@gmod/tabix 1.5.1 → 1.5.4

package/esm/tbi.js

@@ -1,33 +1,9 @@
-"use strict";
-var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[k]; } });
-}) : (function(o, m, k, k2) {
-    if (k2 === undefined) k2 = k;
-    o[k2] = m[k];
-}));
-var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
-    Object.defineProperty(o, "default", { enumerable: true, value: v });
-}) : function(o, v) {
-    o["default"] = v;
-});
-var __importStar = (this && this.__importStar) || function (mod) {
-    if (mod && mod.__esModule) return mod;
-    var result = {};
-    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
-    __setModuleDefault(result, mod);
-    return result;
-};
-var __importDefault = (this && this.__importDefault) || function (mod) {
-    return (mod && mod.__esModule) ? mod : { "default": mod };
-};
-Object.defineProperty(exports, "__esModule", { value: true });
-const long_1 = __importDefault(require("long"));
-const virtualOffset_1 = __importStar(require("./virtualOffset"));
-const chunk_1 = __importDefault(require("./chunk"));
-const bgzf_filehandle_1 = require("@gmod/bgzf-filehandle");
-const util_1 = require("./util");
-const indexFile_1 = __importDefault(require("./indexFile"));
+import Long from 'long';
+import VirtualOffset, { fromBytes } from './virtualOffset';
+import Chunk from './chunk';
+import { unzip } from '@gmod/bgzf-filehandle';
+import { longToNumber, optimizeChunks, checkAbortSignal } from './util';
+import IndexFile from './indexFile';
 const TBI_MAGIC = 21578324; // TBI\1
 const TAD_LIDX_SHIFT = 14;
 /**
@@ -45,7 +21,7 @@ function reg2bins(beg, end) {
         [4681 + (beg >> 14), 4681 + (end >> 14)],
     ];
 }
-class TabixIndex extends indexFile_1.default {
+export default class TabixIndex extends IndexFile {
     async lineCount(refName, opts = {}) {
         const indexData = await this.parse(opts);
         if (!indexData) {
@@ -65,8 +41,8 @@ class TabixIndex extends indexFile_1.default {
     // memoize
     // fetch and parse the index
     async _parse(opts = {}) {
-        const bytes = await (0, bgzf_filehandle_1.unzip)((await this.filehandle.readFile(opts)));
-        (0, util_1.checkAbortSignal)(opts.signal);
+        const bytes = await unzip((await this.filehandle.readFile(opts)));
+        checkAbortSignal(opts.signal);
         // check TBI magic numbers
         if (bytes.readUInt32LE(0) !== TBI_MAGIC /* "TBI\1" */) {
             throw new Error('Not a TBI file');
@@ -127,11 +103,11 @@ class TabixIndex extends indexFile_1.default {
                     currOffset += 4;
                     const chunks = new Array(chunkCount);
                     for (let k = 0; k < chunkCount; k += 1) {
-                        const u = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
-                        const v = (0, virtualOffset_1.fromBytes)(bytes, currOffset + 8);
+                        const u = fromBytes(bytes, currOffset);
+                        const v = fromBytes(bytes, currOffset + 8);
                         currOffset += 16;
                         firstDataLine = this._findFirstData(firstDataLine, u);
-                        chunks[k] = new chunk_1.default(u, v, bin);
+                        chunks[k] = new Chunk(u, v, bin);
                     }
                     binIndex[bin] = chunks;
                 }
@@ -141,7 +117,7 @@ class TabixIndex extends indexFile_1.default {
             currOffset += 4;
             const linearIndex = new Array(linearCount);
             for (let k = 0; k < linearCount; k += 1) {
-                linearIndex[k] = (0, virtualOffset_1.fromBytes)(bytes, currOffset);
+                linearIndex[k] = fromBytes(bytes, currOffset);
                 currOffset += 8;
                 firstDataLine = this._findFirstData(firstDataLine, linearIndex[k]);
             }
@@ -163,7 +139,7 @@ class TabixIndex extends indexFile_1.default {
         };
     }
     parsePseudoBin(bytes, offset) {
-        const lineCount = (0, util_1.longToNumber)(long_1.default.fromBytesLE(bytes.slice(offset + 16, offset + 24), true));
+        const lineCount = longToNumber(Long.fromBytesLE(bytes.slice(offset + 16, offset + 24), true));
         return { lineCount };
     }
     _parseNameBytes(namesBytes) {
@@ -202,7 +178,7 @@ class TabixIndex extends indexFile_1.default {
             ? ba.linearIndex[min >> TAD_LIDX_SHIFT >= ba.linearIndex.length
                 ? ba.linearIndex.length - 1
                 : min >> TAD_LIDX_SHIFT]
-            : new virtualOffset_1.default(0, 0);
+            : new VirtualOffset(0, 0);
         if (!minOffset) {
             console.warn('querying outside of possible tabix range');
         }
@@ -215,7 +191,7 @@ class TabixIndex extends indexFile_1.default {
                 if (ba.binIndex[bin]) {
                     const binChunks = ba.binIndex[bin];
                     for (let c = 0; c < binChunks.length; ++c) {
-                        chunks.push(new chunk_1.default(binChunks[c].minv, binChunks[c].maxv, bin));
+                        chunks.push(new Chunk(binChunks[c].minv, binChunks[c].maxv, bin));
                     }
                 }
             }
@@ -234,7 +210,7 @@ class TabixIndex extends indexFile_1.default {
                 }
             }
         }
-        return (0, util_1.optimizeChunks)(chunks, lowest);
+        return optimizeChunks(chunks, lowest);
     }
 }
-exports.default = TabixIndex;
+//# sourceMappingURL=tbi.js.map

