byteSize() {
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return this.bytes;
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}
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get size() {
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return this.entries.size;
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}
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has(key) {
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return this.entries.has(key);
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}
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get(key) {
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const cached = this.entries.get(key);
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if (cached) {
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// re-insert so Map iteration order stays least-recently-used first
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this.entries.delete(key);
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this.entries.set(key, cached);
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}
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return cached?.entry;
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}
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set(key, entry) {
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this.delete(key);
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const cached = { entry, bytes: 0 };
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this.entries.set(key, cached);
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void entry.promise
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.then(chunk => {
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// a later set() may have replaced this key while the read was in
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// flight; charging these bytes to it would then double-count
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if (this.entries.get(key) === cached) {
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cached.bytes = chunk.buffer.byteLength;
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this.bytes += cached.bytes;
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this.evict();
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}
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})
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.catch(() => {
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// a failed or aborted read caches nothing and costs nothing
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});
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}
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delete(key) {
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const cached = this.entries.get(key);
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if (cached) {
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this.entries.delete(key);
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this.bytes -= cached.bytes;
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}
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}
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keys() {
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return this.entries.keys();
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}
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// Evict from the least-recently-used end. The size > 1 guard means a single
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// chunk larger than the whole budget is still kept: the caller needs it for
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// the query in flight, and dropping it would only force a re-decompress.
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evict() {
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const lru = this.entries.keys();
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while (this.bytes > this.maxBytes && this.entries.size > 1) {
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this.delete(lru.next().value);
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}
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}
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}
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function resolveFilehandle(filehandle, path, url) {
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if (filehandle) {
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return filehandle;
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@@ -126,7 +204,7 @@ class TabixIndexedFile {
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filehandle;
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index;
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chunkCache;
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constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize =
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constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, }) {
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this.filehandle = resolveFilehandle(filehandle, path, url);
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this.index = resolveIndex({
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tbiFilehandle,
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@@ -139,7 +217,7 @@ class TabixIndexedFile {
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url,
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});
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this.chunkCache = new abortable_promise_cache_1.default({
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cache: new
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cache: new ByteBoundedChunkCache(chunkCacheSize),
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fill: (args, signal) => this.readChunk(args, { signal }),
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});
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}
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@@ -349,6 +427,32 @@ class TabixIndexedFile {
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}
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return bytes;
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}
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/**
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* The leading lines the index says to skip — `tabix -S N` — which is where a
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* file whose header row is not commented keeps it. Empty when the index
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* records no skipped lines.
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*
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* Deliberately not part of `getHeader`. htslib draws the same distinction:
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* its indexer treats a line as non-data when `lineno <= line_skip` OR it
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* begins with the meta character (tbx.c), while `tabix -H` prints only the
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* leading meta-character lines and never consults line_skip (tabix.c).
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* `getHeader` mirrors `-H`, so a bare header row is absent from it, and
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* callers that need one were left re-reading the file themselves — guessing
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* at a read size, and unable to tell a headerless file from an uncommented
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* one. PLINK `.ld`, bedGraph and BED deflines are all routinely written this
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* way.
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*/
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async getSkippedLines(opts = {}) {
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const { firstDataLine, skipLines = 0, maxBlockSize, } = await this.getMetadata(opts);
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if (skipLines <= 0) {
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return [];
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}
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// same read getHeaderBuffer makes, and the same caveat: a header spanning
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// more blocks than this is not covered
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const buf = await this.filehandle.read((firstDataLine?.blockPosition ?? 0) + maxBlockSize, 0, opts);
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const bytes = (await (0, bgzf_filehandle_1.unzip)(buf));
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return new TextDecoder().decode(bytes).split(/\r?\n/).slice(0, skipLines);
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}
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async getHeader(opts = {}) {
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const bytes = await this.getHeaderBuffer(opts);
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return new TextDecoder().decode(bytes);
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@@ -1 +1 @@
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-
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|
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1
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|
package/dist/tbi.js
CHANGED
|
@@ -45,8 +45,15 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
45
45
|
const { refNameToId, refIdToName, coordinateType, format, columnNumbers, metaChar, skipLines, } = (0, util_ts_1.parseAuxData)(bytes, 8);
|
|
46
46
|
// nameSectionLength is at TBI offset 32; re-read to find where bin data starts
|
|
47
47
|
const nameSectionLength = dataView.getInt32(32, true);
|
|
48
|
-
// SYNC: ~/src/gmod/bam-js/src/
|
|
49
|
-
// First pass: record per-refId byte offsets and find firstDataLine
|
|
48
|
+
// SYNC: ~/src/gmod/bam-js/src/bai.ts _parse — two-pass structure
|
|
49
|
+
// First pass: record per-refId byte offsets and find firstDataLine.
|
|
50
|
+
//
|
|
51
|
+
// Only the linear index is consulted. Its entry for a window is the
|
|
52
|
+
// smallest virtual offset of any record overlapping that window, so the
|
|
53
|
+
// minimum over the linear index is already the minimum over the bin chunks
|
|
54
|
+
// — walking the chunks too only re-derives it. Checked against every .tbi
|
|
55
|
+
// in test/data: same answer on all 23, and no ref has bins without a
|
|
56
|
+
// linear index.
