@gmod/cram 1.7.3 → 1.7.4
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/CHANGELOG.md +4 -0
- package/dist/cram-bundle.js +1 -1
- package/dist/cram-bundle.js.LICENSE.txt +1 -1
- package/dist/cramFile/file.js +5 -3
- package/dist/cramFile/file.js.map +1 -1
- package/dist/cramFile/record.d.ts +1 -1
- package/dist/cramFile/record.js +1 -1
- package/esm/cramFile/file.js +2 -0
- package/esm/cramFile/file.js.map +1 -1
- package/esm/cramFile/record.d.ts +1 -1
- package/esm/cramFile/record.js +1 -1
- package/package.json +5 -6
- package/src/cramFile/file.ts +2 -0
- package/src/cramFile/record.ts +1 -1
- package/src/typings/bzip2.d.ts +0 -7
package/dist/cramFile/file.js
CHANGED
|
@@ -15,6 +15,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
15
15
|
const unzip_1 = require("../unzip");
|
|
16
16
|
const buffer_crc32_1 = __importDefault(require("buffer-crc32"));
|
|
17
17
|
const quick_lru_1 = __importDefault(require("quick-lru"));
|
|
18
|
+
// @ts-expect-error
|
|
19
|
+
const bzip2_1 = __importDefault(require("bzip2"));
|
|
18
20
|
const errors_1 = require("../errors");
|
|
19
21
|
const rans_1 = __importDefault(require("../rans"));
|
|
20
22
|
const sectionParsers_1 = require("./sectionParsers");
|
|
@@ -256,12 +258,12 @@ class CramFile {
|
|
|
256
258
|
result.copy(outputBuffer);
|
|
257
259
|
}
|
|
258
260
|
else if (compressionMethod === 'bzip2') {
|
|
259
|
-
const bits =
|
|
260
|
-
let size =
|
|
261
|
+
const bits = bzip2_1.default.array(inputBuffer);
|
|
262
|
+
let size = bzip2_1.default.header(bits);
|
|
261
263
|
let j = 0;
|
|
262
264
|
let chunk;
|
|
263
265
|
do {
|
|
264
|
-
chunk =
|
|
266
|
+
chunk = bzip2_1.default.decompress(bits, size);
|
|
265
267
|
if (chunk != -1) {
|
|
266
268
|
Buffer.from(chunk).copy(outputBuffer, j);
|
|
267
269
|
j += chunk.length;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"file.js","sourceRoot":"","sources":["../../src/cramFile/file.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,oCAAgC;AAChC,gEAAgC;AAChC,0DAAgC;
|
|
1
|
+
{"version":3,"file":"file.js","sourceRoot":"","sources":["../../src/cramFile/file.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,oCAAgC;AAChC,gEAAgC;AAChC,0DAAgC;AAChC,mBAAmB;AACnB,kDAAyB;AAEzB,sCAAsE;AACtE,mDAAoC;AACpC,qDAKyB;AACzB,sEAA6C;AAC7C,4DAAuC;AAEvC,8BAA4B;AAC5B,iCAA+C;AAC/C,gCAAwC;AAKxC,+EAA+E;AAC/E,SAAS,aAAa;IACpB,MAAM,MAAM,GAAG,IAAI,WAAW,CAAC,CAAC,UAAU,CAAC,CAAC,CAAA;IAC5C,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;IAE3C,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;QACrB,OAAO,CAAC,CAAA,CAAC,eAAe;KACzB;SAAM,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;QAC5B,OAAO,CAAC,CAAA,CAAC,YAAY;KACtB;SAAM;QACL,OAAO,CAAC,CAAA,CAAC,eAAe;KACzB;AACH,CAAC;AAiCD,MAAqB,QAAQ;IAW3B,YAAY,IAAkB;;QAC5B,IAAI,CAAC,IAAI,GAAG,IAAA,SAAI,EAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QACtD,IAAI,CAAC,iBAAiB,GAAG,IAAI,CAAA;QAC7B,IAAI,CAAC,8BAA8B,GAAG,IAAI,CAAC,QAAQ,CAAA;QACnD,IAAI,CAAC,OAAO,GAAG;YACb,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;YACvC,SAAS,EAAE,MAAA,IAAI,CAAC,SAAS,mCAAI,KAAK;SACnC,CAAA;QAED,6CAA6C;QAC7C,gEAAgE;QAChE,4DAA4D;QAC5D,qCAAqC;QACrC,IAAI,CAAC,YAAY,GAAG,IAAI,mBAAQ,CAAC;YAC/B,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,