package/esm/tbi.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"tbi.js","sourceRoot":"","sources":["../src/tbi.ts"],"names":[],"mappings":"AAAA,OAAO,IAAI,MAAM,MAAM,CAAA;AACvB,OAAO,aAAa,EAAE,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAC1D,OAAO,KAAK,MAAM,SAAS,CAAA;AAC3B,OAAO,EAAE,KAAK,EAAE,MAAM,uBAAuB,CAAA;AAC7C,OAAO,EAAE,YAAY,EAAE,cAAc,EAAE,gBAAgB,EAAE,MAAM,QAAQ,CAAA;AACvE,OAAO,SAAsB,MAAM,aAAa,CAAA;AAEhD,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AACnC,MAAM,cAAc,GAAG,EAAE,CAAA;AAEzB;;GAEG;AACH,SAAS,QAAQ,CAAC,GAAW,EAAE,GAAW;IACxC,GAAG,IAAI,CAAC,CAAA,CAAC,8BAA8B;IACvC,GAAG,IAAI,CAAC,CAAA;IACR,OAAO;QACL,CAAC,CAAC,EAAE,CAAC,CAAC;QACN,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QAClC,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,EAAE,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACpC,CAAC,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,GAAG,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;QACtC,CAAC,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,EAAE,IAAI,GAAG,CAAC,GAAG,IAAI,EAAE,CAAC,CAAC;KACzC,CAAA;AACH,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAAS;IAC/C,KAAK,CAAC,SAAS,CAAC,OAAe,EAAE,OAAgB,EAAE;QACjD,MAAM,SAAS,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACxC,IAAI,CAAC,SAAS,EAAE;YACd,OAAO,CAAC,CAAC,CAAA;SACV;QACD,MAAM,KAAK,GAAG,SAAS,CAAC,WAAW,CAAC,OAAO,CAAC,CAAA;QAC5C,MAAM,GAAG,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QACpC,IAAI,CAAC,GAAG,EAAE;YACR,OAAO,CAAC,CAAC,CAAA;SACV;QACD,MAAM,EAAE,KAAK,EAAE,GAAG,SAAS,CAAC,OAAO,CAAC,KAAK,CAAC,CAAA;QAC1C,IAAI,KAAK,EAAE;YACT,OAAO,KAAK,CAAC,SAAS,CAAA;SACvB;QACD,OAAO,CAAC,CAAC,CAAA;IACX,CAAC;IAED,UAAU;IACV,4BAA4B;IAC5B,KAAK,CAAC,MAAM,CAAC,OAAgB,EAAE;QAC7B,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAW,CAAC,CAAA;QAC3E,gBAAgB,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QAE7B,0BAA0B;QAC1B,IAAI,KAAK,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,CAAC,aAAa,EAAE;YACrD,MAAM,IAAI,KAAK,CAAC,gBAAgB,CAAC,CAAA;YACjC,oDAAoD;SACrD;QAED,6CAA6C;QAC7C,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACrC,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QACxC,MAAM,cAAc,GAClB,WAAW,GAAG,OAAO,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAA;QACnE,MAAM,UAAU,GAA8B;YAC5C,CAAC,EAAE,SAAS;YACZ,CAAC,EAAE,KAAK;YACR,CAAC,EAAE,KAAK;SACT,CAAA;QACD,MAAM,MAAM,GAAG,UAAU,CAAC,WAAW,GAAG,GAAG,CAAC,CAAA;QAC5C,IAAI,CAAC,MAAM,EAAE;YACX,MAAM,IAAI,KAAK,CAAC,qCAAqC,WAAW,EAAE,CAAC,CAAA;SACpE;QACD,MAAM,aAAa,GAAG;YACpB,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;YAC1B,KAAK,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;YAC5B,GAAG,EAAE,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC;SAC3B,CAAA;QACD