@gmod/cram 5.0.0 → 5.0.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/seek-bzip/bitreader.js +2 -2
- package/dist/seek-bzip/bitreader.js.map +1 -1
- package/dist/seek-bzip/index.js +7 -7
- package/dist/seek-bzip/index.js.map +1 -1
- package/esm/seek-bzip/bitreader.js +1 -1
- package/esm/seek-bzip/bitreader.js.map +1 -1
- package/esm/seek-bzip/index.js +3 -3
- package/esm/seek-bzip/index.js.map +1 -1
- package/package.json +2 -2
- package/src/seek-bzip/bitreader.ts +1 -1
- package/src/seek-bzip/index.ts +3 -3
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@@ -33,7 +33,7 @@ Peter Fenwick, Alistair Moffat, Radford Neal, Ian H. Witten,
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Robert Sedgewick, and Jon L. Bentley.
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*/
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Object.defineProperty(exports, "__esModule", { value: true });
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-
const
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+
const toHex_ts_1 = require("./toHex.js");
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const BITMASK = [0x00, 0x01, 0x03, 0x07, 0x0f, 0x1f, 0x3f, 0x7f, 0xff];
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class BitReader {
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constructor(stream) {
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@@ -94,7 +94,7 @@ class BitReader {
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for (let i = 0; i < buf.length; i++) {
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buf[i] = this.read(8);
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}
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-
return (0,
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+
return (0, toHex_ts_1.toHex)(buf);
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}
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}
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exports.default = BitReader;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"bitreader.js","sourceRoot":"","sources":["../../src/seek-bzip/bitreader.ts"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgCE;;AAEF,
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1
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+
{"version":3,"file":"bitreader.js","sourceRoot":"","sources":["../../src/seek-bzip/bitreader.ts"],"names":[],"mappings":";AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgCE;;AAEF,yCAAkC;AAElC,MAAM,OAAO,GAAG,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAA;AAOtE,MAAqB,SAAS;IAM5B,YAAY,MAAc;QACxB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;QACpB,IAAI,CAAC,SAAS,GAAG,CAAC,CAAA;QAClB,IAAI,CAAC,OAAO,GAAG,CAAC,CAAA;QAChB,IAAI,CAAC,OAAO,GAAG,KAAK,CAAA;IACtB,CAAC;IAEO,WAAW;QACjB,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC;YAClB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;YACrC,IAAI,CAAC,OAAO,GAAG,IAAI,CAAA;QACrB,CAAC;IACH,CAAC;IAED;;;OAGG;IACH,IAAI,CAAC,IAAY;QACf,IAAI,MAAM,GAAG,CAAC,CAAA;QACd,OAAO,IAAI,GAAG,CAAC,EAAE,CAAC;YAChB,IAAI,CAAC,WAAW,EAAE,CAAA;YAClB,MAAM,SAAS,GAAG,CAAC,GAAG,IAAI,CAAC,SAAS,CAAA;YACpC,qBAAqB;YACrB,IAAI,IAAI,IAAI,SAAS,EAAE,CAAC;gBACtB,MAAM,KAAK,SAAS,CAAA;gBACpB,MAAM,IAAI,OAAO,CAAC,SAAS,CAAE,GAAG,IAAI,CAAC,OAAO,CAAA;gBAC5C,IAAI,CAAC,OAAO,GAAG,KAAK,CAAA;gBACpB,IAAI,CAAC,SAAS,GAAG,CAAC,CAAA;gBAClB,IAAI,IAAI,SAAS,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,MAAM,KAAK,IAAI,CAAA;gBACf,MAAM,KAAK,GAAG,SAAS,GAAG,IAAI,CAAA;gBAC9B,MAAM,IAAI,CAAC,IAAI,CAAC,OAAO,GAAG,CAAC,OAAO,CAAC,IAAI,CAAE,IAAI,KAAK,CAAC,CAAC,IAAI,KAAK,CAAA;gBAC7D,IAAI,CAAC,SAAS,IAAI,IAAI,CAAA;gBACtB,IAAI,GAAG,CAAC,CAAA;YACV,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAED;;;OAGG;IACH,IAAI,CAAC,GAAW;QACd,MAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACrB,MAAM,MAAM,GAAG,CAAC,GAAG,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;QAChC,IAAI,CAAC,SAAS,GAAG,KAAK,CAAA;QACtB,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACxB,IAAI,CAAC,OAAO,GAAG,KAAK,CAAA;IACtB,CAAC;IAED;;OAEG;IACH,EAAE;QACA,MAAM,GAAG,GAAG,IAAI,UAAU,CAAC,CAAC,CAAC,CAAA;QAC7B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YACpC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACvB,CAAC;QACD,OAAO,IAAA,gBAAK,EAAC,GAAG,CAAC,CAAA;IACnB,CAAC;CACF;AArED,4BAqEC"}
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package/dist/seek-bzip/index.js
CHANGED
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@@ -41,9 +41,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.decode = decode;
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-
const
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-
const
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const
