@gmod/cram 1.5.9 → 1.6.2

package/esm/rans/decoding.js

@@ -0,0 +1,118 @@
+import { CramMalformedError } from '../errors';
+import { RANS_BYTE_L } from './constants';
+class FC {
+    // int F, C;
+    constructor() {
+        this.F = undefined;
+        this.C = undefined;
+    }
+}
+class AriDecoder {
+    // final FC[] fc = new FC[256];
+    // byte[] R;
+    constructor() {
+        this.fc = new Array(256);
+        for (let i = 0; i < this.fc.length; i += 1) {
+            this.fc[i] = new FC();
+        }
+        this.R = null;
+    }
+}
+class Symbol {
+    // int start; // Start of range.
+    // int freq; // Symbol frequency.
+    constructor() {
+        this.start = undefined;
+        this.freq = undefined;
+    }
+}
+// Initialize a decoder symbol to start "start" and frequency "freq"
+function symbolInit(sym, start, freq) {
+    if (!(start <= 1 << 16)) {
+        throw new CramMalformedError(`assertion failed: start <= 1<<16`);
+    }
+    if (!(freq <= (1 << 16) - start)) {
+        throw new CramMalformedError(`assertion failed: freq <= 1<<16`);
+    }
+    sym.start = start;
+    sym.freq = freq;
+}
+// Advances in the bit stream by "popping" a single symbol with range start
+// "start" and frequency "freq". All frequencies are assumed to sum to
+// "1 << scaleBits".
+// No renormalization or output happens.
+/* private static int */ function advanceStep(
+/* final int */ r, 
+/* final int */ start, 
+/* final int */ freq, 
+/* final int */ scaleBits) {
+    /* final int */ const mask = (1 << scaleBits) - 1;
+    // s, x = D(x)
+    return freq * (r >> scaleBits) + (r & mask) - start;
+}
+// Equivalent to RansDecAdvanceStep that takes a symbol.
+/* static int  */ function advanceSymbolStep(
+/* final int */ r, 
+/* final RansDecSymbol */ sym, 
+/* final int */ scaleBits) {
+    return advanceStep(r, sym.start, sym.freq, scaleBits);
+}
+// Returns the current cumulative frequency (map it to a symbol yourself!)
+/* static int */ function get(/* final int */ r, /* final int */ scaleBits) {
+    return r & ((1 << scaleBits) - 1);
+}
+// Advances in the bit stream by "popping" a single symbol with range start
+// "start" and frequency "freq". All frequencies are assumed to sum to
+// "1 << scaleBits",
+// and the resulting bytes get written to ptr (which is updated).
+/* private static int */ function advance(
+/* int */ r, 
+/* final ByteBuffer */ pptr, 
+/* final int */ start, 
+/* final int */ freq, 
+/* final int */ scaleBits) {
+    /* final int */ const mask = (1 << scaleBits) - 1;
+    // s, x = D(x)
+    r = freq * (r >> scaleBits) + (r & mask) - start;
+    // re-normalize
+    if (r < RANS_BYTE_L) {
+        do {
+            /* final int */ const b = 0xff & pptr.get();
+            r = (r << 8) | b;
+        } while (r < RANS_BYTE_L);
+    }
+    return r;
+}
+// Equivalent to RansDecAdvance that takes a symbol.
+/*  static int */ function advanceSymbol(
+/* final int */ r, 
+/* final ByteBuffer */ pptr, 
+/* final RansDecSymbol */ sym, 
+/* final int */ scaleBits) {
+    return advance(r, pptr, sym.start, sym.freq, scaleBits);
+}
+// Re-normalize.
+/*  static int */ function renormalize(
+/* int */ r, 
+/* final ByteBuffer */ pptr) {
+    // re-normalize
+    if (r < RANS_BYTE_L) {
+        do {
+            r = (r << 8) | (0xff & pptr.get());
+        } while (r < RANS_BYTE_L);
+    }
+    return r;
+}
+const Decode = {
+    FC,
+    AriDecoder,
+    Symbol,
+    symbolInit,
+    advanceStep,
+    advanceSymbolStep,
+    get,
+    advanceSymbol,
+    renormalize,
+};
+export default Decode;
+//# sourceMappingURL=decoding.js.map

package/esm/rans/decoding.js.map

@@ -0,0 +1 @@
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package/esm/rans/frequencies.d.ts