,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QACvC,MAAM,KAAK,GAAG,CAAC,CAAA;QACf,MAAM,YAAY,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,CAAA;QACvD,MAAM,YAAY,GAAG,CAAC,IAAI,CAAC,EAAE,GAAG,KAAK,GAAG,CAAC,CAAC,CAAA;QAC1C,MAAM,QAAQ,GAAG,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,YAAY,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,IAAI,CAAA;QAClE,MAAM,SAAS,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QAEvC,2BAA2B;QAC3B,MAAM,iBAAiB,GAAG,KAAK,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;QAC/C,MAAM,EAAE,WAAW,EAAE,WAAW,EAAE,GAAG,IAAI,CAAC,eAAe,CACvD,KAAK,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,GAAG,iBAAiB,CAAC,CACxC,CAAA;QAED,+CAA+C;QAC/C,IAAI,UAAU,GAAG,EAAE,GAAG,iBAAiB,CAAA;QACvC,IAAI,aAAwC,CAAA;QAC5C,MAAM,OAAO,GAAG,IAAI,KAAK,CAAC,QAAQ,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,EAAE;YACnD,oBAAoB;YACpB,MAAM,QAAQ,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YAC9C,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,QAAQ,GAA+B,EAAE,CAAA;YAC/C,IAAI,KAAK,CAAA;YACT,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE;gBACpC,MAAM,GAAG,GAAG,KAAK,CAAC,YAAY,CAAC,UAAU,CAAC,CAAA;gBAC1C,UAAU,IAAI,CAAC,CAAA;gBACf,IAAI,GAAG,GAAG,YAAY,GAAG,CAAC,EAAE;oBAC1B,MAAM,IAAI,KAAK,CACb,4DAA4D,CAC7D,CAAA;iBACF;qBAAM,IAAI,GAAG,KAAK,YAAY,GAAG,CAAC,EAAE;oBACnC,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;oBAChD,UAAU,IAAI,CAAC,CAAA;oBACf,IAAI,UAAU,KAAK,CAAC,EAAE;wBACpB,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;qBAC/C;oBACD,UAAU,IAAI,EAAE,GAAG,UAAU,CAAA;iBAC9B;qBAAM;oBACL,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;oBAChD,UAAU,IAAI,CAAC,CAAA;oBACf,MAAM,MAAM,GAAG,IAAI,KAAK,CAAC,UAAU,CAAC,CAAA;oBACpC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,IAAI,CAAC,EAAE;wBACtC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;wBACtC,MAAM,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,GAAG,CAAC,CAAC,CAAA;wBAC1C,UAAU,IAAI,EAAE,CAAA;wBAChB,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,CAAC,CAAC,CAAA;wBACrD,MAAM,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAA;qBACjC;oBACD,QAAQ,CAAC,GAAG,CAAC,GAAG,MAAM,CAAA;iBACvB;aACF;YAED,mBAAmB;YACnB,MAAM,WAAW,GAAG,KAAK,CAAC,WAAW,CAAC,UAAU,CAAC,CAAA;YACjD,UAAU,IAAI,CAAC,CAAA;YACf,MAAM,WAAW,GAAG,IAAI,KAAK,CAAC,WAAW,CAAC,CAAA;YAC1C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE;gBACvC,WAAW,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,KAAK,EAAE,UAAU,CAAC,CAAA;gBAC7C,UAAU,IAAI,CAAC,CAAA;gBACf,aAAa,GAAG,IAAI,CAAC,cAAc,CAAC,aAAa,EAAE,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;aACnE;YACD,OAAO,EAAE,QAAQ,EAAE,WAAW,EAAE,KAA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package/esm/util.js

