@gmod/tabix 3.5.1 → 3.5.3

package/esm/tabixIndexedFile.js

@@ -1,6 +1,5 @@
 import AbortablePromiseCache from '@gmod/abortable-promise-cache';
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle';
-import LRU from '@jbrowse/quick-lru';
 import { LocalFile, RemoteFile } from 'generic-filehandle2';
 import CSI from "./csi.js";
 import TBI from "./tbi.js";
@@ -13,6 +12,85 @@ const SEMICOLON = 59;
 // is parsing. Six is the HTTP/1.1 per-host connection cap browsers enforce, so
 // going much above it buys nothing on the transport that matters.
 const MAX_READ_AHEAD_CHUNKS = 6;
+// SYNC: ~/src/gmod/bam-js/src/bamFile.ts DEFAULT_MAX_CACHE_BYTES
+//
+// We fetch compressed and cache decompressed, and an entry is a whole chunk, so
+// entry count says nothing about memory. How little is easy to underestimate:
+// a dense VCF (test/data/1kg.chr1.subset.vcf.gz — 213MB over 600kb of chr1)
+// has single index bins of 17MB compressed, 120MB decompressed. Panning it
+// under the old 80-entry cache peaked at 2GB RSS.
+const DEFAULT_CHUNK_CACHE_BYTES = 100 * 2 ** 20;
+/**
+ * Backing store for the chunk cache, bounded by the decompressed size of the
+ * chunks it holds rather than by entry count.
+ *
+ * A chunk's size is only known once its read settles, so `set` records the
+ * entry immediately and charges it to the budget later. Unsettled entries are
+ * therefore free, which is what we want: they are reads a query is waiting on.
+ */
+class ByteBoundedChunkCache {
+    entries = new Map();
+    bytes = 0;
+    maxBytes;
+    constructor(maxBytes) {
+        this.maxBytes = maxBytes;
+    }
+    get byteSize() {
+        return this.bytes;
+    }
+    get size() {
+        return this.entries.size;
+    }
+    has(key) {
+        return this.entries.has(key);
+    }
+    get(key) {
+        const cached = this.entries.get(key);
+        if (cached) {
+            // re-insert so Map iteration order stays least-recently-used first
+            this.entries.delete(key);
+            this.entries.set(key, cached);
+        }
+        return cached?.entry;
+    }
+    set(key, entry) {
+        this.delete(key);
+        const cached = { entry, bytes: 0 };
+        this.entries.set(key, cached);
+        void entry.promise
+            .then(chunk => {
+            // a later set() may have replaced this key while the read was in
+            // flight; charging these bytes to it would then double-count
+            if (this.entries.get(key) === cached) {
+                cached.bytes = chunk.buffer.byteLength;
+                this.bytes += cached.bytes;
+                this.evict();
+            }
+        })
+            .catch(() => {
+            // a failed or aborted read caches nothing and costs nothing
+        });
+    }
+    delete(key) {
+        const cached = this.entries.get(key);
+        if (cached) {
+            this.entries.delete(key);
+            this.bytes -= cached.bytes;
+        }
+    }
+    keys() {
+        return this.entries.keys();
+    }
+    // Evict from the least-recently-used end. The size > 1 guard means a single
+    // chunk larger than the whole budget is still kept: the caller needs it for
+    // the query in flight, and dropping it would only force a re-decompress.
+    evict() {
+        const lru = this.entries.keys();
+        while (this.bytes > this.maxBytes && this.entries.size > 1) {
+            this.delete(lru.next().value);
+        }
+    }
+}
 function resolveFilehandle(filehandle, path, url) {
     if (filehandle) {
         return filehandle;
@@ -121,7 +199,7 @@ export default class TabixIndexedFile {
     filehandle;
     index;
     chunkCache;
-    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = 5 * 2 ** 20, }) {
+    constructor({ path, filehandle, url, tbiPath, tbiUrl, tbiFilehandle, csiPath, csiUrl, csiFilehandle, chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES, }) {
         this.filehandle = resolveFilehandle(filehandle, path, url);
         this.index = resolveIndex({
             tbiFilehandle,
@@ -134,7 +212,7 @@ export default class TabixIndexedFile {
             url,
         });
         this.chunkCache = new AbortablePromiseCache({
-            cache: new LRU({ maxSize: Math.floor(chunkCacheSize / (1 << 16)) }),
+            cache: new ByteBoundedChunkCache(chunkCacheSize),
             fill: (args, signal) => this.readChunk(args, { signal }),
         });
     }
@@ -344,6 +422,32 @@ export default class TabixIndexedFile {
         }
         return bytes;
     }
+    /**
+     * The leading lines the index says to skip — `tabix -S N` — which is where a
+     * file whose header row is not commented keeps it. Empty when the index
+     * records no skipped lines.
+     *
+     * Deliberately not part of `getHeader`. htslib draws the same distinction:
+     * its indexer treats a line as non-data when `lineno <= line_skip` OR it
+     * begins with the meta character (tbx.c), while `tabix -H` prints only the
+     * leading meta-character lines and never consults line_skip (tabix.c).
+     * `getHeader` mirrors `-H`, so a bare header row is absent from it, and
+     * callers that need one were left re-reading the file themselves — guessing
+     * at a read size, and unable to tell a headerless file from an uncommented
+     * one. PLINK `.ld`, bedGraph and BED deflines are all routinely written this
+     * way.
+     */
+    async getSkippedLines(opts = {}) {
+        const { firstDataLine, skipLines = 0, maxBlockSize, } = await this.getMetadata(opts);
+        if (skipLines <= 0) {
+            return [];
+        }
+        // same read getHeaderBuffer makes, and the same caveat: a header spanning
+        // more blocks than this is not covered
+        const buf = await this.filehandle.read((firstDataLine?.blockPosition ?? 0) + maxBlockSize, 0, opts);
+        const bytes = (await unzip(buf));
+        return new TextDecoder().decode(bytes).split(/\r?\n/).slice(0, skipLines);
+    }
     async getHeader(opts = {}) {
         const bytes = await this.getHeaderBuffer(opts);
         return new TextDecoder().decode(bytes);