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const bitreader_ts_1 = __importDefault(require("./bitreader.js"));
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+
const crc32_ts_1 = __importDefault(require("./crc32.js"));
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const stream_ts_1 = __importDefault(require("./stream.js"));
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const MAX_HUFCODE_BITS = 20;
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const MAX_SYMBOLS = 258;
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const SYMBOL_RUNA = 0;
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@@ -101,7 +101,7 @@ class Bunzip {
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this.writeCount = -1;
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return false; /* no more blocks */
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}
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-
this.blockCRC = new
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this.blockCRC = new crc32_ts_1.default();
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return true;
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}
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/* XXX micro-bunzip uses (inputStream, inputBuffer, len) as arguments */
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@@ -116,7 +116,7 @@ class Bunzip {
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if (level < 1 || level > 9) {
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_throw(Err.NOT_BZIP_DATA, 'level out of range');
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}
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-
this.reader = new
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this.reader = new bitreader_ts_1.default(inputStream);
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/* Fourth byte (ascii '1'-'9'), indicates block size in units of 100k of
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uncompressed data. Allocate intermediate buffer for block. */
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this.dbufSize = 100000 * level;
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@@ -487,7 +487,7 @@ const coerceInputStream = function (input) {
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if ('readByte' in input) {
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return input;
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}
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const inputStream = new
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const inputStream = new stream_ts_1.default();
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inputStream.pos = 0;
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inputStream.readByte = function () {
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return input[this.pos++];
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@@ -501,7 +501,7 @@ const coerceInputStream = function (input) {
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return inputStream;
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};
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const coerceOutputStream = function (output) {
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const outputStream = new
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const outputStream = new stream_ts_1.default();
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let resizeOk = true;
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if (output) {
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if (typeof output === 'number') {
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@@ -1 +1 @@
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1
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-
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1
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@@ -31,7 +31,7 @@ which also acknowledges contributions by Mike Burrows, David Wheeler,
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Peter Fenwick, Alistair Moffat, Radford Neal, Ian H. Witten,
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32
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Robert Sedgewick, and Jon L. Bentley.
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*/
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34
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-
import { toHex } from
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34
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+
import { toHex } from "./toHex.js";
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35