@@ -1,14 +1,10 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.optimizeChunks = exports.canMergeBlocks = exports.abortBreakPoint = exports.checkAbortSignal = exports.longToNumber = void 0;
-function longToNumber(long) {
+export function longToNumber(long) {
     if (long.greaterThan(Number.MAX_SAFE_INTEGER) ||
         long.lessThan(Number.MIN_SAFE_INTEGER)) {
         throw new Error('integer overflow');
     }
     return long.toNumber();
 }
-exports.longToNumber = longToNumber;
 class AbortError extends Error {
 }
 /**
@@ -22,7 +18,7 @@ class AbortError extends Error {
  * @param {AbortSignal} [signal] an AbortSignal, or anything with an `aborted` attribute
  * @returns nothing
  */
-function checkAbortSignal(signal) {
+export function checkAbortSignal(signal) {
     if (!signal) {
         return;
     }
@@ -39,24 +35,21 @@ function checkAbortSignal(signal) {
         }
     }
 }
-exports.checkAbortSignal = checkAbortSignal;
 /**
  * Skips to the next tick, then runs `checkAbortSignal`.
  * Await this to inside an otherwise synchronous loop to
  * provide a place to break when an abort signal is received.
  * @param {AbortSignal} signal
  */
-async function abortBreakPoint(signal) {
+export async function abortBreakPoint(signal) {
     await Promise.resolve();
     checkAbortSignal(signal);
 }
-exports.abortBreakPoint = abortBreakPoint;
-function canMergeBlocks(chunk1, chunk2) {
+export function canMergeBlocks(chunk1, chunk2) {
     return (chunk2.minv.blockPosition - chunk1.maxv.blockPosition < 65000 &&
         chunk2.maxv.blockPosition - chunk1.minv.blockPosition < 5000000);
 }
-exports.canMergeBlocks = canMergeBlocks;
-function optimizeChunks(chunks, lowest) {
+export function optimizeChunks(chunks, lowest) {
     const mergedChunks = [];
     let lastChunk = null;
     if (chunks.length === 0) {
@@ -95,4 +88,4 @@ function optimizeChunks(chunks, lowest) {
     });
     return mergedChunks;
 }
-exports.optimizeChunks = optimizeChunks;
+//# sourceMappingURL=util.js.map