package/esm/tabixIndexedFile.js.map

@@ -1 +1 @@
-{"version":3,"file":"tabixIndexedFile.js","sourceRoot":"","sources":["../src/tabixIndexedFile.ts"],"names":[],"mappings":"AAAA,OAAO,qBAAqB,MAAM,+BAA+B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAA;AAC9D,OAAO,GAAG,MAAM,oBAAoB,CAAA;AACpC,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAA;AAE3D,OAAO,GAAG,MAAM,UAAU,CAAA;AAC1B,OAAO,GAAG,MAAM,UAAU,CAAA;AAC1B,OAAO,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAO1C,MAAM,GAAG,GAAG,CAAC,CAAA;AACb,MAAM,OAAO,GAAG,EAAE,CAAA;AAClB,MAAM,eAAe,GAAG,EAAE,CAAA;AAC1B,MAAM,SAAS,GAAG,EAAE,CAAA;AAEpB,+EAA+E;AAC/E,+EAA+E;AAC/E,kEAAkE;AAClE,MAAM,qBAAqB,GAAG,CAAC,CAAA;AA4B/B,SAAS,iBAAiB,CACxB,UAA8B,EAC9B,IAAa,EACb,GAAY;IAEZ,IAAI,UAAU,EAAE,CAAC;QACf,OAAO,UAAU,CAAA;IACnB,CAAC;IACD,IAAI,IAAI,EAAE,CAAC;QACT,OAAO,IAAI,SAAS,CAAC,IAAI,CAAC,CAAA;IAC5B,CAAC;IACD,IAAI,GAAG,EAAE,CAAC;QACR,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,CAAA;IAC5B,CAAC;IACD,MAAM,IAAI,SAAS,CAAC,8CAA8C,CAAC,CAAA;AACrE,CAAC;AAED,mEAAmE;AACnE,sEAAsE;AACtE,SAAS,YAAY,CAAC,EACpB,aAAa,EACb,aAAa,EACb,OAAO,EACP,OAAO,EACP,MAAM,EACN,MAAM,EACN,IAAI,EACJ,GAAG,GAUJ;IACC,IAAI,aAAa,EAAE,CAAC;QAClB,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,aAAa,EAAE,CAAC,CAAA;IAC/C,CAAC;IACD,IAAI,aAAa,EAAE,CAAC;QAClB,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,aAAa,EAAE,CAAC,CAAA;IAC/C,CAAC;IACD,IAAI,OAAO,EAAE,CAAC;QACZ,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,IAAI,SAAS,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;IACxD,CAAC;IACD,IAAI,OAAO,EAAE,CAAC;QACZ,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,IAAI,SAAS,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;IACxD,CAAC;IACD,IAAI,MAAM,EAAE,CAAC;QACX,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,IAAI,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;IACxD,CAAC;IACD,IAAI,MAAM,EAAE,CAAC;QACX,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,IAAI,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;IACxD,CAAC;IACD,IAAI,IAAI,EAAE,CAAC;QACT,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,IAAI,SAAS,CAAC,GAAG,IAAI,MAAM,CAAC,EAAE,CAAC,CAAA;IAC9D,CAAC;IACD,IAAI,GAAG,EAAE,CAAC;QACR,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,IAAI,UAAU,CAAC,GAAG,GAAG,MAAM,CAAC,EAAE,CAAC,CAAA;IAC9D,CAAC;IACD,MAAM,IAAI,SAAS,CACjB,oFAAoF,CACrF,CAAA;AACH,CAAC;AAED,SAAS,mBAAmB,CAC1B,UAAoB,EACpB,UAAoB,EACpB,GAAW,EACX,UAAkB,EAClB,gBAAwB;IAExB,OAAO,CACL,UAAU,CAAC,GAAG,CAAE,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;QAC3B,CAAC,UAAU,GAAG,UAAU,CAAC,GAAG,CAAE,CAAC;QAC/B,gBAAgB;QAChB,CAAC,CACF,CAAA;AACH,CAAC;AAED,SAAS,SAAS,CAChB,MAAkB,EAClB,eAAuB,EACvB,QAAgB,EAChB,MAAc,EACd,SAAiB,EACjB,OAAe;IAEf,MAAM,MAAM,GAAG,MAAM,GAAG,QAAQ,CAAA;IAChC,IAAI,aAAa,GAAG,eAAe,GAAG,MAAM,CAAA;IAE5C,kCAAkC;IAClC,IAAI,MAAM,CAAC,SAAS,CAAC,KAAK,EAAE,EAAE,CAAC;QAC7B,OAAO,aAAa,CAAA;IACtB,CAAC;IAED,iEAAiE;IACjE,kEAAkE;IAClE,4DAA4D;IAC5D,IAAI,UAAU,GAAG,SAAS,CAAA;IAC1B,KAAK,IAAI,CAAC,GAAG,SAAS,EAAE,CAAC,IAAI,OAAO,EAAE,CAAC,EAAE,EAAE,CAAC;QAC1C,IAAI,CAAC,KAAK,OAAO,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE,CAAC;YAC7C,MAAM,QAAQ,GAAG,CAAC,GAAG,UAAU,CAAA;YAC/B,IACE,QAAQ,IAAI,EAAE;gBACd,MAAM,CAAC,UAAU,CAAC,KAAK,EAAE,IAAI,IAAI;gBACjC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,CAAC,IAAI;cAClC,CAAC;gBACD,OAAO,eAAe,GAAG,CAAC,CAAA;YAC5B,CAAC;YACD,IACE,QAAQ,IAAI,CAAC;gBACb,MAAM,CAAC,UAAU,CAAC,KAAK,EAAE,IAAI,IAAI;gBACjC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,CAAC,IAAI;cAClC,CAAC;gBACD,aAAa,GAAG,iBAAiB,CAAC,MAAM,EAAE,UAAU,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;YAC9D,CAAC;YACD,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,OAAO,aAAa,CAAA;AACtB,CAAC;AAED,SAAS,iBAAiB,CAAC,MAAkB,EAAE,KAAa,EAAE,GAAW;IACvE,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,IAAI,CAAC,GAAG,KAAK,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;QACjC,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACpB,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC;YACvB,GAAG,GAAG,GAAG,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QAC3B,CAAC;aAAM,CAAC;YACN,MAAK;QACP,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED;;GAEG;AACH,MAAM,CAAC,OAAO,OAAO,gBAAgB;IAC3B,UAAU,CAAmB;IAC7B,KAAK,CAAW;IAChB,UAAU,CAAyC;IAE3D,YAAY,EACV,IAAI,EACJ,UAAU,EACV,GAAG,EACH,OAAO,EACP,MAAM,EACN,aAAa,EACb,OAAO,EACP,MAAM,EACN,aAAa,EACb,cAAc,GAAG,CAAC,GAAG,CAAC,IAAI,EAAE,GAY7B;QACC,IAAI,CAAC,UAAU,GAAG,iBAAiB,CAAC,UAAU,EAAE,IAAI,EAAE,GAAG,CAAC,CAAA;QAC1D,IAAI,CAAC,KAAK,GAAG,YAAY,CAAC;YACxB,aAAa;YACb,aAAa;YACb,OAAO;YACP,OAAO;YACP,MAAM;YACN,MAAM;YACN,IAAI;YACJ,GAAG;SACJ,CAAC,CAAA;QAEF,IAAI,CAAC,UAAU,GAAG,IAAI,qBAAqB,CAAmB;YAC5D,KAAK,EAAE,IAAI,GAAG,CAAC,EAAE,OAAO,EAAE,IAAI,CAAC,KAAK,CAAC,cAAc,GAAG,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,CAAC;YACnE,IAAI,EAAE,CAAC,IAAW,EAAE,MAAoB,EAAE,EAAE,CAC1C,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,EAAE,MAAM,EAAE,CAAC;SACnC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,eAAe,CACnB,OAA0D,EAC1D,OAAgB,EAAE;QAElB,MAAM,GAAG,GAAY,EAAE,CAAA;QACvB,KAAK,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,OAAO,EAAE,CAAC;YAC9C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;YACzE,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;gBAC3B,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACjB,CAAC;QACH,CAAC;QACD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,cAAc,CAAC,GAAG,CAAC,EAAE,CAAC;YACxC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,QAAQ,CACZ,OAAe,EACf,CAAqB,EACrB,CAAqB,EACrB,IAAqC;QAErC,IAAI,MAA+B,CAAA;QACnC,IAAI,OAAO,GAAY,EAAE,CAAA;QACzB,IAAI,QAA0B,CAAA;QAC9B,IAAI,UAAsC,CAAA;QAE1C,IAAI,OAAO,IAAI,KAAK,UAAU,EAAE,CAAC;YAC/B,QAAQ,GAAG,IAAI,CAAA;QACjB,CAAC;aAAM,CAAC;YACN,OAAO,GAAG,IAAI,CAAA;YACd,QAAQ,GAAG,IAAI,CAAC,YAAY,CAAA;YAC5B,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;YACpB,UAAU,GAAG,IAAI,CAAC,UAAU,CAAA;QAC9B,CAAC;QAED,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QACtD,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;QACpB,MAAM,GAAG,GAAG,CAAC,IAAI,QAAQ,CAAC,YAAY,CAAA;QACtC,IAAI,KAAK,GAAG,GAAG,EAAE,CAAC;YAChB,MAAM,IAAI,SAAS,CACjB,4EAA4E,CAC7E,CAAA;QACH,CAAC;QACD,IAAI,KAAK,KAAK,GAAG,EAAE,CAAC;YAClB,OAAM;QACR,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,CAAC,CAAA;QAE5E,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,KAAK,KAAK,CAAA;QACvC,MAAM,MAAM,GAAG,QAAQ,CAAC,aAAa,CAAC,GAAG,IAAI,CAAC,CAAA;QAC9C,MAAM,QAAQ,GAAG,QAAQ,CAAC,aAAa,CAAC,KAAK,IAAI,CAAC,CAAA;QAClD,MAAM,MAAM,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,aAAa,CAAC,GAAG,IAAI,CAAC,CAAA;QAC1D,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAA;QACpD,MAAM,YAAY,GAAG,QAAQ,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC,CAAC,CAAA;QACrD,MAAM,gBAAgB,GACpB,QAAQ,CAAC,cAAc,KAAK,gBAAgB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEvD,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;QACjC,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;QACjC,MAAM,kBAAkB,GAAG,OAAO,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;QAClD,0EAA0E;QAC1E,6EAA6E;QAC7E,MAAM,IAAI,GAAG,IAAI,UAAU,CAAC,SAAS,GAAG,CAAC,CAAC,CAAA;QAE1C,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;YACvB,UAAU,IAAI,CAAC,CAAC,WAAW,EAAE,CAAA;QAC/B,CAAC;QACD,IAAI,eAAe,GAAG,CAAC,CAAA;QACvB,UAAU,EAAE,CAAC,CAAC,EAAE,UAAU,CAAC,CAAA;QAE3B,yEAAyE;QACzE,2EAA2E;QAC3E,0EAA0E;QAC1E,uEAAuE;QACvE,EAAE;QACF,2EAA2E;QAC3E,4EAA4E;QAC5E,wEAAwE;QACxE,yEAAyE;QACzE,6DAA6D;QAC7D,EAAE;QACF,2EAA2E;QAC3E,wEAAwE;QACxE,2EAA2E;QAC3E,2EAA2E;QAC3E,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,MAAM,KAAK,GAAyB,EAAE,CAAA;QACtC,MAAM,kBAAkB,GAAG,CAAC,KAAa,EAAE,EAAE;YAC3C,OAAO,KAAK,CAAC,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC;gBACrD,MAAM,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,CAAE,CAAA;gBAC/B,MAAM,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,EAAE,MAAM,CAAC,CAAA;gBACzD,KAAK,IAAI,CAAC,KAAK,CAAC,GAAG,EAAE;oBACnB,qEAAqE;oBACrE,sDAAsD;gBACxD,CAAC,CAAC,CAAA;gBACF,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,CAAC;QACH,CAAC,CAAA;QACD,kBAAkB,CAAC,CAAC,CAAC,CAAA;QAErB,KAAK,IAAI,EAAE,GAAG,CAAC,EAAE,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC;YACnD,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,CAAE,CAAA;YACrB,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,GAAG,MAAM,KAAK,CAAC,EAAE,CAAE,CAAA;YAC3D,eAAe,IAAI,CAAC,CAAC,WAAW,EAAE,CAAA;YAClC,UAAU,EAAE,CAAC,eAAe,EAAE,UAAU,CAAC,CAAA;YACzC,MAAM,gBAAgB,GAAG,CAAC,CAAC,IAAI,CAAC,YAAY,CAAA;YAE5C,IAAI,UAAU,GAAG,CAAC,CAAA;YAClB,IAAI,GAAG,GAAG,CAAC,CAAA;YAEX,OAAO,UAAU,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC;gBAClC,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC,OAAO,EAAE,UAAU,CAAC,CAAA;gBAC7C,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC;oBACb,MAAK;gBACP,CAAC;gBAED,MAAM,MAAM,GAAG,UAAU,GAAG,gBAAgB,CAAA;gBAC5C,OAAO,GAAG,GAAG,UAAU,CAAC,MAAM,IAAI,MAAM,IAAI,UAAU,CAAC,GAAG,CAAE,EAAE,CAAC;oBAC7D,GAAG,EAAE,CAAA;gBACP,CAAC;gBAED,kBAAkB;gBAClB,IAAI,YAAY,KAAK,SAAS,IAAI,MAAM,CAAC,UAAU,CAAC,KAAK,YAAY,EAAE,CAAC;oBACtE,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;oBAClB,SAAQ;gBACV,CAAC;gBAED,mEAAmE;gBACnE,qEAAqE;gBACrE,0CAA0C;gBAC1C,IAAI,CAAC,CAAC,CAAC,GAAG,UAAU,GAAG,CAAC,CAAA;gBACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE,CAAC;oBACnC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAE,CAAA;oBACrB,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC5D,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,MAAM,KAAK,CAAC,CAAC,IAAI,MAAM,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;gBACzD,CAAC;gBAED,kCAAkC;gBAClC,MAAM,QAAQ,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,CAAC,CAAA;gBACtC,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAE,CAAA;gBAC5B,MAAM,MAAM,GAAG,MAAM,GAAG,QAAQ,CAAA;gBAChC,IAAI,MAAM,KAAK,kBAAkB,CAAC,MAAM,EAAE,CAAC;oBACzC,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;oBAClB,SAAQ;gBACV,CAAC;gBACD,IAAI,UAAU,GAAG,IAAI,CAAA;gBACrB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;oBAChC,IAAI,MAAM,CAAC,QAAQ,GAAG,CAAC,CAAC,KAAK,kBAAkB,CAAC,CAAC,CAAC,EAAE,CAAC;wBACnD,UAAU,GAAG,KAAK,CAAA;wBAClB,MAAK;oBACP,CAAC;gBACH,CAAC;gBACD,IAAI,CAAC,UAAU,EAAE,CAAC;oBAChB,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;oBAClB,SAAQ;gBACV,CAAC;gBAED,yBAAyB;gBACzB,MAAM,eAAe,GACnB,iBAAiB,CAAC,MAAM,EAAE,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAE,GAAG,CAAC,EAAE,IAAI,CAAC,QAAQ,CAAE,CAAC;oBACnE,gBAAgB,CAAA;gBAElB,IAAI,eAAe,IAAI,GAAG,EAAE,CAAC;oBAC3B,OAAM;gBACR,CAAC;gBAED,uBAAuB;gBACvB,IAAI,aAAqB,CAAA;gBACzB,IAAI,MAAM,KAAK,CAAC,IAAI,MAAM,KAAK,QAAQ,EAAE,CAAC;oBACxC,aAAa,GAAG,eAAe,GAAG,CAAC,CAAA;gBACrC,CAAC;qBAAM,IAAI,KAAK,EAAE,CAAC;oBACjB,aAAa,GAAG,SAAS,CACvB,MAAM,EACN,eAAe,EACf,IAAI,CAAC,CAAC,CAAE,GAAG,CAAC,EACZ,IAAI,CAAC,CAAC,CAAE,EACR,IAAI,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,CAAC,EACrB,IAAI,CAAC,MAAM,CAAE,CACd,CAAA;gBACH,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,iBAAiB,CAC/B,MAAM,EACN,IAAI,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,CAAC,EACrB,IAAI,CAAC,MAAM,CAAE,CACd,CAAA;gBACH,CAAC;gBAED,IAAI,aAAa,GAAG,KAAK,EAAE,CAAC;oBAC1B,wDAAwD;oBACxD,MAAM,OAAO,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,eAAe,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC7D,MAAM,IAAI,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,UAAU,EAAE,OAAO,CAAC,CAAC,CAAA;oBACjE,QAAQ,CACN,IAAI,EACJ,mBAAmB,CACjB,UAAU,EACV,UAAU,EACV,GAAG,EACH,UAAU,EACV,gBAAgB,CACjB,EACD,eAAe,EACf,aAAa,CACd,CAAA;gBACH,CAAC;gBACD,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;YACpB,CAAC;YAED,yEAAyE;YACzE,uEAAuE;YACvE,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,SAAS,GAAG,CAAC,EAAE,qBAAqB,CAAC,CAAA;YAC1D,kBAAkB,CAAC,EAAE,GAAG,CAAC,GAAG,SAAS,CAAC,CAAA;QACxC,CAAC;IACH,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QAClC,OAAO,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,OAAgB,EAAE;QACtC,MAAM,EAAE,aAAa,EAAE,QAAQ,EAAE,YAAY,EAAE,GAC7C,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAE9B,MAAM,QAAQ,GAAG,CAAC,aAAa,EAAE,aAAa,IAAI,CAAC,CAAC,GAAG,YAAY,CAAA;QACnE,uEAAuE;QACvE,8DAA8D;QAE9D,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,QAAQ,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;QACzD,MAAM,KAAK,GAAG,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAe,CAAA;QAE9C,0CAA0C;QAC1C,IAAI,QAAQ,EAAE,CAAC;YACb,IAAI,WAAW,GAAG,CAAC,CAAC,CAAA;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YAEvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC7C,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;gBACrB,IAAI,CAAC,KAAK,WAAW,GAAG,CAAC,IAAI,IAAI,KAAK,QAAQ,EAAE,CAAC;oBAC/C,MAAK;gBACP,CAAC;gBACD,IAAI,IAAI,KAAK,OAAO,EAAE,CAAC;oBACrB,WAAW,GAAG,CAAC,CAAA;gBACjB,CAAC;YACH,CAAC;YACD,OAAO,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;QAC3C,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAgB,EAAE;QAChC,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;QAC9C,OAAO,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;IACxC,CAAC;IAED,KAAK,CAAC,yBAAyB,CAAC,OAAgB,EAAE;QAChD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAC7C,OAAO,QAAQ,CAAC,WAAW,CAAA;IAC7B,CAAC;IAED,6CAA6C;IAC7C,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,OAAO,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,SAAS,CAAC,CAAQ,EAAE,OAAgB,EAAE;QAC1C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,IAAI,CACpC,CAAC,CAAC,WAAW,EAAE,EACf,CAAC,CAAC,IAAI,CAAC,aAAa,EACpB,IAAI,CACL,CAAA;QACD,OAAO,eAAe,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;IAChC,CAAC;CACF"}
+{"version":3,"file":"tabixIndexedFile.js","sourceRoot":"","sources":["../src/tabixIndexedFile.ts"],"names":[],"mappings":"AAAA,OAAO,qBAAqB,MAAM,+BAA+B,CAAA;AACjE,OAAO,EAAE,KAAK,EAAE,eAAe,EAAE,MAAM,uBAAuB,CAAA;AAC9D,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,qBAAqB,CAAA;AAE3D,OAAO,GAAG,MAAM,UAAU,CAAA;AAC1B,OAAO,GAAG,MAAM,UAAU,CAAA;AAC1B,OAAO,EAAE,cAAc,EAAE,MAAM,WAAW,CAAA;AAO1C,MAAM,GAAG,GAAG,CAAC,CAAA;AACb,MAAM,OAAO,GAAG,EAAE,CAAA;AAClB,MAAM,eAAe,GAAG,EAAE,CAAA;AAC1B,MAAM,SAAS,GAAG,EAAE,CAAA;AAEpB,+EAA+E;AAC/E,+EAA+E;AAC/E,kEAAkE;AAClE,MAAM,qBAAqB,GAAG,CAAC,CAAA;AAE/B,iEAAiE;AACjE,EAAE;AACF,gFAAgF;AAChF,8EAA8E;AAC9E,4EAA4E;AAC5E,2EAA2E;AAC3E,kDAAkD;AAClD,MAAM,yBAAyB,GAAG,GAAG,GAAG,CAAC,IAAI,EAAE,CAAA;AAmB/C;;;;;;;GAOG;AACH,MAAM,qBAAqB;IACjB,OAAO,GAAG,IAAI,GAAG,EAAuB,CAAA;IACxC,KAAK,GAAG,CAAC,CAAA;IACT,QAAQ,CAAQ;IAExB,YAAY,QAAgB;QAC1B,IAAI,CAAC,QAAQ,GAAG,QAAQ,CAAA;IAC1B,CAAC;IAED,IAAI,QAAQ;QACV,OAAO,IAAI,CAAC,KAAK,CAAA;IACnB,CAAC;IAED,IAAI,IAAI;QACN,OAAO,IAAI,CAAC,OAAO,CAAC,IAAI,CAAA;IAC1B,CAAC;IAED,GAAG,CAAC,GAAW;QACb,OAAO,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;IAC9B,CAAC;IAED,GAAG,CAAC,GAAW;QACb,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,MAAM,EAAE,CAAC;YACX,mEAAmE;YACnE,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;YACxB,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,EAAE,MAAM,CAAC,CAAA;QAC/B,CAAC;QACD,OAAO,MAAM,EAAE,KAAK,CAAA;IACtB,CAAC;IAED,GAAG,CAAC,GAAW,EAAE,KAAiB;QAChC,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;QAChB,MAAM,MAAM,GAAG,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,EAAE,CAAA;QAClC,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,EAAE,MAAM,CAAC,CAAA;QAC7B,KAAK,KAAK,CAAC,OAAO;aACf,IAAI,CAAC,KAAK,CAAC,EAAE;YACZ,iEAAiE;YACjE,6DAA6D;YAC7D,IAAI,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,KAAK,MAAM,EAAE,CAAC;gBACrC,MAAM,CAAC,KAAK,GAAG,KAAK,CAAC,MAAM,CAAC,UAAU,CAAA;gBACtC,IAAI,CAAC,KAAK,IAAI,MAAM,CAAC,KAAK,CAAA;gBAC1B,IAAI,CAAC,KAAK,EAAE,CAAA;YACd,CAAC;QACH,CAAC,CAAC;aACD,KAAK,CAAC,GAAG,EAAE;YACV,4DAA4D;QAC9D,CAAC,CAAC,CAAA;IACN,CAAC;IAED,MAAM,CAAC,GAAW;QAChB,MAAM,MAAM,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,GAAG,CAAC,CAAA;QACpC,IAAI,MAAM,EAAE,CAAC;YACX,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,GAAG,CAAC,CAAA;YACxB,IAAI,CAAC,KAAK,IAAI,MAAM,CAAC,KAAK,CAAA;QAC5B,CAAC;IACH,CAAC;IAED,IAAI;QACF,OAAO,IAAI,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;IAC5B,CAAC;IAED,4EAA4E;IAC5E,4EAA4E;IAC5E,yEAAyE;IACjE,KAAK;QACX,MAAM,GAAG,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,EAAE,CAAA;QAC/B,OAAO,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,QAAQ,IAAI,IAAI,CAAC,OAAO,CAAC,IAAI,GAAG,CAAC,EAAE,CAAC;YAC3D,IAAI,CAAC,MAAM,CAAC,GAAG,CAAC,IAAI,EAAE,CAAC,KAAM,CAAC,CAAA;QAChC,CAAC;IACH,CAAC;CACF;AA4BD,SAAS,iBAAiB,CACxB,UAA8B,EAC9B,IAAa,EACb,GAAY;IAEZ,IAAI,UAAU,EAAE,CAAC;QACf,OAAO,UAAU,CAAA;IACnB,CAAC;IACD,IAAI,IAAI,EAAE,CAAC;QACT,OAAO,IAAI,SAAS,CAAC,IAAI,CAAC,CAAA;IAC5B,CAAC;IACD,IAAI,GAAG,EAAE,CAAC;QACR,OAAO,IAAI,UAAU,CAAC,GAAG,CAAC,CAAA;IAC5B,CAAC;IACD,MAAM,IAAI,SAAS,CAAC,8CAA8C,CAAC,CAAA;AACrE,CAAC;AAED,mEAAmE;AACnE,sEAAsE;AACtE,SAAS,YAAY,CAAC,EACpB,aAAa,EACb,aAAa,EACb,OAAO,EACP,OAAO,EACP,MAAM,EACN,MAAM,EACN,IAAI,EACJ,GAAG,GAUJ;IACC,IAAI,aAAa,EAAE,CAAC;QAClB,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,aAAa,EAAE,CAAC,CAAA;IAC/C,CAAC;IACD,IAAI,aAAa,EAAE,CAAC;QAClB,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,aAAa,EAAE,CAAC,CAAA;IAC/C,CAAC;IACD,IAAI,OAAO,EAAE,CAAC;QACZ,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,IAAI,SAAS,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;IACxD,CAAC;IACD,IAAI,OAAO,EAAE,CAAC;QACZ,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,IAAI,SAAS,CAAC,OAAO,CAAC,EAAE,CAAC,CAAA;IACxD,CAAC;IACD,IAAI,MAAM,EAAE,CAAC;QACX,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,IAAI,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;IACxD,CAAC;IACD,IAAI,MAAM,EAAE,CAAC;QACX,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,IAAI,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC,CAAA;IACxD,CAAC;IACD,IAAI,IAAI,EAAE,CAAC;QACT,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,IAAI,SAAS,CAAC,GAAG,IAAI,MAAM,CAAC,EAAE,CAAC,CAAA;IAC9D,CAAC;IACD,IAAI,GAAG,EAAE,CAAC;QACR,OAAO,IAAI,GAAG,CAAC,EAAE,UAAU,EAAE,IAAI,UAAU,CAAC,GAAG,GAAG,MAAM,CAAC,EAAE,CAAC,CAAA;IAC9D,CAAC;IACD,MAAM,IAAI,SAAS,CACjB,oFAAoF,CACrF,CAAA;AACH,CAAC;AAED,SAAS,mBAAmB,CAC1B,UAAoB,EACpB,UAAoB,EACpB,GAAW,EACX,UAAkB,EAClB,gBAAwB;IAExB,OAAO,CACL,UAAU,CAAC,GAAG,CAAE,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC;QAC3B,CAAC,UAAU,GAAG,UAAU,CAAC,GAAG,CAAE,CAAC;QAC/B,gBAAgB;QAChB,CAAC,CACF,CAAA;AACH,CAAC;AAED,SAAS,SAAS,CAChB,MAAkB,EAClB,eAAuB,EACvB,QAAgB,EAChB,MAAc,EACd,SAAiB,EACjB,OAAe;IAEf,MAAM,MAAM,GAAG,MAAM,GAAG,QAAQ,CAAA;IAChC,IAAI,aAAa,GAAG,eAAe,GAAG,MAAM,CAAA;IAE5C,kCAAkC;IAClC,IAAI,MAAM,CAAC,SAAS,CAAC,KAAK,EAAE,EAAE,CAAC;QAC7B,OAAO,aAAa,CAAA;IACtB,CAAC;IAED,iEAAiE;IACjE,kEAAkE;IAClE,4DAA4D;IAC5D,IAAI,UAAU,GAAG,SAAS,CAAA;IAC1B,KAAK,IAAI,CAAC,GAAG,SAAS,EAAE,CAAC,IAAI,OAAO,EAAE,CAAC,EAAE,EAAE,CAAC;QAC1C,IAAI,CAAC,KAAK,OAAO,IAAI,MAAM,CAAC,CAAC,CAAC,KAAK,SAAS,EAAE,CAAC;YAC7C,MAAM,QAAQ,GAAG,CAAC,GAAG,UAAU,CAAA;YAC/B,IACE,QAAQ,IAAI,EAAE;gBACd,MAAM,CAAC,UAAU,CAAC,KAAK,EAAE,IAAI,IAAI;gBACjC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,CAAC,IAAI;cAClC,CAAC;gBACD,OAAO,eAAe,GAAG,CAAC,CAAA;YAC5B,CAAC;YACD,IACE,QAAQ,IAAI,CAAC;gBACb,MAAM,CAAC,UAAU,CAAC,KAAK,EAAE,IAAI,IAAI;gBACjC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI;gBACrC,MAAM,CAAC,UAAU,GAAG,CAAC,CAAC,KAAK,EAAE,CAAC,IAAI;cAClC,CAAC;gBACD,aAAa,GAAG,iBAAiB,CAAC,MAAM,EAAE,UAAU,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;YAC9D,CAAC;YACD,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,OAAO,aAAa,CAAA;AACtB,CAAC;AAED,SAAS,iBAAiB,CAAC,MAAkB,EAAE,KAAa,EAAE,GAAW;IACvE,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,KAAK,IAAI,CAAC,GAAG,KAAK,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;QACjC,MAAM,CAAC,GAAG,MAAM,CAAC,CAAC,CAAE,CAAA;QACpB,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,IAAI,EAAE,EAAE,CAAC;YACvB,GAAG,GAAG,GAAG,GAAG,EAAE,GAAG,CAAC,CAAC,GAAG,EAAE,CAAC,CAAA;QAC3B,CAAC;aAAM,CAAC;YACN,MAAK;QACP,CAAC;IACH,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC;AAED;;GAEG;AACH,MAAM,CAAC,OAAO,OAAO,gBAAgB;IAC3B,UAAU,CAAmB;IAC7B,KAAK,CAAW;IAChB,UAAU,CAAyC;IAE3D,YAAY,EACV,IAAI,EACJ,UAAU,EACV,GAAG,EACH,OAAO,EACP,MAAM,EACN,aAAa,EACb,OAAO,EACP,MAAM,EACN,aAAa,EACb,cAAc,GAAG,yBAAyB,GAa3C;QACC,IAAI,CAAC,UAAU,GAAG,iBAAiB,CAAC,UAAU,EAAE,IAAI,EAAE,GAAG,CAAC,CAAA;QAC1D,IAAI,CAAC,KAAK,GAAG,YAAY,CAAC;YACxB,aAAa;YACb,aAAa;YACb,OAAO;YACP,OAAO;YACP,MAAM;YACN,MAAM;YACN,IAAI;YACJ,GAAG;SACJ,CAAC,CAAA;QAEF,IAAI,CAAC,UAAU,GAAG,IAAI,qBAAqB,CAAmB;YAC5D,KAAK,EAAE,IAAI,qBAAqB,CAAC,cAAc,CAAC;YAChD,IAAI,EAAE,CAAC,IAAW,EAAE,MAAoB,EAAE,EAAE,CAC1C,IAAI,CAAC,SAAS,CAAC,IAAI,EAAE,EAAE,MAAM,EAAE,CAAC;SACnC,CAAC,CAAA;IACJ,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,eAAe,CACnB,OAA0D,EAC1D,OAAgB,EAAE;QAElB,MAAM,GAAG,GAAY,EAAE,CAAA;QACvB,KAAK,MAAM,EAAE,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,OAAO,EAAE,CAAC;YAC9C,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,IAAI,CAAC,CAAA;YACzE,KAAK,MAAM,KAAK,IAAI,MAAM,EAAE,CAAC;gBAC3B,GAAG,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YACjB,CAAC;QACH,CAAC;QACD,IAAI,KAAK,GAAG,CAAC,CAAA;QACb,KAAK,MAAM,KAAK,IAAI,cAAc,CAAC,GAAG,CAAC,EAAE,CAAC;YACxC,KAAK,IAAI,KAAK,CAAC,WAAW,EAAE,CAAA;QAC9B,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,QAAQ,CACZ,OAAe,EACf,CAAqB,EACrB,CAAqB,EACrB,IAAqC;QAErC,IAAI,MAA+B,CAAA;QACnC,IAAI,OAAO,GAAY,EAAE,CAAA;QACzB,IAAI,QAA0B,CAAA;QAC9B,IAAI,UAAsC,CAAA;QAE1C,IAAI,OAAO,IAAI,KAAK,UAAU,EAAE,CAAC;YAC/B,QAAQ,GAAG,IAAI,CAAA;QACjB,CAAC;aAAM,CAAC;YACN,OAAO,GAAG,IAAI,CAAA;YACd,QAAQ,GAAG,IAAI,CAAC,YAAY,CAAA;YAC5B,MAAM,GAAG,IAAI,CAAC,MAAM,CAAA;YACpB,UAAU,GAAG,IAAI,CAAC,UAAU,CAAA;QAC9B,CAAC;QAED,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QACtD,MAAM,KAAK,GAAG,CAAC,IAAI,CAAC,CAAA;QACpB,MAAM,GAAG,GAAG,CAAC,IAAI,QAAQ,CAAC,YAAY,CAAA;QACtC,IAAI,KAAK,GAAG,GAAG,EAAE,CAAC;YAChB,MAAM,IAAI,SAAS,CACjB,4EAA4E,CAC7E,CAAA;QACH,CAAC;QACD,IAAI,KAAK,KAAK,GAAG,EAAE,CAAC;YAClB,OAAM;QACR,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,cAAc,CAAC,OAAO,EAAE,KAAK,EAAE,GAAG,EAAE,OAAO,CAAC,CAAA;QAE5E,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,KAAK,KAAK,CAAA;QACvC,MAAM,MAAM,GAAG,QAAQ,CAAC,aAAa,CAAC,GAAG,IAAI,CAAC,CAAA;QAC9C,MAAM,QAAQ,GAAG,QAAQ,CAAC,aAAa,CAAC,KAAK,IAAI,CAAC,CAAA;QAClD,MAAM,MAAM,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,aAAa,CAAC,GAAG,IAAI,CAAC,CAAA;QAC1D,MAAM,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,MAAM,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAA;QACpD,MAAM,YAAY,GAAG,QAAQ,CAAC,QAAQ,EAAE,UAAU,CAAC,CAAC,CAAC,CAAA;QACrD,MAAM,gBAAgB,GACpB,QAAQ,CAAC,cAAc,KAAK,gBAAgB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEvD,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;QACjC,MAAM,OAAO,GAAG,IAAI,WAAW,EAAE,CAAA;QACjC,MAAM,kBAAkB,GAAG,OAAO,CAAC,MAAM,CAAC,OAAO,CAAC,CAAA;QAClD,0EAA0E;QAC1E,6EAA6E;QAC7E,MAAM,IAAI,GAAG,IAAI,UAAU,CAAC,SAAS,GAAG,CAAC,CAAC,CAAA;QAE1C,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,KAAK,MAAM,CAAC,IAAI,MAAM,EAAE,CAAC;YACvB,UAAU,IAAI,CAAC,CAAC,WAAW,EAAE,CAAA;QAC/B,CAAC;QACD,IAAI,eAAe,GAAG,CAAC,CAAA;QACvB,UAAU,EAAE,CAAC,CAAC,EAAE,UAAU,CAAC,CAAA;QAE3B,yEAAyE;QACzE,2EAA2E;QAC3E,0EAA0E;QAC1E,uEAAuE;QACvE,EAAE;QACF,2EAA2E;QAC3E,4EAA4E;QAC5E,wEAAwE;QACxE,yEAAyE;QACzE,6DAA6D;QAC7D,EAAE;QACF,2EAA2E;QAC3E,wEAAwE;QACxE,2EAA2E;QAC3E,2EAA2E;QAC3E,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,MAAM,KAAK,GAAyB,EAAE,CAAA;QACtC,MAAM,kBAAkB,GAAG,CAAC,KAAa,EAAE,EAAE;YAC3C,OAAO,KAAK,CAAC,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,KAAK,EAAE,MAAM,CAAC,MAAM,CAAC,EAAE,CAAC;gBACrD,MAAM,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,CAAE,CAAA;gBAC/B,MAAM,IAAI,GAAG,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,EAAE,MAAM,CAAC,CAAA;gBACzD,KAAK,IAAI,CAAC,KAAK,CAAC,GAAG,EAAE;oBACnB,qEAAqE;oBACrE,sDAAsD;gBACxD,CAAC,CAAC,CAAA;gBACF,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;YAClB,CAAC;QACH,CAAC,CAAA;QACD,kBAAkB,CAAC,CAAC,CAAC,CAAA;QAErB,KAAK,IAAI,EAAE,GAAG,CAAC,EAAE,EAAE,GAAG,MAAM,CAAC,MAAM,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,EAAE,EAAE,CAAC;YACnD,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,CAAE,CAAA;YACrB,MAAM,EAAE,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,GAAG,MAAM,KAAK,CAAC,EAAE,CAAE,CAAA;YAC3D,eAAe,IAAI,CAAC,CAAC,WAAW,EAAE,CAAA;YAClC,UAAU,EAAE,CAAC,eAAe,EAAE,UAAU,CAAC,CAAA;YACzC,MAAM,gBAAgB,GAAG,CAAC,CAAC,IAAI,CAAC,YAAY,CAAA;YAE5C,IAAI,UAAU,GAAG,CAAC,CAAA;YAClB,IAAI,GAAG,GAAG,CAAC,CAAA;YAEX,OAAO,UAAU,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC;gBAClC,MAAM,CAAC,GAAG,MAAM,CAAC,OAAO,CAAC,OAAO,EAAE,UAAU,CAAC,CAAA;gBAC7C,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC;oBACb,MAAK;gBACP,CAAC;gBAED,MAAM,MAAM,GAAG,UAAU,GAAG,gBAAgB,CAAA;gBAC5C,OAAO,GAAG,GAAG,UAAU,CAAC,MAAM,IAAI,MAAM,IAAI,UAAU,CAAC,GAAG,CAAE,EAAE,CAAC;oBAC7D,GAAG,EAAE,CAAA;gBACP,CAAC;gBAED,kBAAkB;gBAClB,IAAI,YAAY,KAAK,SAAS,IAAI,MAAM,CAAC,UAAU,CAAC,KAAK,YAAY,EAAE,CAAC;oBACtE,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;oBAClB,SAAQ;gBACV,CAAC;gBAED,mEAAmE;gBACnE,qEAAqE;gBACrE,0CAA0C;gBAC1C,IAAI,CAAC,CAAC,CAAC,GAAG,UAAU,GAAG,CAAC,CAAA;gBACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,EAAE,EAAE,CAAC;oBACnC,MAAM,IAAI,GAAG,IAAI,CAAC,CAAC,CAAE,CAAA;oBACrB,MAAM,MAAM,GAAG,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,GAAG,EAAE,IAAI,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC5D,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,MAAM,KAAK,CAAC,CAAC,IAAI,MAAM,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAA;gBACzD,CAAC;gBAED,kCAAkC;gBAClC,MAAM,QAAQ,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,CAAC,CAAA;gBACtC,MAAM,MAAM,GAAG,IAAI,CAAC,MAAM,CAAE,CAAA;gBAC5B,MAAM,MAAM,GAAG,MAAM,GAAG,QAAQ,CAAA;gBAChC,IAAI,MAAM,KAAK,kBAAkB,CAAC,MAAM,EAAE,CAAC;oBACzC,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;oBAClB,SAAQ;gBACV,CAAC;gBACD,IAAI,UAAU,GAAG,IAAI,CAAA;gBACrB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;oBAChC,IAAI,MAAM,CAAC,QAAQ,GAAG,CAAC,CAAC,KAAK,kBAAkB,CAAC,CAAC,CAAC,EAAE,CAAC;wBACnD,UAAU,GAAG,KAAK,CAAA;wBAClB,MAAK;oBACP,CAAC;gBACH,CAAC;gBACD,IAAI,CAAC,UAAU,EAAE,CAAC;oBAChB,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;oBAClB,SAAQ;gBACV,CAAC;gBAED,yBAAyB;gBACzB,MAAM,eAAe,GACnB,iBAAiB,CAAC,MAAM,EAAE,IAAI,CAAC,QAAQ,GAAG,CAAC,CAAE,GAAG,CAAC,EAAE,IAAI,CAAC,QAAQ,CAAE,CAAC;oBACnE,gBAAgB,CAAA;gBAElB,IAAI,eAAe,IAAI,GAAG,EAAE,CAAC;oBAC3B,OAAM;gBACR,CAAC;gBAED,uBAAuB;gBACvB,IAAI,aAAqB,CAAA;gBACzB,IAAI,MAAM,KAAK,CAAC,IAAI,MAAM,KAAK,QAAQ,EAAE,CAAC;oBACxC,aAAa,GAAG,eAAe,GAAG,CAAC,CAAA;gBACrC,CAAC;qBAAM,IAAI,KAAK,EAAE,CAAC;oBACjB,aAAa,GAAG,SAAS,CACvB,MAAM,EACN,eAAe,EACf,IAAI,CAAC,CAAC,CAAE,GAAG,CAAC,EACZ,IAAI,CAAC,CAAC,CAAE,EACR,IAAI,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,CAAC,EACrB,IAAI,CAAC,MAAM,CAAE,CACd,CAAA;gBACH,CAAC;qBAAM,CAAC;oBACN,aAAa,GAAG,iBAAiB,CAC/B,MAAM,EACN,IAAI,CAAC,MAAM,GAAG,CAAC,CAAE,GAAG,CAAC,EACrB,IAAI,CAAC,MAAM,CAAE,CACd,CAAA;gBACH,CAAC;gBAED,IAAI,aAAa,GAAG,KAAK,EAAE,CAAC;oBAC1B,wDAAwD;oBACxD,MAAM,OAAO,GAAG,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,eAAe,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;oBAC7D,MAAM,IAAI,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,UAAU,EAAE,OAAO,CAAC,CAAC,CAAA;oBACjE,QAAQ,CACN,IAAI,EACJ,mBAAmB,CACjB,UAAU,EACV,UAAU,EACV,GAAG,EACH,UAAU,EACV,gBAAgB,CACjB,EACD,eAAe,EACf,aAAa,CACd,CAAA;gBACH,CAAC;gBACD,UAAU,GAAG,CAAC,GAAG,CAAC,CAAA;YACpB,CAAC;YAED,yEAAyE;YACzE,uEAAuE;YACvE,SAAS,GAAG,IAAI,CAAC,GAAG,CAAC,SAAS,GAAG,CAAC,EAAE,qBAAqB,CAAC,CAAA;YAC1D,kBAAkB,CAAC,EAAE,GAAG,CAAC,GAAG,SAAS,CAAC,CAAA;QACxC,CAAC;IACH,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,WAAW,CAAC,OAAgB,EAAE;QAClC,OAAO,IAAI,CAAC,KAAK,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;IACrC,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,OAAgB,EAAE;QACtC,MAAM,EAAE,aAAa,EAAE,QAAQ,EAAE,YAAY,EAAE,GAC7C,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAE9B,MAAM,QAAQ,GAAG,CAAC,aAAa,EAAE,aAAa,IAAI,CAAC,CAAC,GAAG,YAAY,CAAA;QACnE,uEAAuE;QACvE,8DAA8D;QAE9D,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,IAAI,CAAC,QAAQ,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;QACzD,MAAM,KAAK,GAAG,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAe,CAAA;QAE9C,0CAA0C;QAC1C,IAAI,QAAQ,EAAE,CAAC;YACb,IAAI,WAAW,GAAG,CAAC,CAAC,CAAA;YACpB,MAAM,QAAQ,GAAG,QAAQ,CAAC,UAAU,CAAC,CAAC,CAAC,CAAA;YAEvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC7C,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAA;gBACrB,IAAI,CAAC,KAAK,WAAW,GAAG,CAAC,IAAI,IAAI,KAAK,QAAQ,EAAE,CAAC;oBAC/C,MAAK;gBACP,CAAC;gBACD,IAAI,IAAI,KAAK,OAAO,EAAE,CAAC;oBACrB,WAAW,GAAG,CAAC,CAAA;gBACjB,CAAC;YACH,CAAC;YACD,OAAO,KAAK,CAAC,QAAQ,CAAC,CAAC,EAAE,WAAW,GAAG,CAAC,CAAC,CAAA;QAC3C,CAAC;QACD,OAAO,KAAK,CAAA;IACd,CAAC;IAED;;;;;;;;;;;;;;OAcG;IACH,KAAK,CAAC,eAAe,CAAC,OAAgB,EAAE;QACtC,MAAM,EACJ,aAAa,EACb,SAAS,GAAG,CAAC,EACb,YAAY,GACb,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAChC,IAAI,SAAS,IAAI,CAAC,EAAE,CAAC;YACnB,OAAO,EAAE,CAAA;QACX,CAAC;QAED,0EAA0E;QAC1E,uCAAuC;QACvC,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,IAAI,CACpC,CAAC,aAAa,EAAE,aAAa,IAAI,CAAC,CAAC,GAAG,YAAY,EAClD,CAAC,EACD,IAAI,CACL,CAAA;QACD,MAAM,KAAK,GAAG,CAAC,MAAM,KAAK,CAAC,GAAG,CAAC,CAAe,CAAA;QAC9C,OAAO,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,SAAS,CAAC,CAAA;IAC3E,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,OAAgB,EAAE;QAChC,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;QAC9C,OAAO,IAAI,WAAW,EAAE,CAAC,MAAM,CAAC,KAAK,CAAC,CAAA;IACxC,CAAC;IAED,KAAK,CAAC,yBAAyB,CAAC,OAAgB,EAAE;QAChD,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;QAC7C,OAAO,QAAQ,CAAC,WAAW,CAAA;IAC7B,CAAC;IAED,6CAA6C;IAC7C,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,OAAO,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,OAAO,EAAE,IAAI,CAAC,CAAA;IAC5C,CAAC;IAED,gBAAgB;IAChB,KAAK,CAAC,SAAS,CAAC,CAAQ,EAAE,OAAgB,EAAE;QAC1C,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,UAAU,CAAC,IAAI,CACpC,CAAC,CAAC,WAAW,EAAE,EACf,CAAC,CAAC,IAAI,CAAC,aAAa,EACpB,IAAI,CACL,CAAA;QACD,OAAO,eAAe,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;IAChC,CAAC;CACF"}