SAAS;SAChC,CAAC,CAAA;QACF,IAAI,aAAa,EAAE,GAAG,CAAC,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;SACrE;IACH,CAAC;IAED,eAAe;IACf,8BAA8B;IAC9B,gCAAgC;IAChC,MAAM;IACN,yBAAyB;IACzB,2BAA2B;IAC3B,MAAM;IACN,EAAE;IACF,yBAAyB;IACzB,IAAI;IAEJ,8CAA8C;IAC9C,IAAI,CACF,MAAc,EACd,MAAc,EACd,MAAc,EACd,QAAgB;QAKhB,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;IACzD,CAAC;IAED,8CAA8C;IAC9C,IAAI;QACF,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACzB,CAAC;IAED,WAAW;IACL,aAAa;;YACjB,MAAM,SAAS,GAAG,MAAM,CAAC,WAAW,CAAC,mCAAwB,CAAC,SAAS,CAAC,CAAA;YACxE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC,EAAE,mCAAwB,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;YACzE,MAAM,UAAU,GAAG,mCAAwB,CAAC,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC;iBAChE,MAAa,CAAA;YAChB,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,EAAE;gBAClE,MAAM,IAAI,+BAAsB,CAC9B,gBAAgB,UAAU,CAAC,YAAY,gBAAgB,CACxD,CAAA;aACF;YACD,OAAO,UAAU,CAAA;QACnB,CAAC;KAAA;IAED,UAAU;IACJ,YAAY;;YAChB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAA;YACrD,IAAI,CAAC,cAAc,EAAE;gBACnB,MAAM,IAAI,2BAAkB,CAAC,6BAA6B,CAAC,CAAA;aAC5D;YAED,MAAM,UAAU,GAAG,MAAM,cAAc,CAAC,aAAa,EAAE,CAAA;YACvD,IAAI,UAAU,KAAK,SAAS,EAAE;gBAC5B,OAAO,IAAA,qBAAe,EAAC,EAAE,CAAC,CAAA;aAC3B;YACD,MAAM,OAAO,GAAG,UAAU,CAAC,OAAO,CAAA;YAClC,wDAAwD;YACxD,MAAM,YAAY,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;YAC3C,MAAM,SAAS,GAAG,CAAC,CAAA;YACnB,mCAAmC;YACnC,iEAAiE;YACjE,8BAA8B;YAC9B,MAAM,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,MAAM,EAAE,SAAS,EAAE,SAAS,GAAG,YAAY,CAAC,CAAA;YAC1E,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;YAClB,OAAO,IAAA,qBAAe,EAAC,IAAI,CAAC,CAAA;QAC9B,CAAC;KAAA;IAEK,aAAa;;YACjB,MAAM,IAAI,CAAC,YAAY,EAAE,CAAA;YACzB,OAAO,IAAI,CAAC,MAAM,CAAA;QACpB,CAAC;KAAA;IAED,UAAU;IACJ,iBAAiB;;YACrB,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;YACnD,OAAO,IAAA,kCAAiB,EAAC,YAAY,CAAC,CAAA;QACxC,CAAC;KAAA;IAEK,gBAAgB,CAAC,eAAuB;;YAC5C,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;YACrD,IAAI,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;YAC1D,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;YACjD,MAAM,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;YAE/C,sDAAsD;YACtD,IAAI,gBAAgB,CAAA;YACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,eAAe,EAAE,CAAC,IAAI,CAAC,EAAE;gBAC5C,gDAAgD;gBAChD,uDAAuD;gBACvD,IAAI,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,IAAI,QAAQ,EAAE;oBAC7D,OAAO,SAAS,CAAA;iBACjB;gBAED,gBAAgB,GAAG,IAAI,CAAC,sBAAsB,CAAC,QAAQ,CAAC,CAAA;gBACxD,MAAM,aAAa,GAAG,MAAM,gBAAgB,CAAC,SAAS,EAAE,CAAA;gBACxD,IAAI,CAAC,aAAa,EAAE;oBAClB,MAAM,IAAI,2BAAkB,CAC1B,aAAa,eAAe,oBAAoB,CACjD,CAAA;iBACF;gBACD,6DAA6D;gBAC7D,6DAA6D;gBAC7D,6DAA6D;gBAC7D,YAAY;gBACZ,IAAI,CAAC,KAAK,CAAC,EAAE;oBACX,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;oBACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;wBACnD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;wBAC5C,IAAI,KAAK,KAAK,SAAS,EAAE;4BACvB,OAAO,SAAS,CAAA;yBACjB;wBACD,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;qBAC9B;iBACF;qBAAM;oBACL,8EAA8E;oBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;iBACvD;aACF;YAED,OAAO,gBAAgB,CAAA;QACzB,CAAC;KAAA;IAEK,UAAU,CACd,QAAgB,EAChB,MAAc,EACd,aAAqB,EACrB,WAAmB;;YAEnB,