package/esm/util.js.map

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package/esm/virtualOffset.js

@@ -1,7 +1,4 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.fromBytes = void 0;
-class VirtualOffset {
+export default class VirtualOffset {
     constructor(blockPosition, dataPosition) {
         this.blockPosition = blockPosition; // < offset of the compressed data block
         this.dataPosition = dataPosition; // < offset into the uncompressed data
@@ -26,8 +23,7 @@ class VirtualOffset {
         return min;
     }
 }
-exports.default = VirtualOffset;
-function fromBytes(bytes, offset = 0, bigendian = false) {
+export function fromBytes(bytes, offset = 0, bigendian = false) {
     if (bigendian) {
         throw new Error('big-endian virtual file offsets not implemented');
     }
@@ -38,4 +34,4 @@ function fromBytes(bytes, offset = 0, bigendian = false) {
         bytes[offset + 3] * 0x100 +
         bytes[offset + 2], (bytes[offset + 1] << 8) | bytes[offset]);
 }
-exports.fromBytes = fromBytes;
+//# sourceMappingURL=virtualOffset.js.map

package/esm/virtualOffset.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/tabix",
-  "version": "1.5.1",
+  "version": "1.5.4",
   "description": "Read Tabix-indexed files, supports both .tbi and .csi indexes",
   "license": "MIT",
   "repository": "GMOD/tabix-js",
@@ -16,7 +16,8 @@
   },
   "files": [
     "dist",
-    "esm"
+    "esm",
+    "src"
   ],
   "scripts": {
     "test": "jest",
@@ -41,28 +42,28 @@
     "@gmod/bgzf-filehandle": "^1.3.3",
     "abortable-promise-cache": "^1.4.1",
     "es6-promisify": "^6.0.1",
-    "generic-filehandle": "^2.0.1",
+    "generic-filehandle": "^3.0.0",
     "long": "^4.0.0",
     "quick-lru": "^4.0.0"
   },
   "devDependencies": {
-    "@types/jest": "^27.0.3",
+    "@types/jest": "^28.1.6",
     "@types/long": "^4.0.0",
-    "@types/node": "^12.7.11",
+    "@types/node": "^18.0.6",
     "@types/quick-lru": "2.0.0",
-    "@typescript-eslint/eslint-plugin": "^5.7.0",
-    "@typescript-eslint/parser": "^5.7.0",
-    "documentation": "^9.1.1",
-    "eslint": "^7.0.0",
+    "@typescript-eslint/eslint-plugin": "^5.30.7",
+    "@typescript-eslint/parser": "^5.30.7",
+    "eslint": "^8.20.0",
     "eslint-config-prettier": "^8.3.0",
     "eslint-plugin-import": "^2.25.3",
-    "eslint-plugin-prettier": "^4.0.0",
-    "jest": "^27.4.3",
-    "prettier": "^2.5.1",
-    "rimraf": "^2.6.2",
-    "standard-changelog": "^1.0.0",
-    "ts-jest": "^27.0.7",
-    "typescript": "^4.5.2"
+    "eslint-plugin-prettier": "^4.2.1",
+    "jest": "^28.1.3",
+    "jest-environment-jsdom": "^28.1.3",
+    "prettier": "^2.7.1",
+    "rimraf": "^3.0.2",
+    "standard-changelog": "^2.0.27",
+    "ts-jest": "^28.0.7",
+    "typescript": "^4.7.4"
   },
   "publishConfig": {
     "access": "public"

package/src/chunk.ts

@@ -0,0 +1,52 @@
+import VirtualOffset from './virtualOffset'
+
+// little class representing a chunk in the index
+export default class Chunk {
+  public minv: VirtualOffset
+  public maxv: VirtualOffset
+  public bin: number
+  public _fetchedSize?: number
+
+  /**
+   * @param {VirtualOffset} minv
+   * @param {VirtualOffset} maxv
+   * @param {number} bin
+   * @param {number} [fetchedSize]
+   */
+  constructor(
+    minv: VirtualOffset,
+    maxv: VirtualOffset,
+    bin: number,
+    fetchedSize = undefined,
+  ) {
+    this.minv = minv
+    this.maxv = maxv
+    this.bin = bin
+    this._fetchedSize = fetchedSize
+  }
+
+  toUniqueString() {
+    return `${this.minv}..${this.maxv} (bin ${
+      this.bin
+    }, fetchedSize ${this.fetchedSize()})`
+  }
+
+  toString() {
+    return this.toUniqueString()
+  }
+
+  compareTo(b: Chunk) {
+    return (
+      this.minv.compareTo(b.minv) ||
+      this.maxv.compareTo(b.maxv) ||
+      this.bin - b.bin
+    )
+  }
+
+  fetchedSize() {
+    if (this._fetchedSize !== undefined) {
+      return this._fetchedSize
+    }
+    return this.maxv.blockPosition + (1 << 16) - this.minv.blockPosition
+  }
+}