@@ -0,0 +1,2 @@
+export function readStatsO0(cp: any, decoder: any, syms: any): void;
+export function readStatsO1(cp: any, D: any, syms: any): void;

package/esm/rans/frequencies.js

@@ -0,0 +1,110 @@
+import { CramMalformedError } from '../errors';
+import { TOTFREQ } from './constants';
+import Decoding from './decoding';
+function assert(result) {
+    if (!result) {
+        throw new CramMalformedError('assertion failed');
+    }
+}
+export function readStatsO0(
+/* ByteBuffer */ cp, 
+/* Decoding.AriDecoder */ decoder, 
+/* Decoding.RansDecSymbol[] */ syms) {
+    // Pre-compute reverse lookup of frequency.
+    let rle = 0;
+    let x = 0;
+    let j = cp.get() & 0xff;
+    do {
+        if (decoder.fc[j] == null) {
+            decoder.fc[j] = new Decoding.FC();
+        }
+        decoder.fc[j].F = cp.get() & 0xff;
+        if (decoder.fc[j].F >= 128) {
+            decoder.fc[j].F &= ~128;
+            decoder.fc[j].F = ((decoder.fc[j].F & 127) << 8) | (cp.get() & 0xff);
+        }
+        decoder.fc[j].C = x;
+        Decoding.symbolInit(syms[j], decoder.fc[j].C, decoder.fc[j].F);
+        /* Build reverse lookup table */
+        if (!decoder.R) {
+            decoder.R = new Array(TOTFREQ);
+        }
+        decoder.R.fill(j, x, x + decoder.fc[j].F);
+        x += decoder.fc[j].F;
+        if (rle === 0 && j + 1 === (0xff & cp.getByteAt(cp.position()))) {
+            j = cp.get() & 0xff;
+            rle = cp.get() & 0xff;
+        }
+        else if (rle !== 0) {
+            rle -= 1;
+            j += 1;
+        }
+        else {
+            j = cp.get() & 0xff;
+        }
+    } while (j !== 0);
+    assert(x < TOTFREQ);
+}
+export function readStatsO1(
+/* ByteBuffer */ cp, 
+/*  Decoding.AriDecoder[] */ D, 
+/* Decoding.RansDecSymbol[][] */ syms) {
+    let rlei = 0;
+    let i = 0xff & cp.get();
+    do {
+        let rlej = 0;
+        let x = 0;
+        let j = 0xff & cp.get();
+        if (D[i] == null) {
+            D[i] = new Decoding.AriDecoder();
+        }
+        do {
+            if (D[i].fc[j] == null) {
+                D[i].fc[j] = new Decoding.FC();
+            }
+            D[i].fc[j].F = 0xff & cp.get();
+            if (D[i].fc[j].F >= 128) {
+                D[i].fc[j].F &= ~128;
+                D[i].fc[j].F = ((D[i].fc[j].F & 127) << 8) | (0xff & cp.get());
+            }
+            D[i].fc[j].C = x;
+            if (D[i].fc[j].F === 0) {
+                D[i].fc[j].F = TOTFREQ;
+            }
+            if (syms[i][j] == null) {
+                syms[i][j] = new Decoding.RansDecSymbol();
+            }
+            Decoding.symbolInit(syms[i][j], D[i].fc[j].C, D[i].fc[j].F);
+            /* Build reverse lookup table */
+            if (D[i].R == null) {
+                D[i].R = new Array(TOTFREQ);
+            }
+            D[i].R.fill(j, x, x + D[i].fc[j].F);
+            x += D[i].fc[j].F;
+            assert(x <= TOTFREQ);
+            if (rlej === 0 && j + 1 === (0xff & cp.getByteAt(cp.position()))) {
+                j = 0xff & cp.get();
+                rlej = 0xff & cp.get();
+            }
+            else if (rlej !== 0) {
+                rlej -= 1;
+                j += 1;
+            }
+            else {
+                j = 0xff & cp.get();
+            }
+        } while (j !== 0);
+        if (rlei === 0 && i + 1 === (0xff & cp.getByteAt(cp.position()))) {
+            i = 0xff & cp.get();
+            rlei = 0xff & cp.get();
+        }
+        else if (rlei !== 0) {
+            rlei -= 1;
+            i += 1;
+        }
+        else {
+            i = 0xff & cp.get();
+        }
+    } while (i !== 0);
+}
+//# sourceMappingURL=frequencies.js.map

package/esm/rans/frequencies.js.map

@@ -0,0 +1 @@
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package/esm/rans/index.d.ts