|
|
50
57
|
let curr = 36 + nameSectionLength;
|
|
51
58
|
let firstDataLine;
|
|
52
59
|
const offsets = [];
|
|
@@ -62,22 +69,12 @@ class TabixIndex extends indexFile_ts_1.default {
|
|
|
62
69
|
if (bin > maxBinNumber + 1) {
|
|
63
70
|
throw new Error('tabix index contains too many bins, please use a CSI index');
|
|
64
71
|
}
|
|
65
|
-
|
|
66
|
-
curr += 16 * chunkCount;
|
|
67
|
-
}
|
|
68
|
-
else {
|
|
69
|
-
for (let k = 0; k < chunkCount; k++) {
|
|
70
|
-
firstDataLine = (0, util_ts_1.findFirstData)(firstDataLine, (0, virtualOffset_ts_1.fromBytes)(bytes, curr));
|
|
71
|
-
curr += 16;
|
|
72
|
-
}
|
|
73
|
-
}
|
|
72
|
+
curr += 16 * chunkCount;
|
|
74
73
|
}
|
|
75
74
|
const linearCount = dataView.getInt32(curr, true);
|
|
76
75
|
curr += 4;
|
|
77
|
-
|
|
78
|
-
|
|
79
|
-
curr += 8;
|
|
80
|
-
}
|
|
76
|
+
firstDataLine = (0, util_ts_1.minVirtualOffset)(bytes, curr, linearCount, firstDataLine);
|
|
77
|
+
curr += 8 * linearCount;
|
|
81
78
|
}
|
|
82
79
|
function getIndices(refId) {
|
|
83
80
|
const start = offsets[refId];
|
package/dist/tbi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,kEAAsC;AACtC,uCAOkB;AAClB,yDAA8C;AAK9C,MAAM,SAAS,GAAG,UAAU,CAAA,CAAC,QAAQ;AAErC,8DAA8D;AAC9D,MAAM,SAAS,GAAG,CAAC,CAAA;AACnB,MAAM,kBAAkB,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,SAAS,GAAG,CAAC,CAAC,CAAA;AAEpD;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,qEAAqE;IACrE,yEAAyE;IACzE,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,EAAE,kBAAkB,CAAC,CAAA;IACxD,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAC/C,MAAM,IAAI,GAAkC,EAAE,CAAA;IAC9C,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QACX,IAAI,CAAC,IAAI,CACP,CAAC,CAAC,EAAE,CAAC,CAAC,EACN,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAC9B,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAC9B,CAAC,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAChC,CAAC,GAAG,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAClC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CACrC,CAAA;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED,MAAqB,UAAW,SAAQ,sBAAS;IAC/C,gBAAgB;IAChB,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,UAAU,EAAE,IAAI,CAAC,UAAU;SAC5B,CAAC,CAAA;QACF,MAAM,KAAK,GAAG,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAe,CAAA;QAC9C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QAED,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC9C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC5C,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAE3D,oEAAoE;QACpE,MAAM,EACJ,WAAW,EACX,WAAW,EACX,cAAc,EACd,MAAM,EACN,aAAa,EACb,QAAQ,EACR,SAAS,GACV,GAAG,IAAA,sBAAY,EAAC,KAAK,EAAE,CAAC,CAAC,CAAA;QAC1B,+EAA+E;QAC/E,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAErD,iEAAiE;QACjE,
|
|
1
|
+
{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":";;;;;AAAA,2DAA6C;AAE7C,0DAA8B;AAC9B,kEAAsC;AACtC,uCAOkB;AAClB,yDAA8C;AAK9C,MAAM,SAAS,GAAG,UAAU,CAAA,CAAC,QAAQ;AAErC,8DAA8D;AAC9D,MAAM,SAAS,GAAG,CAAC,CAAA;AACnB,MAAM,kBAAkB,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,SAAS,GAAG,CAAC,CAAC,CAAA;AAEpD;;;GAGG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,qEAAqE;IACrE,yEAAyE;IACzE,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,EAAE,kBAAkB,CAAC,CAAA;IACxD,MAAM,CAAC,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,kBAAkB,CAAC,GAAG,CAAC,CAAA;IAC/C,MAAM,IAAI,GAAkC,EAAE,CAAA;IAC9C,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;QACX,IAAI,CAAC,IAAI,CACP,CAAC,CAAC,EAAE,CAAC,CAAC,EACN,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAC9B,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAC9B,CAAC,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAChC,CAAC,GAAG,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAClC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CACrC,CAAA;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAED,MAAqB,UAAW,SAAQ,sBAAS;IAC/C,gBAAgB;IAChB,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,UAAU,EAAE,IAAI,CAAC,UAAU;SAC5B,CAAC,CAAA;QACF,MAAM,KAAK,GAAG,CAAC,MAAM,IAAA,uBAAK,EAAC,GAAG,CAAC,CAAe,CAAA;QAC9C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QAED,IAAI,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;YAC9C,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;QACnC,CAAC;QAED,MAAM,QAAQ,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC5C,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAE3D,oEAAoE;QACpE,MAAM,EACJ,WAAW,EACX,WAAW,EACX,cAAc,EACd,MAAM,EACN,aAAa,EACb,QAAQ,EACR,SAAS,GACV,GAAG,IAAA,sBAAY,EAAC,KAAK,EAAE,CAAC,CAAC,CAAA;QAC1B,+EAA+E;QAC/E,