MAAM,CAAC,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;YACpC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;YAC5C,MAAM,eAAe,GAAG,sBAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;YACzC,IAAI,eAAe,KAAK,aAAa,EAAE;gBACrC,MAAM,IAAI,2BAAkB,CAC1B,mBAAmB,WAAW,sBAAsB,aAAa,4BAA4B,eAAe,EAAE,CAC/G,CAAA;aACF;QACH,CAAC;KAAA;IAED;;OAEG;IACG,cAAc;;YAClB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;YACrD,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;YACjD,MAAM,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;YAE/C,IAAI,cAAc,GAAG,CAAC,CAAA;YACtB,IAAI,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;YAC1D,OAAO,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,GAAG,QAAQ,EAAE;gBAC/D,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,sBAAsB,CACrD,QAAQ,CACT,CAAC,SAAS,EAAE,CAAA;gBACb,IAAI,CAAC,aAAa,EAAE;oBAClB,MAAK;iBACN;gBACD,6DAA6D;gBAC7D,mDAAmD;gBACnD,yDAAyD;gBACzD,IAAI,cAAc,KAAK,CAAC,EAAE;oBACxB,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;oBACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;wBACnD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;wBAC5C,IAAI,KAAK,KAAK,SAAS,EAAE;4BACvB,OAAO,SAAS,CAAA;yBACjB;wBACD,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;qBAC9B;iBACF;qBAAM;oBACL,8EAA8E;oBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;iBACvD;gBACD,cAAc,IAAI,CAAC,CAAA;aACpB;YAED,OAAO,cAAc,CAAA;QACvB,CAAC;KAAA;IAED,sBAAsB,CAAC,QAAgB;QACrC,OAAO,IAAI,mBAAa,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAA;IAC1C,CAAC;IAEK,eAAe,CAAC,QAAgB;;YACpC,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;YACrD,MAAM,EAAE,eAAe,EAAE,GAAG,cAAc,CAAA;YAC1C,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;YAEjD,IAAI,QAAQ,GAAG,eAAe,CAAC,SAAS,IAAI,QAAQ,EAAE;gBACpD,OAAO,SAAS,CAAA;aACjB;YAED,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,eAAe,CAAC,SAAS,CAAC,CAAA;YAC5D,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,eAAe,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;YACpE,OAAO,IAAA,gBAAS,EAAC,MAAM,EAAE,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QAC/D,CAAC;KAAA;IAEK,aAAa,CACjB,OAAiD,EACjD,QAAgB,EAChB,IAAI,GAAG,OAAO,CAAC,SAAS,EACxB,aAAa,GAAG,SAAS;;YAEzB,IAAI,MAAM,CAAA;YACV,IAAI,aAAa,EAAE;gBACjB,MAAM,GAAG,aAAa,CAAA;aACvB;iBAAM;gBACL,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;gBACjD,IAAI,QAAQ,GAAG,IAAI,IAAI,QAAQ,EAAE;oBAC/B,OAAO,SAAS,CAAA;iBACjB;gBACD,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;gBACjC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,IAAI,EAAE,QAAQ,CAAC,CAAA;aAChD;YACD,MAAM,IAAI,GAAG,IAAA,gBAAS,EAAC,MAAM,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;YAC3D,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;gBACvB,MAAM,IAAI,2BAAkB,CAC1B,sCAAsC,IAAI,+BAA+B,IAAI,CAAC,KAAK,EAAE,CACtF,CAAA;aACF;YACD,OAAO,IAAI,CAAA;QACb,CAAC;KAAA;IAED,WAAW,CACT,iBAAoC,EACpC,WAAmB,EACnB,YAAoB;QAEpB,IAAI,iBAAiB,KAAK,MAAM,EAAE;YAChC,MAAM,MAAM,GAAG,IAAA,aAAK,EAAC,WAAW,CAAC,CAAA;YACjC,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;SAC1B;aAAM,IAAI,iBAAiB,KAAK,OAAO,EAAE;YACxC,MAAM,IAAI,GAAG,eAAK,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;YACrC,IAAI,IAAI,GAAG,eAAK,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YAC7B,IAAI,CAAC,GAAG,CAAC,CAAA;YACT,IAAI,KAAK,CAAA;YACT,GAAG;gBACD,KAAK,GAAG,eAAK,CAAC,UAAU,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBACpC,IAAI,KAAK,IAAI,CAAC,CAAC,EAAE;oBACf,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,CAAC,CAAA;oBACxC,CAAC,IAAI,KAAK,CAAC,MAAM,CAAA;oBACjB,IAAI,IAAI,KAAK,CAAC,MAAM,CAAA;iBACrB;aACF,QAAQ,KAAK,IAAI,CAAC,CAAC,EAAC;SACtB;aAAM,IAAI,iBAAiB,KAAK,MAAM,EAAE;YACvC,IAAA,cAAc,EAAC,WAAW,EAAE,YAAY,CAAC,CAAA;YACzC,2CAA2C;YAC3C,uDAAuD;SACxD;aAAM,IAAI,iBAAiB,KAAK,UAAU,EAAE;YAC3C,mBAAS,CAAC,gBAAgB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACtD;aAAM,IAAI,iBAAiB,KAAK,OAAO,EAAE;YACxC,mBAAS,CAAC,gBAAgB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACtD;aAAM,IAAI,iBAAiB,KAAK,SAAS,EAAE;YAC1C,mBAAS,CAAC,kBAAkB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACxD;aAAM,IAAI,iBAAiB,KAAK,MAAM,EAAE;YACvC,mBAAS,CAAC,eAAe,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACrD;aAAM;YACL,MAAM,IAAI,+BAAsB,CAC9B,GAAG,iBAAiB,oCAAoC,CACzD,CAAA;SACF;IACH,CAAC;IAEK,SAAS,CAAC,QAAgB;;YAC9B,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;YACnD,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;YACrD,MAAM,WAAW,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,QAAQ,CAAC,CAAA;YACxD,IAAI,WAAW,KAAK,SAAS,EAAE;gBAC7B,OAAO,SAAS,CAAA;aACjB;YACD,MAAM,oBAAoB,GAAG,WAAW,CAAC,YAAY,CAAA;YAErD,MAAM,gBAAgB,GAAG,MAAM,CAAC,WAAW,CAAC,WAAW,CAAC,gBAAgB,CAAC,CAAA;YAEzE,MAAM,KAAK,mCACN,WAAW,KACd,YAAY,EAAE,oBAAoB,EAClC,eAAe,EAAE,oBAAoB,EACrC,OAAO,EAAE,gBAAgB,GAC1B,CAAA;YAED,IAAI,WAAW,CAAC,iBAAiB,KAAK,KAAK,EAAE;gBAC3C,MAAM,cAAc,GAAG,MAAM,CAAC,WAAW,CAAC,WAAW,CAAC,cAAc,CAAC,CAAA;gBACrE,MAAM,IAAI,CAAC,IAAI,CACb,cAAc,EACd,CAAC,EACD,WAAW,CAAC,cAAc,EAC1B,oBAAoB,CACrB,CAAA;gBAED,IAAI,CAAC,WAAW,CACd,WAAW,CAAC,iBAAiB,EAC7B,cAAc,EACd,gBAAgB,CACjB,CAAA;aACF;iBAAM;gBACL,MAAM,IAAI,CAAC,IAAI,CACb,gBAAgB,EAChB,CAAC,EACD,WAAW,CAAC,gBAAgB,EAC5B,oBAAoB,CACrB,CAAA;aACF;YAED,IAAI,YAAY,IAAI,CAAC,EAAE;gBACrB,kBAAkB;gBAClB,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,aAAa,CAClC,cAAc,CAAC,cAAc,EAC7B,oBAAoB,GAAG,WAAW,CAAC,cAAc,CAClD,CAAA;gBACD,IAAI,GAAG,KAAK,SAAS,EAAE;oBACrB,OAAO,SAAS,CAAA;iBACjB;gBACD,KAAK,CAAC,KAAK,GAAG,GAAG,CAAC,KAAK,CAAA;gBAEvB,6BAA6B;gBAC7B,IAAI,IAAI,CAAC,iBAAiB,EAAE;oBAC1B,MAAM,IAAI,CAAC,UAAU,CACnB,QAAQ,EACR,WAAW,CAAC,KAAK,GAAG,WAAW,CAAC,cAAc,EAC9C,GAAG,CAAC,KAAK,EACT,YAAY,CACb,CAAA;iBACF;gBAED,wDAAwD;gBACxD,KAAK,CAAC,YAAY,GAAG,GAAG,CAAC,YAAY,CAAA;gBACrC,KAAK,CAAC,KAAK;oBACT,KAAK,CAAC,cAAc,GAAG,cAAc,CAAC,cAAc,CAAC,SAAS,CAAA;aACjE;iBAAM;gBACL,KAAK,CAAC,YAAY,GAAG,oBAAoB,GAAG,KAAK,CAAC,cAAc,CAAA;gBAChE,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,cAAc,CAAA;aACnC;YAED,OAAO,KAAK,CAAA;QACd,CAAC;KAAA;CACF;AA7WD,2BA6WC;AAED,8CAA8C;KAC3C,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,IAAA,kBAAW,EAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAAA"}
|
|
@@ -107,7 +107,7 @@ export default class CramRecord {
|
|
|
107
107
|
/**
|
|
108
108
|
* Annotates this feature with the given reference sequence basepair
|
|
109
109
|
* information. This will add a `sub` and a `ref` item to base
|
|
110
|
-
*
|
|
110
|
+
* substitution read features given the actual substituted and reference
|
|
111
111
|
* base pairs, and will make the `getReadSequence()` method work.