@@ -0,0 +1 @@
+export default function uncompress(inputBuffer: any, outputBuffer: any, initialInputPosition?: number): any;

package/esm/rans/index.js

@@ -0,0 +1,195 @@
+import { CramMalformedError } from '../errors';
+import Decoding from './decoding';
+import { readStatsO0, readStatsO1 } from './frequencies';
+import D04 from './d04';
+import D14 from './d14';
+// const /* int */ ORDER_BYTE_LENGTH = 1
+// const /* int */ COMPRESSED_BYTE_LENGTH = 4
+const /* int */ RAW_BYTE_LENGTH = 4;
+// const /* int */ PREFIX_BYTE_LENGTH =
+//   ORDER_BYTE_LENGTH + COMPRESSED_BYTE_LENGTH + RAW_BYTE_LENGTH
+// enum ORDER {
+//     ZERO, ONE;
+//     static ORDER fromInt(const /* int */ value) {
+//         try {
+//             return ORDER.values()[value];
+//         } catch (const ArrayIndexOutOfBoundsException e) {
+//             throw new RuntimeException("Unknown rANS order: " + value);
+//         }
+//     }
+// }
+// static ByteBuffer compress(const ByteBuffer input, const ORDER order, const ByteBuffer out) {
+//     if (input.remaining() == 0)
+//         return EMPTY_BUFFER;
+//     if (input.remaining() < 4)
+//         return encode_order0_way4(input, out);
+//     switch (order) {
+//         case ZERO:
+//             return encode_order0_way4(input, out);
+//         case ONE:
+//             return encode_order1_way4(input, out);
+//         default:
+//             throw new RuntimeException("Unknown rANS order: " + order);
+//     }
+// }
+// static /* ByteBuffer */ allocateIfNeeded(/* const int */ in_size,
+//                                            /* const ByteBuffer */ out_buf) {
+//     const /* int */ compressedSize = (/* int */) (1.05 * in_size + 257 * 257 * 3 + 4);
+//     if (out_buf == null)
+//         return ByteBuffer.allocate(compressedSize);
+//     if (out_buf.remaining() < compressedSize)
+//         throw new RuntimeException("Insufficient buffer size.");
+//     out_buf.order(ByteOrder.LITTLE_ENDIAN);
+//     return out_buf;
+// }
+// static ByteBuffer encode_order0_way4(const ByteBuffer input,
+//                                              ByteBuffer out_buf) {
+//     const /* int */ in_size = input.remaining();
+//     out_buf = allocateIfNeeded(in_size, out_buf);
+//     const /* int */ freqTableStart = PREFIX_BYTE_LENGTH;
+//     out_buf.position(freqTableStart);
+//     const /* int */[] F = Frequencies.calcFrequencies_o0(in);
+//     const RansEncSymbol[] syms = Frequencies.buildSyms_o0(F);
+//     const ByteBuffer cp = out_buf.slice();
+//     const /* int */ frequencyTable_size = Frequencies.writeFrequencies_o0(cp, F);
+//     input.rewind();
+//     const /* int */ compressedBlob_size = E04.compress(input, syms, cp);
+//     finalizeCompressed(0, out_buf, in_size, frequencyTable_size,
+//             compressedBlob_size);
+//     return out_buf;
+// }
+// static ByteBuffer encode_order1_way4(const ByteBuffer input,
+//                                              ByteBuffer out_buf) {
+//     const /* int */ in_size = input.remaining();
+//     out_buf = allocateIfNeeded(in_size, out_buf);
+//     const /* int */ freqTableStart = PREFIX_BYTE_LENGTH;
+//     out_buf.position(freqTableStart);
+//     const /* int */[][] F = Frequencies.calcFrequencies_o1(in);
+//     const RansEncSymbol[][] syms = Frequencies.buildSyms_o1(F);
+//     const ByteBuffer cp = out_buf.slice();
+//     const /* int */ frequencyTable_size = Frequencies.writeFrequencies_o1(cp, F);
+//     input.rewind();
+//     const /* int */ compressedBlob_size = E14.compress(input, syms, cp);
+//     finalizeCompressed(1, out_buf, in_size, frequencyTable_size,
+//             compressedBlob_size);
+//     return out_buf;
+// }
+// static void finalizeCompressed(const /* int */ order, const ByteBuffer out_buf,
+//                                        const /* int */ in_size, const /* int */ frequencyTable_size, const /* int */ compressedBlob_size) {