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAErD,iEAAiE;QACjE,oEAAoE;QACpE,EAAE;QACF,oEAAoE;QACpE,wEAAwE;QACxE,2EAA2E;QAC3E,0EAA0E;QAC1E,qEAAqE;QACrE,gBAAgB;QAChB,IAAI,IAAI,GAAG,EAAE,GAAG,iBAAiB,CAAA;QACjC,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAa,EAAE,CAAA;QAE5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAChD,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;gBACH,CAAC;gBACD,IAAI,IAAI,EAAE,GAAG,UAAU,CAAA;YACzB,CAAC;YACD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,aAAa,GAAG,IAAA,0BAAgB,EAAC,KAAK,EAAE,IAAI,EAAE,WAAW,EAAE,aAAa,CAAC,CAAA;YACzE,IAAI,IAAI,CAAC,GAAG,WAAW,CAAA;QACzB,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YAC5B,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,IAAI,GAAG,GAAG,KAAK,CAAA;YACf,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YAC7C,GAAG,IAAI,CAAC,CAAA;YACR,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;gBACzC,GAAG,IAAI,CAAC,CAAA;gBACR,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE,CAAC;oBAC3B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;gBACH,CAAC;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;oBACpC,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;oBAC/C,GAAG,IAAI,CAAC,CAAA;oBACR,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;wBACrB,KAAK,GAAG,IAAA,wBAAc,EAAC,KAAK,EAAE,GAAG,GAAG,EAAE,CAAC,CAAA;oBACzC,CAAC;oBACD,GAAG,IAAI,EAAE,GAAG,UAAU,CAAA;gBACxB,CAAC;qBAAM,CAAC;oBACN,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;oBAC/C,GAAG,IAAI,CAAC,CAAA;oBACR,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC,CAAA;oBACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAK,CACnB,IAAA,4BAAS,EAAC,KAAK,EAAE,GAAG,CAAC,EACrB,IAAA,4BAAS,EAAC,KAAK,EAAE,GAAG,GAAG,CAAC,CAAC,EACzB,GAAG,CACJ,CAAA;wBACD,GAAG,IAAI,EAAE,CAAA;oBACX,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YACD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YAChD,GAAG,IAAI,CAAC,CAAA;YACR,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAgB,EAAE,MAAM,EAAE,WAAW,EAAE,CAAC,CAAA;YACtE,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,WAAW,CAAC,CAAC,CAAC,GAAG,IAAA,4BAAS,EAAC,KAAK,EAAE,GAAG,CAAC,CAAA;gBACtC,GAAG,IAAI,CAAC,CAAA;YACV,CAAC;YACD,IAAA,wBAAc,EACZ,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,EAC9B,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,aAAa,CAAC,CACtC,CAAA;YACD,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,KAAK,EAAE,CAAA;QACzC,CAAC;QAED,OAAO;YACL,OAAO,EAAE,IAAA,wBAAc,EAAC,UAAU,CAAC;YACnC,QAAQ;YACR,YAAY;YACZ,YAAY,EAAE,kBAAkB;YAChC,SAAS;YACT,aAAa;YACb,aAAa;YACb,cAAc;YACd,MAAM;YACN,WAAW;YACX,WAAW;YACX,YAAY,EAAE,CAAC,IAAI,EAAE;SACtB,CAAA;IACH,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,OAAe,EACf,GAAW,EACX,GAAW,EACX,OAAgB,EAAE;QAElB,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;YACxB,OAAO,EAAE,CAAA;QACX,CAAC;QACD,MAAM,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACnC,IAAI,CAAC,EAAE,EAAE,CAAC;YACR,OAAO,EAAE,CAAA;QACX,CAAC;QAED,IAAI,GAAG,GAAG,kBAAkB,EAAE,CAAC;YAC7B,OAAO,CAAC,IAAI,CAAC,0CAA0C,CAAC,CAAA;QAC1D,CAAC;QACD,qEAAqE;QACrE,sBAAsB;QACtB,MAAM,GAAG,GAAG,IAAI,CAAC,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,EAAE,CAAC,CAAC,EAAE,kBAAkB,CAAC,CAAA;QAC1D,MAAM,eAAe,GAAG,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAA,CAAC,uCAAuC;QAClF,MAAM,MAAM,GAAY,EAAE,CAAA;QAE1B,sEAAsE;QACtE,KAAK,MAAM,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,eAAe,EAAE,CAAC;YAC3C,KAAK,IAAI,GAAG,GAAG,KAAK,EAAE,GAAG,IAAI,GAAG,EAAE,GAAG,EAAE,EAAE,CAAC;gBACxC,MAAM,SAAS,GAAG,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;gBAClC,IAAI,SAAS,EAAE,CAAC;oBACd,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;wBAC1B,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;oBAChB,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QAED,2EAA2E;QAC3E,sEAAsE;QACtE,oDAAoD;QACpD,MAAM,WAAW,GAAG,EAAE,CAAC,WAAW,CAAA;QAClC,MAAM,MAAM,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,EAAE,WAAW,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QAEzE,OAAO,IAAA,wBAAc,EAAC,MAAM,EAAE,MAAM,CAAC,CAAA;IACvC,CAAC;CACF;AAvLD,6BAuLC"}
|
package/dist/util.d.ts
CHANGED
|
@@ -1,8 +1,17 @@
|
|
|
1
1
|
import Chunk from './chunk.ts';
|
|
2
|
-
import
|
|
2
|
+
import VirtualOffset from './virtualOffset.ts';
|
|
3
3
|
export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
|
|
4
4
|
export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number[]): void;
|
|
5
|
-
|
|
5
|
+
/**
|
|
6
|
+
* The smallest of `current` and the `count` packed virtual offsets starting at
|
|
7
|
+
* `offset`, allocating at most one VirtualOffset rather than one per entry.