package/src/csi.ts

@@ -0,0 +1,277 @@
+import Long from 'long'
+import { unzip } from '@gmod/bgzf-filehandle'
+
+import VirtualOffset, { fromBytes } from './virtualOffset'
+import Chunk from './chunk'
+import { longToNumber, optimizeChunks } from './util'
+
+import IndexFile, { Options } from './indexFile'
+
+const CSI1_MAGIC = 21582659 // CSI\1
+const CSI2_MAGIC = 38359875 // CSI\2
+
+function lshift(num: number, bits: number) {
+  return num * 2 ** bits
+}
+function rshift(num: number, bits: number) {
+  return Math.floor(num / 2 ** bits)
+}
+
+export default class CSI extends IndexFile {
+  private maxBinNumber: number
+  private depth: number
+  private minShift: number
+  constructor(args: any) {
+    super(args)
+    this.maxBinNumber = 0
+    this.depth = 0
+    this.minShift = 0
+  }
+  async lineCount(refName: string, opts: Options = {}): Promise<number> {
+    const indexData = await this.parse(opts)
+    if (!indexData) {
+      return -1
+    }
+    const refId = indexData.refNameToId[refName]
+    const idx = indexData.indices[refId]
+    if (!idx) {
+      return -1
+    }
+    const { stats } = indexData.indices[refId]
+    if (stats) {
+      return stats.lineCount
+    }
+    return -1
+  }
+  async indexCov() {
+    throw new Error('CSI indexes do not support indexcov')
+    return []
+  }
+
+  parseAuxData(bytes: Buffer, offset: number, auxLength: number) {
+    if (auxLength < 30) {
+      return {
+        refIdToName: [],
+        refNameToId: {},
+      }
+    }
+
+    const formatFlags = bytes.readInt32LE(offset)
+    const coordinateType =
+      formatFlags & 0x10000 ? 'zero-based-half-open' : '1-based-closed'
+    const format = (
+      { 0: 'generic', 1: 'SAM', 2: 'VCF' } as {
+        [key: number]: string
+      }
+    )[formatFlags & 0xf]
+    if (!format) {
+      throw new Error(`invalid Tabix preset format flags ${formatFlags}`)
+    }
+    const columnNumbers = {
+      ref: bytes.readInt32LE(offset + 4),
+      start: bytes.readInt32LE(offset + 8),
+      end: bytes.readInt32LE(offset + 12),
+    }
+    const metaValue = bytes.readInt32LE(offset + 16)
+    const metaChar = metaValue ? String.fromCharCode(metaValue) : ''
+    const skipLines = bytes.readInt32LE(offset + 20)
+    const nameSectionLength = bytes.readInt32LE(offset + 24)
+
+    const { refIdToName, refNameToId } = this._parseNameBytes(
+      bytes.slice(offset + 28, offset + 28 + nameSectionLength),
+    )
+
+    return {
+      refIdToName,
+      refNameToId,
+      skipLines,
+      metaChar,
+      columnNumbers,
+      format,
+      coordinateType,
+    }
+  }
+
+  _parseNameBytes(namesBytes: Buffer) {
+    let currRefId = 0
+    let currNameStart = 0
+    const refIdToName = []
+    const refNameToId: { [key: string]: number } = {}
+    for (let i = 0; i < namesBytes.length; i += 1) {
+      if (!namesBytes[i]) {
+        if (currNameStart < i) {
+          let refName = namesBytes.toString('utf8', currNameStart, i)
+          refName = this.renameRefSeq(refName)
+          refIdToName[currRefId] = refName
+          refNameToId[refName] = currRefId
+        }
+        currNameStart = i + 1
+        currRefId += 1
+      }
+    }
+    return { refNameToId, refIdToName }
+  }
+
+  // fetch and parse the index
+
+  async _parse(opts: Options = {}) {
+    const bytes = await unzip((await this.filehandle.readFile(opts)) as Buffer)
+
+    // check TBI magic numbers
+    let csiVersion
+    if (bytes.readUInt32LE(0) === CSI1_MAGIC) {
+      csiVersion = 1
+    } else if (bytes.readUInt32LE(0) === CSI2_MAGIC) {
+      csiVersion = 2
+    } else {
+      throw new Error('Not a CSI file')
+      // TODO: do we need to support big-endian CSI files?
+    }
+
+    this.minShift = bytes.readInt32LE(4)
+    this.depth = bytes.readInt32LE(8)
+    this.maxBinNumber = ((1 << ((this.depth + 1) * 3)) - 1) / 7
+    const maxRefLength = 2 ** (this.minShift + this.depth * 3)
+
+    const auxLength = bytes.readInt32LE(12)
+    let aux: {
+      refIdToName: string[]
+      refNameToId: { [key: string]: number }
+    } = {
+      refIdToName: [],
+      refNameToId: {},
+    }
+    if (auxLength) {
+      aux = this.parseAuxData(bytes, 16, auxLength)
+    }
+    const refCount = bytes.readInt32LE(16 + auxLength)