+//     out_buf.limit(PREFIX_BYTE_LENGTH + frequencyTable_size
+//             + compressedBlob_size);
+//     out_buf.put(0, (byte) order);
+//     out_buf.order(ByteOrder.LITTLE_ENDIAN);
+//     const /* int */ compressedSizeOffset = ORDER_BYTE_LENGTH;
+//     out_buf.putInt(compressedSizeOffset, frequencyTable_size
+//             + compressedBlob_size);
+//     const /* int */ rawSizeOffset = ORDER_BYTE_LENGTH + COMPRESSED_BYTE_LENGTH;
+//     out_buf.putInt(rawSizeOffset, in_size);
+//     out_buf.rewind();
+// }
+function uncompressOrder0Way4(
+/* const ByteBuffer  */ input, 
+/* const ByteBuffer  */ out) {
+    // input.order(ByteOrder.LITTLE_ENDIAN);
+    const D = new Decoding.AriDecoder();
+    const syms = new Array(256);
+    for (let i = 0; i < syms.length; i += 1) {
+        syms[i] = new Decoding.Symbol();
+    }
+    readStatsO0(input, D, syms);
+    D04(input, D, syms, out);
+    return out;
+}
+function uncompressOrder1Way4(
+/* const ByteBuffer */ input, 
+/* const ByteBuffer */ output) {
+    const D = new Array(256);
+    for (let i = 0; i < D.length; i += 1) {
+        D[i] = new Decoding.AriDecoder();
+    }
+    const /* Decoding.RansDecSymbol[][]  */ syms = new Array(256);
+    for (let i = 0; i < syms.length; i += 1) {
+        syms[i] = new Array(256);
+        for (let j = 0; j < syms[i].length; j += 1) {
+            syms[i][j] = new Decoding.Symbol();
+        }
+    }
+    readStatsO1(input, D, syms);
+    D14(input, output, D, syms);
+    return output;
+}
+/* compat layer to make a node buffer act like a java ByteBuffer */
+class ByteBuffer {
+    constructor(nodeBuffer, initialInputPosition = 0) {
+        this._buffer = nodeBuffer;
+        this._position = initialInputPosition;
+        this.length = nodeBuffer.length;
+    }
+    get() {
+        const b = this._buffer[this._position];
+        this._position += 1;
+        return b;
+    }
+    getByte() {
+        return this.get();
+    }
+    getByteAt(position) {
+        return this._buffer[position];
+    }
+    position() {
+        return this._position;
+    }
+    put(val) {
+        this._buffer[this._position] = val;
+        this._position += 1;
+        return val;
+    }
+    putAt(position, val) {
+        this._buffer[position] = val;
+        return val;
+    }
+    setPosition(pos) {
+        this._position = pos;
+        return pos;
+    }
+    getInt() {
+        const i = this._buffer.readInt32LE(this._position);
+        this._position += 4;
+        return i;
+    }
+    remaining() {
+        return this._buffer.length - this._position;
+    }
+}
+// static /* const */ ByteBuffer EMPTY_BUFFER = ByteBuffer.allocate(0);
+export default function uncompress(inputBuffer, outputBuffer, initialInputPosition = 0) {
+    if (inputBuffer.length === 0) {
+        outputBuffer.fill(0);
+        return outputBuffer;
+    }
+    const input = new ByteBuffer(inputBuffer, initialInputPosition);
+    // input.order(ByteOrder.LITTLE_ENDIAN);
+    const order = input.get();
+    if (order !== 0 && order !== 1) {
+        throw new CramMalformedError(`Invalid rANS order ${order}`);
+    }
+    const /* int */ inputSize = input.getInt();
+    if (inputSize !== input.remaining() - RAW_BYTE_LENGTH) {
+        throw new CramMalformedError('Incorrect input length.');
+    }
+    const /* int */ outputSize = input.getInt();
+    const output = new ByteBuffer(outputBuffer || Buffer.allocUnsafe(outputSize));
+    // TODO output.limit(outputSize)
+    if (output.length < outputSize) {
+        throw new CramMalformedError(`Output buffer too small to fit ${outputSize} bytes.`);
+    }
+    switch (order) {
+        case 0:
+            return uncompressOrder0Way4(input, output);
+        case 1:
+            return uncompressOrder1Way4(input, output);
+        default:
+            throw new CramMalformedError(`Invalid rANS order: ${order}`);
+    }
+}
+//# sourceMappingURL=index.js.map