|
|
8
|
+
*
|
|
9
|
+
* The index first pass exists only to find this minimum, and it visits every
|
|
10
|
+
* linear-index entry in the file to do it — 301k of them on
|
|
11
|
+
* test/data/failing_tabix.vcf.gz.tbi against 19k bin chunks. Building a
|
|
12
|
+
* VirtualOffset per entry to compare and discard it is the bulk of that pass.
|
|
13
|
+
*/
|
|
14
|
+
export declare function minVirtualOffset(bytes: Uint8Array, offset: number, count: number, current: VirtualOffset | undefined): VirtualOffset | undefined;
|
|
6
15
|
export declare function parseNameBytes(namesBytes: Uint8Array): {
|
|
7
16
|
refNameToId: Record<string, number>;
|
|
8
17
|
refIdToName: string[];
|
package/dist/util.js
CHANGED
|
@@ -5,7 +5,7 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
6
|
exports.optimizeChunks = optimizeChunks;
|
|
7
7
|
exports.clampChunkEnds = clampChunkEnds;
|
|
8
|
-
exports.
|
|
8
|
+
exports.minVirtualOffset = minVirtualOffset;
|
|
9
9
|
exports.parseNameBytes = parseNameBytes;
|
|
10
10
|
exports.parseAuxData = parseAuxData;
|
|
11
11
|
exports.parsePseudoBin = parsePseudoBin;
|
|
@@ -13,6 +13,7 @@ exports.memoizeByRefId = memoizeByRefId;
|
|
|
13
13
|
const quick_lru_1 = __importDefault(require("@jbrowse/quick-lru"));
|
|
14
14
|
const chunk_ts_1 = __importDefault(require("./chunk.js"));
|
|
15
15
|
const long_ts_1 = require("./long.js");
|
|
16
|
+
const virtualOffset_ts_1 = __importDefault(require("./virtualOffset.js"));
|
|
16
17
|
// SYNC: ~/src/gmod/bam-js/src/util.ts optimizeChunks
|
|
17
18
|
function optimizeChunks(chunks, lowest) {
|
|
18
19
|
const n = chunks.length;
|
|
@@ -109,10 +110,35 @@ function clampChunkEnds(chunks, extraBoundaries = []) {
|
|
|
109
110
|
}
|
|
110
111
|
}
|
|
111
112
|
}
|
|
112
|
-
|
|
113
|
-
|
|
114
|
-
|
|
115
|
-
|
|
113
|
+
/**
|
|
114
|
+
* The smallest of `current` and the `count` packed virtual offsets starting at
|
|
115
|
+
* `offset`, allocating at most one VirtualOffset rather than one per entry.
|
|
116
|
+
*
|
|
117
|
+
* The index first pass exists only to find this minimum, and it visits every
|
|
118
|
+
* linear-index entry in the file to do it — 301k of them on
|
|
119
|
+
* test/data/failing_tabix.vcf.gz.tbi against 19k bin chunks. Building a
|
|
120
|
+
* VirtualOffset per entry to compare and discard it is the bulk of that pass.
|
|
121
|
+
*/
|
|
122
|
+
function minVirtualOffset(bytes, offset, count, current) {
|
|
123
|
+
let minBlock = current ? current.blockPosition : Infinity;
|
|
124
|
+
let minData = current ? current.dataPosition : 0;
|
|
125
|
+
let found = false;
|
|
126
|
+
for (let i = 0; i < count; i++) {
|
|
127
|
+
const p = offset + i * 8;
|
|
128
|
+
const block = bytes[p + 7] * 0x1_00_00_00_00_00 +
|
|
129
|
+
bytes[p + 6] * 0x1_00_00_00_00 +
|
|
130
|
+
bytes[p + 5] * 0x1_00_00_00 +
|
|
131
|
+
bytes[p + 4] * 0x1_00_00 +
|
|
132
|
+
bytes[p + 3] * 0x1_00 +
|
|
133
|
+
bytes[p + 2];
|
|
134
|
+
const data = (bytes[p + 1] << 8) | bytes[p];
|
|
135
|
+
if (block < minBlock || (block === minBlock && data < minData)) {
|
|
136
|
+
minBlock = block;
|
|
137
|
+
minData = data;
|
|
138
|
+
found = true;
|
|
139
|
+
}
|
|
140
|
+
}
|
|
141
|
+
return found ? new virtualOffset_ts_1.default(minBlock, minData) : current;
|
|
116
142
|
}
|
|
117
143
|
function parseNameBytes(namesBytes) {
|
|
118
144
|
const decoder = new TextDecoder('utf-8');
|
package/dist/util.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;
|
|
1
|
+
{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":";;;;;AAOA,wCAuEC;AASD,wCA8BC;AAWD,4CA0BC;AAED,wCAoBC;AAQD,oCAkCC;AAED,wCAEC;AAGD,wCAgBC;AAjPD,mEAAoC;AAEpC,0DAA8B;AAC9B,uCAAmD;AACnD,0EAA8C;AAE9C,qDAAqD;AACrD,SAAgB,cAAc,CAAC,MAAe,EAAE,MAAsB;IACpE,MAAM,CAAC,GAAG,MAAM,CAAC,MAAM,CAAA;IACvB,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;QACZ,OAAO,MAAM,CAAA;IACf,CAAC;IAED,uEAAuE;IACvE,wEAAwE;IACxE,2EAA2E;IAC3E,IAAI,QAAiB,CAAA;IACrB,IAAI,MAAM,EAAE,CAAC;QACX,MAAM,WAAW,GAAG,MAAM,CAAC,aAAa,CAAA;QACxC,MAAM,UAAU,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,QAAQ,GAAG,EAAE,CAAA;QACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;YAC3B,MAAM,KAAK,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;YACxB,MAAM,GAAG,GACP,KAAK,CAAC,