|
|
112
112
|
*
|
|
113
113
|
* @param {object} refRegion
|
package/dist/cramFile/record.js
CHANGED
|
@@ -336,7 +336,7 @@ class CramRecord {
|
|
|
336
336
|
/**
|
|
337
337
|
* Annotates this feature with the given reference sequence basepair
|
|
338
338
|
* information. This will add a `sub` and a `ref` item to base
|
|
339
|
-
*
|
|
339
|
+
* substitution read features given the actual substituted and reference
|
|
340
340
|
* base pairs, and will make the `getReadSequence()` method work.
|
|
341
341
|
*
|
|
342
342
|
* @param {object} refRegion
|
package/esm/cramFile/file.js
CHANGED
|
@@ -1,6 +1,8 @@
|
|
|
1
1
|
import { unzip } from '../unzip';
|
|
2
2
|
import crc32 from 'buffer-crc32';
|
|
3
3
|
import QuickLRU from 'quick-lru';
|
|
4
|
+
// @ts-expect-error
|
|
5
|
+
import bzip2 from 'bzip2';
|
|
4
6
|
import { CramMalformedError, CramUnimplementedError } from '../errors';
|
|
5
7
|
import ransuncompress from '../rans';
|
|
6
8
|
import { cramFileDefinition as cramFileDefinitionParser, getSectionParsers, } from './sectionParsers';
|
package/esm/cramFile/file.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"file.js","sourceRoot":"","sources":["../../src/cramFile/file.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,UAAU,CAAA;AAChC,OAAO,KAAK,MAAM,cAAc,CAAA;AAChC,OAAO,QAAQ,MAAM,WAAW,CAAA;AAEhC,OAAO,EAAE,kBAAkB,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AACtE,OAAO,cAAc,MAAM,SAAS,CAAA;AACpC,OAAO,EAGL,kBAAkB,IAAI,wBAAwB,EAC9C,iBAAiB,GAClB,MAAM,kBAAkB,CAAA;AACzB,OAAO,SAAS,MAAM,uBAAuB,CAAA;AAC7C,OAAO,aAAa,MAAM,aAAa,CAAA;AAEvC,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAC5B,OAAO,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,QAAQ,CAAA;AAKxC,+EAA+E;AAC/E,SAAS,aAAa;IACpB,MAAM,MAAM,GAAG,IAAI,WAAW,CAAC,CAAC,UAAU,CAAC,CAAC,CAAA;IAC5C,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;IAE3C,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;QACrB,OAAO,CAAC,CAAA,CAAC,eAAe;KACzB;SAAM,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;QAC5B,OAAO,CAAC,CAAA,CAAC,YAAY;KACtB;SAAM;QACL,OAAO,CAAC,CAAA,CAAC,eAAe;KACzB;AACH,CAAC;AAiCD,MAAM,CAAC,OAAO,OAAO,QAAQ;IAW3B,YAAY,IAAkB;;QAC5B,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QACtD,IAAI,CAAC,iBAAiB,GAAG,IAAI,CAAA;QAC7B,IAAI,CAAC,8BAA8B,GAAG,IAAI,CAAC,QAAQ,CAAA;QACnD,IAAI,CAAC,OAAO,GAAG;YACb,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;YACvC,SAAS,EAAE,MAAA,IAAI,CAAC,SAAS,mCAAI,KAAK;SACnC,CAAA;QAED,6CAA6C;QAC7C,gEAAgE;QAChE,4DAA4D;QAC5D,qCAAqC;QACrC,IAAI,CAAC,YAAY,GAAG,IAAI,QAAQ,CAAC;YAC/B,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,SAAS;SAChC,CAAC,CAAA;QACF,IAAI,aAAa,EAAE,GAAG,CAAC,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;SACrE;IACH,CAAC;IAED,eAAe;IACf,8BAA8B;IAC9B,gCAAgC;IAChC,MAAM;IACN,yBAAyB;IACzB,2BAA2B;IAC3B,MAAM;IACN,EAAE;IACF,yBAAyB;IACzB,IAAI;IAEJ,8CAA8C;IAC9C,IAAI,CACF,MAAc,EACd,MAAc,EACd,MAAc,EACd,QAAgB;QAKhB,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;IACzD,CAAC;IAED,8CAA8C;IAC9C,IAAI;QACF,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACzB,CAAC;IAED,WAAW;IACX,KAAK,CAAC,aAAa;QACjB,MAAM,SAAS,GAAG,MAAM,CAAC,WAAW,CAAC,wBAAwB,CAAC,SAAS,CAAC,CAAA;QACxE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC,EAAE,wBAAwB,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QACzE,MAAM,UAAU,GAAG,wBAAwB,CAAC,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC;aAChE,MAAa,CAAA;QAChB,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,EAAE;YAClE,MAAM,IAAI,sBAAsB,CAC9B,gBAAgB,UAAU,CAAC,YAAY,gBAAgB,CACxD,CAAA;SACF;QACD,OAAO,UAAU,CAAA;IACnB,CAAC;IAED,UAAU;IACV,KAAK,CAAC,YAAY;QAChB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAA;QACrD,IAAI,CAAC,cAAc,EAAE;YACnB,MAAM,IAAI,kBAAkB,CAAC,6BAA6B,CAAC,CAAA;SAC5D;QAED,MAAM,UAAU,GAAG,MAAM,cAAc,CAAC,aAAa,EAAE,CAAA;QACvD,IAAI,UAAU,KAAK,SAAS,EAAE;YAC5B,OAAO,eAAe,CAAC,EAAE,CAAC,CAAA;SAC3B;QACD,MAAM,OAAO,GAAG,UAAU,CAAC,OAAO,CAAA;QAClC,wDAAwD;QACxD,MAAM,YAAY,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC3C,MAAM,SAAS,GAAG,CAAC,CAAA;QACnB,mCAAmC;QACnC,iEAAiE;QACjE,8BAA8B;QAC9B,MAAM,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,MAAM,EAAE,SAAS,EAAE,SAAS,GAAG,YAAY,CAAC,CAAA;QAC1E,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;QAClB,OAAO,eAAe,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,IAAI,CAAC,YAAY,EAAE,CAAA;QACzB,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,UAAU;IACV,KAAK,CAAC,iBAAiB;QACrB,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACnD,OAAO,iBAAiB,CAAC,YAAY,CAAC,CAAA;IACxC,CAAC;IAED,KAAK,CAAC,gBAAgB,CAAC,eAAuB;QAC5C,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,IAAI,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;QAC1D,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QACjD,MAAM,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QAE/C,sDAAsD;QACtD,IAAI,gBAAgB,CAAA;QACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,eAAe,EAAE,CAAC,IAAI,CAAC,EAAE;YAC5C,gDAAgD;YAChD,uDAAuD;YACvD,IAAI,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,IAAI,QAAQ,EAAE;gBAC7D,OAAO,SAAS,CAAA;aACjB;YAED,gBAAgB,GAAG,IAAI,CAAC,sBAAsB,CAAC,QAAQ,CAAC,CAAA;YACxD,MAAM,aAAa,GAAG,MAAM,gBAAgB,CAAC,SAAS,EAAE,CAAA;YACxD,IAAI,CAAC,aAAa,EAAE;gBAClB,MAAM,IAAI,kBAAkB,CAC1B,aAAa,eAAe,oBAAoB,CACjD,CAAA;aACF;YACD,6DAA6D;YAC7D,6DAA6D;YAC7D,6DAA6D;YAC7D,YAAY;YACZ,IAAI,CAAC,KAAK,CAAC,EAAE;gBACX,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;gBACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;oBACnD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;oBAC5C,IAAI,KAAK,KAAK,SAAS,EAAE;wBACvB,OAAO,SAAS,CAAA;qBACjB;oBACD,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;iBAC9B;aACF;iBAAM;gBACL,8EAA8E;gBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;aACvD;SACF;QAED,OAAO,gBAAgB,CAAA;IACzB,CAAC;IAED,KAAK,CAAC,UAAU,CACd,QAAgB,EAChB,MAAc,EACd,aAAqB,EACrB,WAAmB;QAEnB,MAAM,CAAC,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QACpC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;QAC5C,MAAM,eAAe,GAAG,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QACzC,IAAI,eAAe,KAAK,aAAa,EAAE;YACrC,MAAM,IAAI,kBAAkB,CAC1B,mBAAmB,WAAW,sBAAsB,aAAa,4BAA4B,eAAe,EAAE,CAC/G,CAAA;SACF;IACH,CAAC;IAED;;OAEG;IACH,KAAK,CAAC,cAAc;QAClB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