package/esm/tbi.js

@@ -1,7 +1,7 @@
 import { unzip } from '@gmod/bgzf-filehandle';
 import Chunk from "./chunk.js";
 import IndexFile from "./indexFile.js";
-import { clampChunkEnds, findFirstData, memoizeByRefId, optimizeChunks, parseAuxData, parsePseudoBin, } from "./util.js";
+import { clampChunkEnds, memoizeByRefId, minVirtualOffset, optimizeChunks, parseAuxData, parsePseudoBin, } from "./util.js";
 import { fromBytes } from "./virtualOffset.js";
 const TBI_MAGIC = 21_578_324; // TBI\1
 // TBI is always the fixed depth-5, 14-bit-leaf binning scheme
@@ -40,8 +40,15 @@ export default class TabixIndex extends IndexFile {
         const { refNameToId, refIdToName, coordinateType, format, columnNumbers, metaChar, skipLines, } = parseAuxData(bytes, 8);
         // nameSectionLength is at TBI offset 32; re-read to find where bin data starts
         const nameSectionLength = dataView.getInt32(32, true);
-        // SYNC: ~/src/gmod/bam-js/src/csi.ts _parse — two-pass structure
-        // First pass: record per-refId byte offsets and find firstDataLine
+        // SYNC: ~/src/gmod/bam-js/src/bai.ts _parse — two-pass structure
+        // First pass: record per-refId byte offsets and find firstDataLine.
+        //
+        // Only the linear index is consulted. Its entry for a window is the
+        // smallest virtual offset of any record overlapping that window, so the
+        // minimum over the linear index is already the minimum over the bin chunks
+        // — walking the chunks too only re-derives it. Checked against every .tbi
+        // in test/data: same answer on all 23, and no ref has bins without a
+        // linear index.
         let curr = 36 + nameSectionLength;
         let firstDataLine;
         const offsets = [];
@@ -57,22 +64,12 @@ export default class TabixIndex extends IndexFile {
                 if (bin > maxBinNumber + 1) {
                     throw new Error('tabix index contains too many bins, please use a CSI index');
                 }
-                else if (bin === maxBinNumber + 1) {
-                    curr += 16 * chunkCount;
-                }
-                else {
-                    for (let k = 0; k < chunkCount; k++) {
-                        firstDataLine = findFirstData(firstDataLine, fromBytes(bytes, curr));
-                        curr += 16;
-                    }
-                }
+                curr += 16 * chunkCount;
             }
             const linearCount = dataView.getInt32(curr, true);
             curr += 4;
-            for (let k = 0; k < linearCount; k++) {
-                firstDataLine = findFirstData(firstDataLine, fromBytes(bytes, curr));
-                curr += 8;
-            }
+            firstDataLine = minVirtualOffset(bytes, curr, linearCount, firstDataLine);
+            curr += 8 * linearCount;
         }
         function getIndices(refId) {
             const start = offsets[refId];