IAAI,CAAC,aAAa,GAAG,WAAW;gBACtC,KAAK,CAAC,IAAI,CAAC,YAAY,GAAG,UAAU,CAAA;YACtC,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACtB,CAAC;QACH,CAAC;QACD,IAAI,QAAQ,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC1B,OAAO,QAAQ,CAAA;QACjB,CAAC;IACH,CAAC;SAAM,CAAC;QACN,QAAQ,GAAG,MAAM,CAAA;IACnB,CAAC;IAED,QAAQ,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,EAAE,EAAE;QACvB,MAAM,GAAG,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,GAAG,EAAE,CAAC,IAAI,CAAC,aAAa,CAAA;QACzD,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,IAAI,CAAC,YAAY,GAAG,EAAE,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,CAAC,GAAG,CAAA;IACtE,CAAC,CAAC,CAAA;IAEF,4EAA4E;IAC5E,0DAA0D;IAC1D,oEAAoE;IACpE,MAAM,YAAY,GAAY,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,CAAA;IAC5C,IAAI,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,CAAC,aAAa,CAAA;IAClD,IAAI,YAAY,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAC,IAAI,CAAC,aAAa,CAAA;IAElD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACzC,MAAM,KAAK,GAAG,QAAQ,CAAC,CAAC,CAAE,CAAA;QAC1B,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,MAAM,aAAa,GAAG,KAAK,CAAC,IAAI,CAAC,aAAa,CAAA;QAC9C,IACE,aAAa,GAAG,YAAY,GAAG,MAAM;YACrC,aAAa,GAAG,YAAY,GAAG,SAAS,EACxC,CAAC;YACD,MAAM,SAAS,GAAG,YAAY,CAAC,EAAE,CAAC,CAAC,CAAC,CAAE,CAAA;YACtC,MAAM,GAAG,GACP,aAAa,GAAG,YAAY;gBAC5B,KAAK,CAAC,IAAI,CAAC,YAAY,GAAG,SAAS,CAAC,IAAI,CAAC,YAAY,CAAA;YACvD,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,YAAY,CAAC,YAAY,CAAC,MAAM,GAAG,CAAC,CAAC,GAAG,IAAI,kBAAK,CAC/C,SAAS,CAAC,IAAI,EACd,KAAK,CAAC,IAAI,EACV,SAAS,CAAC,GAAG,EACb,KAAK,CAAC,WAAW,CAClB,CAAA;gBACD,YAAY,GAAG,aAAa,CAAA;YAC9B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACxB,YAAY,GAAG,aAAa,CAAA;YAC5B,YAAY,GAAG,aAAa,CAAA;QAC9B,CAAC;IACH,CAAC;IAED,OAAO,YAAY,CAAA;AACrB,CAAC;AAED,6EAA6E;AAC7E,kFAAkF;AAClF,kFAAkF;AAClF,iFAAiF;AACjF,kFAAkF;AAClF,iFAAiF;AACjF,yEAAyE;AACzE,SAAgB,cAAc,CAC5B,MAAe,EACf,kBAA4B,EAAE;IAE9B,uEAAuE;IACvE,wEAAwE;IACxE,qDAAqD;IACrD,MAAM,UAAU,GAAG,CAAC,GAAG,eAAe,CAAC,CAAA;IACvC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,aAAa,EAAE,CAAC,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;IAC7D,CAAC;IACD,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,CAAC,CAAA;IAEhC,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;QACvB,MAAM,GAAG,GAAG,CAAC,CAAC,IAAI,CAAC,aAAa,CAAA;QAChC,2CAA2C;QAC3C,IAAI,EAAE,GAAG,CAAC,CAAA;QACV,IAAI,EAAE,GAAG,UAAU,CAAC,MAAM,CAAA;QAC1B,OAAO,EAAE,GAAG,EAAE,EAAE,CAAC;YACf,MAAM,GAAG,GAAG,CAAC,EAAE,GAAG,EAAE,CAAC,KAAK,CAAC,CAAA;YAC3B,IAAI,UAAU,CAAC,GAAG,CAAE,GAAG,GAAG,EAAE,CAAC;gBAC3B,EAAE,GAAG,GAAG,CAAA;YACV,CAAC;iBAAM,CAAC;gBACN,EAAE,GAAG,GAAG,GAAG,CAAC,CAAA;YACd,CAAC;QACH,CAAC;QACD,IAAI,EAAE,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC;YAC3B,CAAC,CAAC,WAAW,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,UAAU,CAAC,EAAE,CAAE,CAAC,CAAA;QAC1D,CAAC;IACH,CAAC;AACH,CAAC;AAED;;;;;;;;GAQG;AACH,SAAgB,gBAAgB,CAC9B,KAAiB,EACjB,MAAc,EACd,KAAa,EACb,OAAkC;IAElC,IAAI,QAAQ,GAAG,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,QAAQ,CAAA;IACzD,IAAI,OAAO,GAAG,OAAO,CAAC,CAAC,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAA;IAChD,IAAI,KAAK,GAAG,KAAK,CAAA;IACjB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,EAAE,CAAC,EAAE,EAAE,CAAC;QAC/B,MAAM,CAAC,GAAG,MAAM,GAAG,CAAC,GAAG,CAAC,CAAA;QACxB,MAAM,KAAK,GACT,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,kBAAkB;YAClC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,eAAe;YAC/B,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,YAAY;YAC5B,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,SAAS;YACzB,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,GAAG,MAAM;YACtB,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,CAAA;QACf,MAAM,IAAI,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAE,IAAI,CAAC,CAAC,GAAG,KAAK,CAAC,CAAC,CAAE,CAAA;QAC7C,IAAI,KAAK,GAAG,QAAQ,IAAI,CAAC,KAAK,KAAK,QAAQ,IAAI,IAAI,GAAG,OAAO,CAAC,EAAE,CAAC;YAC/D,QAAQ,GAAG,KAAK,CAAA;YAChB,OAAO,GAAG,IAAI,CAAA;YACd,KAAK,GAAG,IAAI,CAAA;QACd,CAAC;IACH,CAAC;IACD,OAAO,KAAK,CAAC,CAAC,CAAC,IAAI,0BAAa,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,OAAO,CAAA;AAC/D,CAAC;AAED,SAAgB,cAAc,CAAC,UAAsB;IACnD,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,OAAO,CAAC,CAAA;IACxC,MAAM,WAAW,GAAa,EAAE,CAAA;IAChC,MAAM,WAAW,GAA2B,EAAE,CAAA;IAC9C,IAAI,SAAS,GAAG,CAAC,CAAA;IACjB,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,OAAO,GAAG,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC;QAC/B,MAAM,GAAG,GAAG,UAAU,CAAC,OAAO,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;QACtC,IAAI,GAAG,KAAK,CAAC,CAAC,EAAE,CAAC;YACf,MAAK;QACP,CAAC;QACD,IAAI,GAAG,GAAG,GAAG,EAAE,CAAC;YACd,MAAM,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,UAAU,CAAC,QAAQ,CAAC,GAAG,EAAE,GAAG,CAAC,CAAC,CAAA;YAC7D,WAAW,CAAC,SAAS,CAAC,GAAG,OAAO,CAAA;YAChC,WAAW,CAAC,OAAO,CAAC,GAAG,SAAS,CAAA;QAClC,CAAC;QACD,GAAG,GAAG,GAAG,GAAG,CAAC,CAAA;QACb,SAAS,EAAE,CAAA;IACb,CAAC;IACD,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,CAAA;AACrC,CAAC;AAED,MAAM,YAAY,GAA2B;IAC3C,CAAC,EAAE,SAAS;IACZ,CAAC,EAAE,KAAK;IACR,CAAC,EAAE,KAAK;CACT,CAAA;AAED,SAAgB,YAAY,CAAC,KAAiB,EAAE,MAAc;IAC5D,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;IACD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IACnD,MAAM,cAAc,GAClB,WAAW,GAAG,SAAS,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;IACrE,MAAM,MAAM,GAAG,YAAY,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;IAC9C,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;IACrE,CAAC;IACD,MAAM,aAAa,GAAG;QACpB,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;QACxC,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,IAAI,CAAC;QAC1C,GAAG,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC;KAC1C,CAAA;IACD,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACtD,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;IACvE,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IACtD,MAAM,iBAAiB,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,IAAI,CAAC,CAAA;IAC9D,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,cAAc,CACjD,KAAK,CAAC,QAAQ,CAAC,MAAM,GAAG,EAAE,EAAE,MAAM,GAAG,EAAE,GAAG,iBAAiB,CAAC,CAC7D,CAAA;IACD,OAAO;QACL,WAAW;QACX,WAAW;QACX,SAAS;QACT,QAAQ;QACR,aAAa;QACb,MAAM;QACN,cAAc;KACf,CAAA;AACH,CAAC;AAED,SAAgB,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO,EAAE,SAAS,EAAE,IAAA,iCAAuB,EAAC,KAAK,EAAE,MAAM,CAAC,EAAE,CAAA;AAC9D,CAAC;AAED,0DAA0D;AAC1D,SAAgB,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,GAAG,GAAG,IAAI,mBAAG,CAAY,EAAE,OAAO,EAAE,CAAC,CAAA;IAC3C,OAAO,CAAC,KAAa,EAAE,EAAE;QACvB,MAAM,MAAM,GAAG,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,CAAA;QAC7B,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,OAAO,MAAM,CAAA;QACf,CAAC;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,KAAK,CAAC,CAAA;QAChC,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACzB,GAAG,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QACxB,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC,CAAA;AACH,CAAC"}
|
package/esm/csi.js
CHANGED
|
@@ -1,7 +1,7 @@
|
|
|
1
1
|
import { unzip } from '@gmod/bgzf-filehandle';
|
|
2
2
|
import Chunk from "./chunk.js";
|
|
3
3
|
import IndexFile from "./indexFile.js";
|
|
4
|
-
import { clampChunkEnds,
|
|
4
|
+
import { clampChunkEnds, memoizeByRefId, minVirtualOffset, optimizeChunks, parseAuxData, parsePseudoBin, } from "./util.js";
|
|
5
5
|
import { fromBytes } from "./virtualOffset.js";
|
|
6
6
|
const CSI1_MAGIC = 21_582_659; // CSI\1
|
|
7
7
|
const CSI2_MAGIC = 38_359_875; // CSI\2
|
|
@@ -69,7 +69,7 @@ export default class CSI extends IndexFile {
|
|
|
69
69
|
curr += 28 + 16; // skip pseudo-bin (loffset + nchunk + 2 chunks)
|
|
70
70
|
}
|
|
71
71
|
else {
|
|
72
|
-
firstDataLine =
|
|
72
|
+
firstDataLine = minVirtualOffset(bytes, curr, 1, firstDataLine);
|
|
73
73
|
curr += 8; // loffset
|
|
74
74
|
const chunkCount = dataView.getInt32(curr, true);
|
|
75
75
|
curr += 4 + 16 * chunkCount;
|
package/esm/csi.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EACL,cAAc,EACd,
|
|
1
|
+