package/esm/rans/index.js.map

@@ -0,0 +1 @@
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package/esm/sam.d.ts

@@ -0,0 +1 @@
+export function parseHeaderText(text: any): any[];

package/esm/sam.js

@@ -0,0 +1,16 @@
+export function parseHeaderText(text) {
+    const lines = text.split(/\r?\n/);
+    const data = [];
+    lines.forEach(line => {
+        const [tag, ...fields] = line.split(/\t/);
+        const parsedFields = fields.map(f => {
+            const [fieldTag, value] = f.split(':', 2);
+            return { tag: fieldTag, value };
+        });
+        if (tag) {
+            data.push({ tag: tag.substr(1), data: parsedFields });
+        }
+    });
+    return data;
+}
+//# sourceMappingURL=sam.js.map

package/esm/sam.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.js"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAI;IAClC,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAAG,EAAE,CAAA;IACf,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;QACnB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,MAAM,YAAY,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;YAClC,MAAM,CAAC,QAAQ,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,GAAG,EAAE,CAAC,CAAC,CAAA;YACzC,OAAO,EAAE,GAAG,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAA;QACjC,CAAC,CAAC,CAAA;QACF,IAAI,GAAG,EAAE;YACP,IAAI,CAAC,IAAI,CAAC,EAAE,GAAG,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC,CAAA;SACtD;IACH,CAAC,CAAC,CAAA;IACF,OAAO,IAAI,CAAA;AACb,CAAC"}

package/esm/unzip-pako.d.ts

@@ -0,0 +1,2 @@
+/// <reference types="node" />
+export declare function unzip(input: Buffer): Buffer;

package/esm/unzip-pako.js

@@ -0,0 +1,5 @@
+import { inflate } from 'pako';
+export function unzip(input) {
+    return Buffer.from(inflate(input));
+}
+//# sourceMappingURL=unzip-pako.js.map

package/esm/unzip-pako.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,OAAO,EAAE,MAAM,MAAM,CAAA;AAE9B,MAAM,UAAU,KAAK,CAAC,KAAa;IACjC,OAAO,MAAM,CAAC,IAAI,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,CAAA;AACpC,CAAC"}

package/esm/unzip.d.ts

@@ -0,0 +1,2 @@
+import { gunzipSync } from 'zlib';
+export { gunzipSync as unzip };

package/esm/unzip.js

@@ -0,0 +1,3 @@
+import { gunzipSync } from 'zlib';
+export { gunzipSync as unzip };
+//# sourceMappingURL=unzip.js.map

package/esm/unzip.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,UAAU,EAAE,MAAM,MAAM,CAAA;AACjC,OAAO,EAAE,UAAU,IAAI,KAAK,EAAE,CAAA"}