package/esm/tbi.js.map

@@ -1 +1 @@
-{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.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,aAAa,EACb,cAAc,EACd,cAAc,EACd,YAAY,EACZ,cAAc,GACf,MAAM,WAAW,CAAA;AAClB,OAAO,EAAE,SAAS,EAAE,MAAM,oBAAoB,CAAA;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,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAAS;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,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,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,YAAY,CAAC,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,mEAAmE;QACnE,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;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE,CAAC;oBACpC,IAAI,IAAI,EAAE,GAAG,UAAU,CAAA;gBACzB,CAAC;qBAAM,CAAC;oBACN,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;wBACpC,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;wBACpE,IAAI,IAAI,EAAE,CAAA;oBACZ,CAAC;gBACH,CAAC;YACH,CAAC;YACD,MAAM,WAAW,GAAG,QAAQ,CAAC,QAAQ,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;YACjD,IAAI,IAAI,CAAC,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,EAAE,EAAE,CAAC;gBACrC,aAAa,GAAG,aAAa,CAAC,aAAa,EAAE,SAAS,CAAC,KAAK,EAAE,IAAI,CAAC,CAAC,CAAA;gBACpE,IAAI,IAAI,CAAC,CAAA;YACX,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,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,cAAc,CAAC,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,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,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,SAAS,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;gBACtC,GAAG,IAAI,CAAC,CAAA;YACV,CAAC;YACD,cAAc,CACZ,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,cAAc,CAAC,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,cAAc,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;IACvC,CAAC;CACF"}
+{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.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,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,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAAS;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,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,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,YAAY,CAAC,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,gBAAgB,CAAC,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,cAAc,CAAC,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,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,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,SAAS,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;gBACtC,GAAG,IAAI,CAAC,CAAA;YACV,CAAC;YACD,cAAc,CACZ,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,cAAc,CAAC,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,cAAc,CAAC,MAAM,EAAE,MAAM,CAAC,CAAA;IACvC,CAAC;CACF"}

package/esm/util.d.ts

@@ -1,8 +1,17 @@
 import Chunk from './chunk.ts';
-import type VirtualOffset from './virtualOffset.ts';
+import VirtualOffset from './virtualOffset.ts';
 export declare function optimizeChunks(chunks: Chunk[], lowest?: VirtualOffset): Chunk[];
 export declare function clampChunkEnds(chunks: Chunk[], extraBoundaries?: number[]): void;
-export declare function findFirstData(currentFdl: VirtualOffset | undefined, virtualOffset: VirtualOffset): VirtualOffset;
+/**
+ * The smallest of `current` and the `count` packed virtual offsets starting at
+ * `offset`, allocating at most one VirtualOffset rather than one per entry.
+ *
+ * The index first pass exists only to find this minimum, and it visits every
+ * linear-index entry in the file to do it — 301k of them on
+ * test/data/failing_tabix.vcf.gz.tbi against 19k bin chunks. Building a
+ * VirtualOffset per entry to compare and discard it is the bulk of that pass.
+ */
+export declare function minVirtualOffset(bytes: Uint8Array, offset: number, count: number, current: VirtualOffset | undefined): VirtualOffset | undefined;
 export declare function parseNameBytes(namesBytes: Uint8Array): {
     refNameToId: Record<string, number>;
     refIdToName: string[];

package/esm/util.js

@@ -1,6 +1,7 @@
 import LRU from '@jbrowse/quick-lru';
 import Chunk from "./chunk.js";
 import { longFromBytesToUnsigned } from "./long.js";
+import VirtualOffset from "./virtualOffset.js";
 // SYNC: ~/src/gmod/bam-js/src/util.ts optimizeChunks
 export function optimizeChunks(chunks, lowest) {
     const n = chunks.length;
@@ -97,10 +98,35 @@ export function clampChunkEnds(chunks, extraBoundaries = []) {
         }
     }
 }
-export function findFirstData(currentFdl, virtualOffset) {
-    return !currentFdl || currentFdl.compareTo(virtualOffset) > 0
-        ? virtualOffset
-        : currentFdl;
+/**
+ * The smallest of `current` and the `count` packed virtual offsets starting at
+ * `offset`, allocating at most one VirtualOffset rather than one per entry.
+ *
+ * The index first pass exists only to find this minimum, and it visits every
+ * linear-index entry in the file to do it — 301k of them on
+ * test/data/failing_tabix.vcf.gz.tbi against 19k bin chunks. Building a
+ * VirtualOffset per entry to compare and discard it is the bulk of that pass.
+ */
+export function minVirtualOffset(bytes, offset, count, current) {
+    let minBlock = current ? current.blockPosition : Infinity;
+    let minData = current ? current.dataPosition : 0;
+    let found = false;
+    for (let i = 0; i < count; i++) {
+        const p = offset + i * 8;
+        const block = bytes[p + 7] * 0x1_00_00_00_00_00 +
+            bytes[p + 6] * 0x1_00_00_00_00 +
+            bytes[p + 5] * 0x1_00_00_00 +
+            bytes[p + 4] * 0x1_00_00 +
+            bytes[p + 3] * 0x1_00 +
+            bytes[p + 2];
+        const data = (bytes[p + 1] << 8) | bytes[p];
+        if (block < minBlock || (block === minBlock && data < minData)) {
+            minBlock = block;
+            minData = data;
+            found = true;
+        }
+    }
+    return found ? new VirtualOffset(minBlock, minData) : current;
 }
 export function parseNameBytes(namesBytes) {
     const decoder = new TextDecoder('utf-8');

package/esm/util.js.map

@@ -1 +1 @@
-{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,oBAAoB,CAAA;AAEpC,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AAInD,qDAAqD;AACrD,MAAM,UAAU,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,KAAK,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,MAAM,UAAU,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,MAAM,UAAU,aAAa,CAC3B,UAAqC,EACrC,aAA4B;IAE5B,OAAO,CAAC,UAAU,IAAI,UAAU,CAAC,SAAS,CAAC,aAAa,CAAC,GAAG,CAAC;QAC3D,CAAC,CAAC,aAAa;QACf,CAAC,CAAC,UAAU,CAAA;AAChB,CAAC;AAED,MAAM,UAAU,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,MAAM,UAAU,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,MAAM,UAAU,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO,EAAE,SAAS,EAAE,uBAAuB,CAAC,KAAK,EAAE,MAAM,CAAC,EAAE,CAAA;AAC9D,CAAC;AAED,0DAA0D;AAC1D,MAAM,UAAU,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,GAAG,GAAG,IAAI,GAAG,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"}
+{"version":3,"file":"util.js","sourceRoot":"","sources":["../src/util.ts"],"names":[],"mappings":"AAAA,OAAO,GAAG,MAAM,oBAAoB,CAAA;AAEpC,OAAO,KAAK,MAAM,YAAY,CAAA;AAC9B,OAAO,EAAE,uBAAuB,EAAE,MAAM,WAAW,CAAA;AACnD,OAAO,aAAa,MAAM,oBAAoB,CAAA;AAE9C,qDAAqD;AACrD,MAAM,UAAU,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,KAAK,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,MAAM,UAAU,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,MAAM,UAAU,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,aAAa,CAAC,QAAQ,EAAE,OAAO,CAAC,CAAC,CAAC,CAAC,OAAO,CAAA;AAC/D,CAAC;AAED,MAAM,UAAU,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,MAAM,UAAU,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,MAAM,UAAU,cAAc,CAAC,KAAiB,EAAE,MAAc;IAC9D,OAAO,EAAE,SAAS,EAAE,uBAAuB,CAAC,KAAK,EAAE,MAAM,CAAC,EAAE,CAAA;AAC9D,CAAC;AAED,0DAA0D;AAC1D,MAAM,UAAU,cAAc,CAC5B,UAA4C,EAC5C,OAAO,GAAG,CAAC;IAEX,MAAM,GAAG,GAAG,IAAI,GAAG,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/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "3.5.1",
+  "version": "3.5.3",
   "packageManager": "pnpm@11.15.1",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "type": "module",
@@ -37,12 +37,11 @@
     "preversion": "pnpm lint && pnpm test --run && pnpm build",
     "postversion": "git push --follow-tags",
     "build": "pnpm build:esm && pnpm build:es5",
+    "differential": "vite-node scripts/differential.mjs",
     "benchonly": "vitest bench",
     "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
-    "build:docs": "typedoc && node scripts/build-docs.mjs",
     "postbuild": "webpack",
-    "prepublishOnly": "pnpm lint && pnpm test run && pnpm build",
-    "version": "standard-changelog && git add CHANGELOG.md"
+    "version": "git-cliff --tag v$npm_package_version --unreleased --prepend CHANGELOG.md && git add CHANGELOG.md"
   },
   "keywords": [
     "bionode",
@@ -62,11 +61,9 @@
     "eslint": "^10.7.0",
     "eslint-plugin-import-x": "^4.17.1",
     "eslint-plugin-unicorn": "^72.0.0",
+    "git-cliff": "^2.13.1",
     "prettier": "^3.9.6",
     "rimraf": "^6.1.3",
-    "standard-changelog": "^8.1.0",
-    "typedoc": "^0.28.20",
-    "typedoc-plugin-markdown": "^4.12.0",
     "typescript": "^6.0.0",
     "typescript-eslint": "^8.65.0",
     "vitest": "^4.1.10",