{"version":3,"file":"csi.js","sourceRoot":"","sources":["../src/csi.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAE7C,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,SAAS,MAAM,gBAAgB,CAAA;AACtC,OAAO,EACL,cAAc,EACd,cAAc,EACd,gBAAgB,EAChB,cAAc,EACd,YAAY,EACZ,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;AAK9C,MAAM,UAAU,GAAG,UAAU,CAAA,CAAC,QAAQ;AACtC,MAAM,UAAU,GAAG,UAAU,CAAA,CAAC,QAAQ;AAEtC,gFAAgF;AAChF,wDAAwD;AACxD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,GAAG,GAAG,CAAC,IAAI,IAAI,CAAA;AACxB,CAAC;AACD,SAAS,MAAM,CAAC,GAAW,EAAE,IAAY;IACvC,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,IAAI,CAAC,CAAA;AACpC,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,GAAI,SAAQ,SAAS;IAChC,YAAY,GAAG,CAAC,CAAA;IAChB,KAAK,GAAG,CAAC,CAAA;IACT,QAAQ,GAAG,CAAC,CAAA;IAEpB,gBAAgB;IAChB,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC;YACzC,MAAM,EAAE,IAAI,CAAC,MAAM;YACnB,UAAU,EAAE,IAAI,CAAC,UAAU;SAC5B,CAAC,CAAA;QACF,MAAM,KAAK,GAAG,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAe,CAAA;QAC9C,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAC3B,KAAK,CAAC,MAAM,EACZ,KAAK,CAAC,UAAU,EAChB,KAAK,CAAC,UAAU,CACjB,CAAA;QAED,MAAM,KAAK,GAAG,QAAQ,CAAC,SAAS,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACzC,IAAI,UAAU,CAAA;QACd,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YACzB,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,IAAI,KAAK,KAAK,UAAU,EAAE,CAAC;YAChC,UAAU,GAAG,CAAC,CAAA;QAChB,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,KAAK,CAAC,yBAAyB,KAAK,GAAG,CAAC,CAAA;QACpD,CAAC;QAED,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QAC1C,IAAI,CAAC,KAAK,GAAG,QAAQ,CAAC,QAAQ,CAAC,CAAC,EAAE,IAAI,CAAC,CAAA;QACvC,IAAI,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QAC3D,MAAM,YAAY,GAAG,IAAI,CAAC,YAAY,CAAA;QACtC,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,QAAQ,GAAG,IAAI,CAAC,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1D,MAAM,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,EAAE,IAAI,CAAC,CAAA;QAC7C,MAAM,GAAG,GACP,SAAS,IAAI,EAAE;YACb,CAAC,CAAC,YAAY,CAAC,KAAK,EAAE,EAAE,CAAC;YACzB,CAAC,CAAC;gBACE,WAAW,EAAE,EAAc;gBAC3B,WAAW,EAAE,EAA4B;gBACzC,QAAQ,EAAE,SAAS;gBACnB,aAAa,EAAE,EAAE,GAAG,EAAE,CAAC,EAAE,KAAK,EAAE,CAAC,EAAE,GAAG,EAAE,CAAC,EAAE;gBAC3C,cAAc,EAAE,sBAAsB;gBACtC,MAAM,EAAE,SAAS;aAClB,CAAA;QACP,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,EAAE,GAAG,SAAS,EAAE,IAAI,CAAC,CAAA;QAExD,iEAAiE;QACjE,gFAAgF;QAChF,IAAI,IAAI,GAAG,EAAE,GAAG,SAAS,GAAG,CAAC,CAAA;QAC7B,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAa,EAAE,CAAA;QAE5B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;YAClC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YAC9C,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBAC1C,IAAI,IAAI,CAAC,CAAA;gBACT,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,IAAI,IAAI,EAAE,GAAG,EAAE,CAAA,CAAC,gDAAgD;gBAClE,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,gBAAgB,CAAC,KAAK,EAAE,IAAI,EAAE,CAAC,EAAE,aAAa,CAAC,CAAA;oBAC/D,IAAI,IAAI,CAAC,CAAA,CAAC,UAAU;oBACpB,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;oBAChD,IAAI,IAAI,CAAC,GAAG,EAAE,GAAG,UAAU,CAAA;gBAC7B,CAAC;YACH,CAAC;QACH,CAAC;QAED,SAAS,UAAU,CAAC,KAAa;YAC/B,MAAM,KAAK,GAAG,OAAO,CAAC,KAAK,CAAC,CAAA;YAC5B,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,IAAI,GAAG,GAAG,KAAK,CAAA;YACf,MAAM,QAAQ,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;YAC7C,GAAG,IAAI,CAAC,CAAA;YACR,MAAM,QAAQ,GAA4B,EAAE,CAAA;YAC5C,MAAM,QAAQ,GAAkC,EAAE,CAAA;YAClD,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,EAAE,EAAE,CAAC;gBAClC,MAAM,GAAG,GAAG,QAAQ,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;gBACzC,GAAG,IAAI,CAAC,CAAA;gBACR,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;oBACvB,KAAK,GAAG,cAAc,CAAC,KAAK,EAAE,GAAG,GAAG,EAAE,CAAC,CAAA;oBACvC,GAAG,IAAI,EAAE,GAAG,EAAE,CAAA;gBAChB,CAAC;qBAAM,CAAC;oBACN,QAAQ,CAAC,GAAG,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;oBACrC,GAAG,IAAI,CAAC,CAAA;oBACR,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE,IAAI,CAAC,CAAA;oBAC/C,GAAG,IAAI,CAAC,CAAA;oBACR,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAQ,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC,CAAA;oBACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CACnB,SAAS,CAAC,KAAK,EAAE,GAAG,CAAC,EACrB,SAAS,CAAC,KAAK,EAAE,GAAG,GAAG,CAAC,CAAC,EACzB,GAAG,CACJ,CAAA;wBACD,GAAG,IAAI,EAAE,CAAA;oBACX,CAAC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;gBACxB,CAAC;YACH,CAAC;YACD,cAAc,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,CAAC,CAAA;YAC9C,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QACtC,CAAC;QAED,OAAO;YACL,GAAG,GAAG;YACN,GAAG,EAAE,IAAI;YACT,QAAQ;YACR,YAAY,EAAE,CAAC,IAAI,EAAE;YACrB,aAAa;YACb,UAAU;YACV,OAAO,EAAE,cAAc,CAAC,UAAU,CAAC;YACnC,KAAK,EAAE,IAAI,CAAC,KAAK;YACjB,YAAY;YACZ,YAAY;SACb,CAAA;IACH,CAAC;IAED,KAAK,CAAC,cAAc,CAClB,OAAe,EACf,GAAW,EACX,GAAW,EACX,OAAgB,EAAE;QAElB,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;YACZ,GAAG,GAAG,CAAC,CAAA;QACT,CAAC;QAED,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,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@@ -31,6 +31,7 @@ export default class TabixIndexedFile {