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const BITMASK = [0x00, 0x01, 0x03, 0x07, 0x0f, 0x1f, 0x3f, 0x7f, 0xff];
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36
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export default class BitReader {
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37
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constructor(stream) {
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"bitreader.js","sourceRoot":"","sources":["../../src/seek-bzip/bitreader.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgCE;AAEF,OAAO,EAAE,KAAK,EAAE,MAAM,
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1
|
+
{"version":3,"file":"bitreader.js","sourceRoot":"","sources":["../../src/seek-bzip/bitreader.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgCE;AAEF,OAAO,EAAE,KAAK,EAAE,MAAM,YAAY,CAAA;AAElC,MAAM,OAAO,GAAG,CAAC,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,EAAE,IAAI,CAAC,CAAA;AAOtE,MAAM,CAAC,OAAO,OAAO,SAAS;IAM5B,YAAY,MAAc;QACxB,IAAI,CAAC,MAAM,GAAG,MAAM,CAAA;QACpB,IAAI,CAAC,SAAS,GAAG,CAAC,CAAA;QAClB,IAAI,CAAC,OAAO,GAAG,CAAC,CAAA;QAChB,IAAI,CAAC,OAAO,GAAG,KAAK,CAAA;IACtB,CAAC;IAEO,WAAW;QACjB,IAAI,CAAC,IAAI,CAAC,OAAO,EAAE,CAAC;YAClB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,MAAM,CAAC,QAAQ,EAAE,CAAA;YACrC,IAAI,CAAC,OAAO,GAAG,IAAI,CAAA;QACrB,CAAC;IACH,CAAC;IAED;;;OAGG;IACH,IAAI,CAAC,IAAY;QACf,IAAI,MAAM,GAAG,CAAC,CAAA;QACd,OAAO,IAAI,GAAG,CAAC,EAAE,CAAC;YAChB,IAAI,CAAC,WAAW,EAAE,CAAA;YAClB,MAAM,SAAS,GAAG,CAAC,GAAG,IAAI,CAAC,SAAS,CAAA;YACpC,qBAAqB;YACrB,IAAI,IAAI,IAAI,SAAS,EAAE,CAAC;gBACtB,MAAM,KAAK,SAAS,CAAA;gBACpB,MAAM,IAAI,OAAO,CAAC,SAAS,CAAE,GAAG,IAAI,CAAC,OAAO,CAAA;gBAC5C,IAAI,CAAC,OAAO,GAAG,KAAK,CAAA;gBACpB,IAAI,CAAC,SAAS,GAAG,CAAC,CAAA;gBAClB,IAAI,IAAI,SAAS,CAAA;YACnB,CAAC;iBAAM,CAAC;gBACN,MAAM,KAAK,IAAI,CAAA;gBACf,MAAM,KAAK,GAAG,SAAS,GAAG,IAAI,CAAA;gBAC9B,MAAM,IAAI,CAAC,IAAI,CAAC,OAAO,GAAG,CAAC,OAAO,CAAC,IAAI,CAAE,IAAI,KAAK,CAAC,CAAC,IAAI,KAAK,CAAA;gBAC7D,IAAI,CAAC,SAAS,IAAI,IAAI,CAAA;gBACtB,IAAI,GAAG,CAAC,CAAA;YACV,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAA;IACf,CAAC;IAED;;;OAGG;IACH,IAAI,CAAC,GAAW;QACd,MAAM,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;QACrB,MAAM,MAAM,GAAG,CAAC,GAAG,GAAG,KAAK,CAAC,GAAG,CAAC,CAAA;QAChC,IAAI,CAAC,SAAS,GAAG,KAAK,CAAA;QACtB,IAAI,CAAC,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACxB,IAAI,CAAC,OAAO,GAAG,KAAK,CAAA;IACtB,CAAC;IAED;;OAEG;IACH,EAAE;QACA,MAAM,GAAG,GAAG,IAAI,UAAU,CAAC,CAAC,CAAC,CAAA;QAC7B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;YACpC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACvB,CAAC;QACD,OAAO,KAAK,CAAC,GAAG,CAAC,CAAA;IACnB,CAAC;CACF"}
|
package/esm/seek-bzip/index.js
CHANGED
|
@@ -35,9 +35,9 @@ which also acknowledges contributions by Mike Burrows, David Wheeler,
|
|
|
35
35
|
Peter Fenwick, Alistair Moffat, Radford Neal, Ian H. Witten,
|
|
36
36
|
Robert Sedgewick, and Jon L. Bentley.
|
|
37
37
|
*/
|
|
38
|
-
import BitReader from
|
|
39
|
-
import CRC32 from
|
|
40
|
-
import Stream from
|
|
38
|
+
import BitReader from "./bitreader.js";
|
|
39
|
+
import CRC32 from "./crc32.js";
|
|
40
|
+
import Stream from "./stream.js";
|
|
41
41
|
const MAX_HUFCODE_BITS = 20;
|
|
42
42
|
const MAX_SYMBOLS = 258;
|
|
43
43
|
const SYMBOL_RUNA = 0;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/cram",
|
|
3
|
-
"version": "5.0.
|
|
3
|
+
"version": "5.0.2",
|
|
4
4
|
"description": "read CRAM files with pure Javascript",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/cram-js",
|
|
@@ -56,7 +56,7 @@
|
|
|
56
56
|
"xz-decompress": "^0.2.1"
|
|
57
57
|
},
|
|
58
58
|
"devDependencies": {
|
|
59
|
-
"@gmod/indexedfasta": "^
|
|
59
|
+
"@gmod/indexedfasta": "^4.0.1",
|
|
60
60
|
"@types/md5": "^2.3.2",
|
|
61
61
|
"@types/pako": "^1.0.3",
|
|
62
62
|
"@vitest/coverage-v8": "^3.0.1",
|
|
@@ -32,7 +32,7 @@ Peter Fenwick, Alistair Moffat, Radford Neal, Ian H. Witten,
|
|
|
32
32
|
Robert Sedgewick, and Jon L. Bentley.
|
|
33
33
|
*/
|
|
34
34
|
|
|
35
|
-
import { toHex } from './toHex'
|
|
35
|
+
import { toHex } from './toHex.ts'
|
|
36
36
|
|
|
37
37
|
const BITMASK = [0x00, 0x01, 0x03, 0x07, 0x0f, 0x1f, 0x3f, 0x7f, 0xff]
|
|
38
38
|
|
package/src/seek-bzip/index.ts
CHANGED
|
@@ -36,9 +36,9 @@ Peter Fenwick, Alistair Moffat, Radford Neal, Ian H. Witten,
|
|
|
36
36
|
Robert Sedgewick, and Jon L. Bentley.
|
|
37
37
|
*/
|
|
38
38
|
|
|
39
|
-
import BitReader from './bitreader'
|
|
40
|
-
import CRC32 from './crc32'
|
|
41
|
-
import Stream from './stream'
|
|
39
|
+
import BitReader from './bitreader.ts'
|
|
40
|
+
import CRC32 from './crc32.ts'
|
|
41
|
+
import Stream from './stream.ts'
|
|
42
42
|
|
|
43
43
|
const MAX_HUFCODE_BITS = 20
|
|
44
44
|
const MAX_SYMBOLS = 258
|