+
+    // read the indexes for each reference sequence
+    let firstDataLine: VirtualOffset | undefined
+    let currOffset = 16 + auxLength + 4
+    const indices = new Array(refCount).fill(0).map(() => {
+      // the binning index
+      const binCount = bytes.readInt32LE(currOffset)
+      currOffset += 4
+      const binIndex: { [key: string]: Chunk[] } = {}
+      let stats // < provided by parsing a pseudo-bin, if present
+      for (let j = 0; j < binCount; j += 1) {
+        const bin = bytes.readUInt32LE(currOffset)
+        if (bin > this.maxBinNumber) {
+          // this is a fake bin that actually has stats information
+          // about the reference sequence in it
+          stats = this.parsePseudoBin(bytes, currOffset + 4)
+          currOffset += 4 + 8 + 4 + 16 + 16
+        } else {
+          const loffset = fromBytes(bytes, currOffset + 4)
+          firstDataLine = this._findFirstData(firstDataLine, loffset)
+          const chunkCount = bytes.readInt32LE(currOffset + 12)
+          currOffset += 16
+          const chunks = new Array(chunkCount)
+          for (let k = 0; k < chunkCount; k += 1) {
+            const u = fromBytes(bytes, currOffset)
+            const v = fromBytes(bytes, currOffset + 8)
+            currOffset += 16
+            // this._findFirstData(data, u)
+            chunks[k] = new Chunk(u, v, bin)
+          }
+          binIndex[bin] = chunks
+        }
+      }
+
+      return { binIndex, stats }
+    })
+
+    return {
+      ...aux,
+      csi: true,
+      refCount,
+      maxBlockSize: 1 << 16,
+      firstDataLine,
+      csiVersion,
+      indices,
+      depth: this.depth,
+      maxBinNumber: this.maxBinNumber,
+      maxRefLength,
+    }
+  }
+
+  parsePseudoBin(bytes: Buffer, offset: number) {
+    const lineCount = longToNumber(
+      Long.fromBytesLE(
+        Array.prototype.slice.call(bytes, offset + 28, offset + 36),
+        true,
+      ),
+    )
+    return { lineCount }
+  }
+
+  async blocksForRange(
+    refName: string,
+    min: number,
+    max: number,
+    opts: Options = {},
+  ) {
+    if (min < 0) {
+      min = 0
+    }
+
+    const indexData = await this.parse(opts)
+    if (!indexData) {
+      return []
+    }
+    const refId = indexData.refNameToId[refName]
+    const ba = indexData.indices[refId]
+    if (!ba) {
+      return []
+    }
+
+    // const { linearIndex, binIndex } = indexes
+
+    const overlappingBins = this.reg2bins(min, max) // List of bin #s that overlap min, max
+    const chunks: Chunk[] = []
+
+    // Find chunks in overlapping bins.  Leaf bins (< 4681) are not pruned
+    for (const [start, end] of overlappingBins) {
+      for (let bin = start; bin <= end; bin++) {
+        if (ba.binIndex[bin]) {
+          const binChunks = ba.binIndex[bin]
+          for (let c = 0; c < binChunks.length; ++c) {
+            chunks.push(new Chunk(binChunks[c].minv, binChunks[c].maxv, bin))
+          }
+        }
+      }
+    }
+
+    return optimizeChunks(chunks, new VirtualOffset(0, 0))
+  }
+
+  /**
+   * calculate the list of bins that may overlap with region [beg,end) (zero-based half-open)
+   */
+  reg2bins(beg: number, end: number) {
+    beg -= 1 // < convert to 1-based closed
+    if (beg < 1) {
+      beg = 1
+    }
+    if (end > 2 ** 50) {
+      end = 2 ** 34
+    } // 17 GiB ought to be enough for anybody
+    end -= 1
+    let l = 0
+    let t = 0
+    let s = this.minShift + this.depth * 3
+    const bins = []
+    for (; l <= this.depth; s -= 3, t += lshift(1, l * 3), l += 1) {
+      const b = t + rshift(beg, s)
+      const e = t + rshift(end, s)
+      if (e - b + bins.length > this.maxBinNumber) {
+        throw new Error(
+          `query ${beg}-${end} is too large for current binning scheme (shift ${this.minShift}, depth ${this.depth}), try a smaller query or a coarser index binning scheme`,
+        )
+      }
+      bins.push([b, e])
+    }
+    return bins
+  }
+}

package/src/declare.d.ts

@@ -0,0 +1,2 @@
+declare module 'abortable-promise-cache'
+declare module '@gmod/bgzf-filehandle'

package/src/index.ts

@@ -0,0 +1,5 @@
+import TabixIndexedFile from './tabixIndexedFile'
+import TBI from './tbi'
+import CSI from './csi'
+
+export { TabixIndexedFile, TBI, CSI }