package/src/csi.ts

@@ -4,8 +4,8 @@ import Chunk from './chunk.ts'
 import IndexFile from './indexFile.ts'
 import {
   clampChunkEnds,
-  findFirstData,
   memoizeByRefId,
+  minVirtualOffset,
   optimizeChunks,
   parseAuxData,
   parsePseudoBin,
@@ -90,7 +90,7 @@ export default class CSI extends IndexFile {
         if (bin > maxBinNumber) {
           curr += 28 + 16 // skip pseudo-bin (loffset + nchunk + 2 chunks)
         } else {
-          firstDataLine = findFirstData(firstDataLine, fromBytes(bytes, curr))
+          firstDataLine = minVirtualOffset(bytes, curr, 1, firstDataLine)
           curr += 8 // loffset
           const chunkCount = dataView.getInt32(curr, true)
           curr += 4 + 16 * chunkCount

package/src/tabixIndexedFile.ts

@@ -1,6 +1,5 @@
 import AbortablePromiseCache from '@gmod/abortable-promise-cache'
 import { unzip, unzipChunkSlice } from '@gmod/bgzf-filehandle'
-import LRU from '@jbrowse/quick-lru'
 import { LocalFile, RemoteFile } from 'generic-filehandle2'
 
 import CSI from './csi.ts'
@@ -22,6 +21,113 @@ const SEMICOLON = 59
 // going much above it buys nothing on the transport that matters.
 const MAX_READ_AHEAD_CHUNKS = 6
 
+// SYNC: ~/src/gmod/bam-js/src/bamFile.ts DEFAULT_MAX_CACHE_BYTES
+//
+// We fetch compressed and cache decompressed, and an entry is a whole chunk, so
+// entry count says nothing about memory. How little is easy to underestimate:
+// a dense VCF (test/data/1kg.chr1.subset.vcf.gz — 213MB over 600kb of chr1)
+// has single index bins of 17MB compressed, 120MB decompressed. Panning it
+// under the old 80-entry cache peaked at 2GB RSS.
+const DEFAULT_CHUNK_CACHE_BYTES = 100 * 2 ** 20
+
+// The entry type AbortablePromiseCache stores in its backing cache. Not exported
+// by the package, so it is recovered from the constructor signature rather than
+// restated (and left to drift) here.
+type CacheEntry = NonNullable<
+  ReturnType<
+    ConstructorParameters<
+      typeof AbortablePromiseCache<Chunk, ReadChunk>
+    >[0]['cache']['get']
+  >
+>
+
+interface CachedChunk {
+  entry: CacheEntry
+  /** 0 until the read settles and the decompressed size is known */
+  bytes: number
+}
+
+/**
+ * Backing store for the chunk cache, bounded by the decompressed size of the
+ * chunks it holds rather than by entry count.
+ *
+ * A chunk's size is only known once its read settles, so `set` records the
+ * entry immediately and charges it to the budget later. Unsettled entries are
+ * therefore free, which is what we want: they are reads a query is waiting on.
+ */
+class ByteBoundedChunkCache {
+  private entries = new Map<string, CachedChunk>()
+  private bytes = 0
+  private maxBytes: number
+
+  constructor(maxBytes: number) {
+    this.maxBytes = maxBytes
+  }
+
+  get byteSize() {
+    return this.bytes
+  }
+
+  get size() {
+    return this.entries.size
+  }
+
+  has(key: string) {
+    return this.entries.has(key)
+  }
+
+  get(key: string) {
+    const cached = this.entries.get(key)
+    if (cached) {
+      // re-insert so Map iteration order stays least-recently-used first
+      this.entries.delete(key)
+      this.entries.set(key, cached)
+    }
+    return cached?.entry
+  }
+
+  set(key: string, entry: CacheEntry) {
+    this.delete(key)
+    const cached = { entry, bytes: 0 }
+    this.entries.set(key, cached)
+    void entry.promise
+      .then(chunk => {
+        // a later set() may have replaced this key while the read was in
+        // flight; charging these bytes to it would then double-count
+        if (this.entries.get(key) === cached) {
+          cached.bytes = chunk.buffer.byteLength
+          this.bytes += cached.bytes
+          this.evict()
+        }
+      })
+      .catch(() => {
+        // a failed or aborted read caches nothing and costs nothing
+      })
+  }
+
+  delete(key: string) {
+    const cached = this.entries.get(key)
+    if (cached) {
+      this.entries.delete(key)
+      this.bytes -= cached.bytes
+    }
+  }
+
+  keys() {
+    return this.entries.keys()
+  }
+
+  // Evict from the least-recently-used end. The size > 1 guard means a single
+  // chunk larger than the whole budget is still kept: the caller needs it for
+  // the query in flight, and dropping it would only force a re-decompress.
+  private evict() {
+    const lru = this.entries.keys()
+    while (this.bytes > this.maxBytes && this.entries.size > 1) {
+      this.delete(lru.next().value!)
+    }
+  }
+}
+
 type GetLinesCallback = (
   line: string,
   fileOffset: number,
@@ -214,7 +320,7 @@ export default class TabixIndexedFile {
     csiPath,
     csiUrl,
     csiFilehandle,
-    chunkCacheSize = 5 * 2 ** 20,
+    chunkCacheSize = DEFAULT_CHUNK_CACHE_BYTES,
   }: {
     path?: string
     filehandle?: GenericFilehandle
@@ -225,6 +331,7 @@ export default class TabixIndexedFile {
     csiPath?: string
     csiUrl?: string
     csiFilehandle?: GenericFilehandle
+    /** budget for the decompressed chunk cache, in bytes */
     chunkCacheSize?: number
   }) {
     this.filehandle = resolveFilehandle(filehandle, path, url)
@@ -240,7 +347,7 @@ export default class TabixIndexedFile {
     })
 
     this.chunkCache = new AbortablePromiseCache<Chunk, ReadChunk>({
-      cache: new LRU({ maxSize: Math.floor(chunkCacheSize / (1 << 16)) }),
+      cache: new ByteBoundedChunkCache(chunkCacheSize),
       fill: (args: Chunk, signal?: AbortSignal) =>
         this.readChunk(args, { signal }),
     })
@@ -511,6 +618,42 @@ export default class TabixIndexedFile {
     return bytes
   }
 
+  /**
+   * The leading lines the index says to skip — `tabix -S N` — which is where a
+   * file whose header row is not commented keeps it. Empty when the index
+   * records no skipped lines.
+   *
+   * Deliberately not part of `getHeader`. htslib draws the same distinction:
+   * its indexer treats a line as non-data when `lineno <= line_skip` OR it
+   * begins with the meta character (tbx.c), while `tabix -H` prints only the
+   * leading meta-character lines and never consults line_skip (tabix.c).
+   * `getHeader` mirrors `-H`, so a bare header row is absent from it, and
+   * callers that need one were left re-reading the file themselves — guessing
+   * at a read size, and unable to tell a headerless file from an uncommented
+   * one. PLINK `.ld`, bedGraph and BED deflines are all routinely written this
+   * way.
+   */
+  async getSkippedLines(opts: Options = {}) {
+    const {
+      firstDataLine,
+      skipLines = 0,
+      maxBlockSize,
+    } = await this.getMetadata(opts)
+    if (skipLines <= 0) {
+      return []
+    }
+
+    // same read getHeaderBuffer makes, and the same caveat: a header spanning
+    // more blocks than this is not covered
+    const buf = await this.filehandle.read(
+      (firstDataLine?.blockPosition ?? 0) + maxBlockSize,
+      0,
+      opts,
+    )
+    const bytes = (await unzip(buf)) as Uint8Array
+    return new TextDecoder().decode(bytes).split(/\r?\n/).slice(0, skipLines)
+  }
+
   async getHeader(opts: Options = {}) {
     const bytes = await this.getHeaderBuffer(opts)
     return new TextDecoder().decode(bytes)