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31
31
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csiPath?: string;
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32
32
|
csiUrl?: string;
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33
33
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csiFilehandle?: GenericFilehandle;
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34
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+
/** budget for the decompressed chunk cache, in bytes */
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34
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chunkCacheSize?: number;
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35
36
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});
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36
37
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/**
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@@ -73,6 +74,22 @@ export default class TabixIndexedFile {
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73
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depth?: number;
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74
75
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}>;
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75
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getHeaderBuffer(opts?: Options): Promise<Uint8Array<ArrayBufferLike>>;
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77
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+
/**
|
|
78
|
+
* The leading lines the index says to skip — `tabix -S N` — which is where a
|
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79
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+
* file whose header row is not commented keeps it. Empty when the index
|
|
80
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+
* records no skipped lines.
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81
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+
*
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82
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+
* Deliberately not part of `getHeader`. htslib draws the same distinction:
|
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83
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+
* its indexer treats a line as non-data when `lineno <= line_skip` OR it
|
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84
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+
* begins with the meta character (tbx.c), while `tabix -H` prints only the
|
|
85
|
+
* leading meta-character lines and never consults line_skip (tabix.c).
|
|
86
|
+
* `getHeader` mirrors `-H`, so a bare header row is absent from it, and
|
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87
|
+
* callers that need one were left re-reading the file themselves — guessing
|
|
88
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+
* at a read size, and unable to tell a headerless file from an uncommented
|
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89
|
+
* one. PLINK `.ld`, bedGraph and BED deflines are all routinely written this
|
|
90
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+
* way.
|
|
91
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+
*/
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92
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+
getSkippedLines(opts?: Options): Promise<string[]>;
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76
93
|
getHeader(opts?: Options): Promise<string>;
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|
77
94
|
getReferenceSequenceNames(opts?: Options): Promise<string[]>;
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78
95
|
/** @param refName reference sequence name */
|