package/package.json

@@ -1,10 +1,11 @@
 {
   "name": "@gmod/cram",
-  "version": "1.5.9",
+  "version": "1.6.2",
   "description": "read CRAM files with pure Javascript",
   "license": "MIT",
   "repository": "GMOD/cram-js",
   "main": "dist/index.js",
+  "module": "esm/index.js",
   "author": {
     "name": "Robert Buels",
     "email": "rbuels@gmail.com",
@@ -15,26 +16,23 @@
   },
   "files": [
     "errors.js",
-    "dist"
+    "src",
+    "dist",
+    "esm"
   ],
   "scripts": {
-    "test": "node ./node_modules/.bin/mocha",
-    "coverage": "rm -rf coverage; nyc ./node_modules/.bin/mocha; nyc report --reporter=lcov",
+    "test": "jest",
     "lint": "eslint src test",
     "docs": "documentation readme --shallow src/indexedCramFile.js --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.js --section=CramFile; documentation readme --shallow src/craiIndex.js --section=CraiIndex;  documentation readme --shallow errors.js '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.js --section=CramFile; documentation readme --shallow src/cramFile/record.js --section=CramRecord",
-    "clean": "rimraf dist",
     "prebuild": "npm run clean",
-    "build": "babel src -d dist && webpack",
-    "built-tests": "rm -rf built-tests; mkdir built-tests; ln -s ../test/data built-tests/data; babel test/*.js -d built-tests; babel test/lib/*.js -d built-tests/lib;babel test/lib/fasta/*.js -d built-tests/lib/fasta;node ./node_modules/.bin/mocha built-tests",
-    "watch": "npm-watch",
+    "clean": "rimraf dist esm",
+    "build:esm": "tsc --target es2018 --outDir esm",
+    "build:es5": "tsc --target es5 --outDir dist",
+    "build": "npm run build:esm && npm run build:es5",
+    "postbuild": "webpack",
     "prepublishOnly": "npm test && npm run build && cp dist/errors.js errors.js",
     "postpublish": "rm errors.js",
-    "postversion": "git push origin master --follow-tags"
-  },
-  "watch": {
-    "test": "{src,test}/*.js",
-    "lint": "{src,test}/*.js",
-    "build": "src"
+    "postversion": "git push --follow-tags"
   },
   "keywords": [
     "cram",
@@ -43,41 +41,46 @@
     "biojs"
   ],
   "dependencies": {
-    "@babel/runtime-corejs3": "^7.4.5",
     "@gmod/binary-parser": "^1.3.5",
+    "@jkbonfield/htscodecs": "^0.5.1",
     "abortable-promise-cache": "^1.2.0",
     "buffer-crc32": "^0.2.13",
+    "bzip2": "^0.1.1",
     "cross-fetch": "^3.0.0",
     "es6-promisify": "^6.0.1",
     "long": "^4.0.0",
     "md5": "^2.2.1",
+    "pako": "^1.0.4",
     "quick-lru": "^2.0.0"
   },
   "devDependencies": {
-    "@babel/cli": "^7.4.4",
-    "@babel/core": "^7.4.5",
-    "@babel/plugin-transform-runtime": "^7.4.4",
-    "@babel/preset-env": "^7.4.5",
-    "chai": "^4.1.2",
-    "documentation": "^9.1.1",
-    "eslint": "^5.12.0",
-    "eslint-config-airbnb-base": "^13.1.0",
-    "eslint-config-prettier": "^4.1.0",
-    "eslint-plugin-import": "^2.2.0",
-    "eslint-plugin-prettier": "^3.0.1",
-    "get-stream": "^4.1.0",
-    "glob": "^7.1.2",
-    "imports-loader": "^0.8.0",
-    "mocha": "^6.0.0",
-    "mock-fs": "^4.12.0",
-    "npm-watch": "^0.5.0",
-    "nyc": "^13.0.0",
-    "prettier": "^1.10.2",
-    "rimraf": "^2.6.1",
+    "@gmod/indexedfasta": "^2.0.2",
+    "@types/jest": "^27.4.0",
+    "@types/pako": "^1.0.3",
+    "@typescript-eslint/eslint-plugin": "^5.9.1",
+    "@typescript-eslint/parser": "^5.9.1",
+    "documentation": "^13.2.5",
+    "eslint": "^7.0.0",
+    "eslint-config-prettier": "^8.3.0",
+    "eslint-plugin-import": "^2.25.4",
+    "eslint-plugin-prettier": "^4.0.0",
+    "glob": "^7.2.0",
+    "jest": "^27.4.7",
+    "mock-fs": "^5.1.2",
+    "prettier": "^2.5.1",
+    "rimraf": "^3.0.2",
+    "ts-jest": "^27.1.2",
+    "typescript": "^4.5.4",
     "webpack": "4",
     "webpack-cli": "^3.2.1"
   },
   "publishConfig": {
     "access": "public"
+  },
+  "browser": {
+    "./dist/io/localFile.js": false,
+    "./esm/io/localFile.js": false,
+    "./esm/unzip.js": "./esm/unzip-pako.js",
+    "./dist/unzip.js": "./dist/unzip-pako.js"
   }
 }