QACjD,MAAM,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QAE/C,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,IAAI,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;QAC1D,OAAO,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,GAAG,QAAQ,EAAE;YAC/D,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,sBAAsB,CACrD,QAAQ,CACT,CAAC,SAAS,EAAE,CAAA;YACb,IAAI,CAAC,aAAa,EAAE;gBAClB,MAAK;aACN;YACD,6DAA6D;YAC7D,mDAAmD;YACnD,yDAAyD;YACzD,IAAI,cAAc,KAAK,CAAC,EAAE;gBACxB,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;gBACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;oBACnD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;oBAC5C,IAAI,KAAK,KAAK,SAAS,EAAE;wBACvB,OAAO,SAAS,CAAA;qBACjB;oBACD,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;iBAC9B;aACF;iBAAM;gBACL,8EAA8E;gBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;aACvD;YACD,cAAc,IAAI,CAAC,CAAA;SACpB;QAED,OAAO,cAAc,CAAA;IACvB,CAAC;IAED,sBAAsB,CAAC,QAAgB;QACrC,OAAO,IAAI,aAAa,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAA;IAC1C,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,QAAgB;QACpC,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,MAAM,EAAE,eAAe,EAAE,GAAG,cAAc,CAAA;QAC1C,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QAEjD,IAAI,QAAQ,GAAG,eAAe,CAAC,SAAS,IAAI,QAAQ,EAAE;YACpD,OAAO,SAAS,CAAA;SACjB;QAED,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,eAAe,CAAC,SAAS,CAAC,CAAA;QAC5D,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,eAAe,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;QACpE,OAAO,SAAS,CAAC,MAAM,EAAE,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;IAC/D,CAAC;IAED,KAAK,CAAC,aAAa,CACjB,OAAiD,EACjD,QAAgB,EAChB,IAAI,GAAG,OAAO,CAAC,SAAS,EACxB,aAAa,GAAG,SAAS;QAEzB,IAAI,MAAM,CAAA;QACV,IAAI,aAAa,EAAE;YACjB,MAAM,GAAG,aAAa,CAAA;SACvB;aAAM;YACL,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;YACjD,IAAI,QAAQ,GAAG,IAAI,IAAI,QAAQ,EAAE;gBAC/B,OAAO,SAAS,CAAA;aACjB;YACD,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;YACjC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,IAAI,EAAE,QAAQ,CAAC,CAAA;SAChD;QACD,MAAM,IAAI,GAAG,SAAS,CAAC,MAAM,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QAC3D,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,MAAM,IAAI,kBAAkB,CAC1B,sCAAsC,IAAI,+BAA+B,IAAI,CAAC,KAAK,EAAE,CACtF,CAAA;SACF;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,WAAW,CACT,iBAAoC,EACpC,WAAmB,EACnB,YAAoB;QAEpB,IAAI,iBAAiB,KAAK,MAAM,EAAE;YAChC,MAAM,MAAM,GAAG,KAAK,CAAC,WAAW,CAAC,CAAA;YACjC,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;SAC1B;aAAM,IAAI,iBAAiB,KAAK,OAAO,EAAE;YACxC,MAAM,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;YACrC,IAAI,IAAI,GAAG,KAAK,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YAC7B,IAAI,CAAC,GAAG,CAAC,CAAA;YACT,IAAI,KAAK,CAAA;YACT,GAAG;gBACD,KAAK,GAAG,KAAK,CAAC,UAAU,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBACpC,IAAI,KAAK,IAAI,CAAC,CAAC,EAAE;oBACf,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,CAAC,CAAA;oBACxC,CAAC,IAAI,KAAK,CAAC,MAAM,CAAA;oBACjB,IAAI,IAAI,KAAK,CAAC,MAAM,CAAA;iBACrB;aACF,QAAQ,KAAK,IAAI,CAAC,CAAC,EAAC;SACtB;aAAM,IAAI,iBAAiB,KAAK,MAAM,EAAE;YACvC,cAAc,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;YACzC,2CAA2C;YAC3C,uDAAuD;SACxD;aAAM,IAAI,iBAAiB,KAAK,UAAU,EAAE;YAC3C,SAAS,CAAC,gBAAgB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACtD;aAAM,IAAI,iBAAiB,KAAK,OAAO,EAAE;YACxC,SAAS,CAAC,gBAAgB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACtD;aAAM,IAAI,iBAAiB,KAAK,SAAS,EAAE;YAC1C,SAAS,CAAC,kBAAkB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACxD;aAAM,IAAI,iBAAiB,KAAK,MAAM,EAAE;YACvC,SAAS,CAAC,eAAe,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACrD;aAAM;YACL,MAAM,IAAI,sBAAsB,CAC9B,GAAG,iBAAiB,oCAAoC,CACzD,CAAA;SACF;IACH,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,QAAgB;QAC9B,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACnD,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,QAAQ,CAAC,CAAA;QACxD,IAAI,WAAW,KAAK,SAAS,EAAE;YAC7B,OAAO,SAAS,CAAA;SACjB;QACD,MAAM,oBAAoB,GAAG,WAAW,CAAC,YAAY,CAAA;QAErD,MAAM,gBAAgB,GAAG,MAAM,CAAC,WAAW,CAAC,WAAW,CAAC,gBAAgB,CAAC,CAAA;QAEzE,MAAM,KAAK,GAAkB;YAC3B,GAAG,WAAW;YACd,YAAY,EAAE,oBAAoB;YAClC,eAAe,EAAE,oBAAoB;YACrC,OAAO,EAAE,gBAAgB;SAC1B,CAAA;QAED,IAAI,WAAW,CAAC,iBAAiB,KAAK,KAAK,EAAE;YAC3C,MAAM,cAAc,GAAG,MAAM,CAAC,WAAW,CAAC,WAAW,CAAC,cAAc,CAAC,CAAA;YACrE,MAAM,IAAI,CAAC,IAAI,CACb,cAAc,EACd,CAAC,EACD,WAAW,CAAC,cAAc,EAC1B,oBAAoB,CACrB,CAAA;YAED,IAAI,CAAC,WAAW,CACd,WAAW,CAAC,iBAAiB,EAC7B,cAAc,EACd,gBAAgB,CACjB,CAAA;SACF;aAAM;YACL,MAAM,IAAI,CAAC,IAAI,CACb,gBAAgB,EAChB,CAAC,EACD,WAAW,CAAC,gBAAgB,EAC5B,oBAAoB,CACrB,CAAA;SACF;QAED,IAAI,YAAY,IAAI,CAAC,EAAE;YACrB,kBAAkB;YAClB,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,aAAa,CAClC,cAAc,CAAC,cAAc,EAC7B,oBAAoB,GAAG,WAAW,CAAC,cAAc,CAClD,CAAA;YACD,IAAI,GAAG,KAAK,SAAS,EAAE;gBACrB,OAAO,SAAS,CAAA;aACjB;YACD,KAAK,CAAC,KAAK,GAAG,GAAG,CAAC,KAAK,CAAA;YAEvB,6BAA6B;YAC7B,IAAI,IAAI,CAAC,iBAAiB,EAAE;gBAC1B,MAAM,IAAI,CAAC,UAAU,CACnB,QAAQ,EACR,WAAW,CAAC,KAAK,GAAG,WAAW,CAAC,cAAc,EAC9C,GAAG,CAAC,KAAK,EACT,YAAY,CACb,CAAA;aACF;YAED,wDAAwD;YACxD,KAAK,CAAC,YAAY,GAAG,GAAG,CAAC,YAAY,CAAA;YACrC,KAAK,CAAC,KAAK;gBACT,KAAK,CAAC,cAAc,GAAG,cAAc,CAAC,cAAc,CAAC,SAAS,CAAA;SACjE;aAAM;YACL,KAAK,CAAC,YAAY,GAAG,oBAAoB,GAAG,KAAK,CAAC,cAAc,CAAA;YAChE,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,cAAc,CAAA;SACnC;QAED,OAAO,KAAK,CAAA;IACd,CAAC;CACF;AAED,8CAA8C;KAC3C,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAAA"}
|
|
1
|
+
{"version":3,"file":"file.js","sourceRoot":"","sources":["../../src/cramFile/file.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,KAAK,EAAE,MAAM,UAAU,CAAA;AAChC,OAAO,KAAK,MAAM,cAAc,CAAA;AAChC,OAAO,QAAQ,MAAM,WAAW,CAAA;AAChC,mBAAmB;AACnB,OAAO,KAAK,MAAM,OAAO,CAAA;AAEzB,OAAO,EAAE,kBAAkB,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AACtE,OAAO,cAAc,MAAM,SAAS,CAAA;AACpC,OAAO,EAGL,kBAAkB,IAAI,wBAAwB,EAC9C,iBAAiB,GAClB,MAAM,kBAAkB,CAAA;AACzB,OAAO,SAAS,MAAM,uBAAuB,CAAA;AAC7C,OAAO,aAAa,MAAM,aAAa,CAAA;AAEvC,OAAO,EAAE,IAAI,EAAE,MAAM,OAAO,CAAA;AAC5B,OAAO,EAAE,SAAS,EAAE,WAAW,EAAE,MAAM,QAAQ,CAAA;AAC/C,OAAO,EAAE,eAAe,EAAE,MAAM,QAAQ,CAAA;AAKxC,+EAA+E;AAC/E,SAAS,aAAa;IACpB,MAAM,MAAM,GAAG,IAAI,WAAW,CAAC,CAAC,UAAU,CAAC,CAAC,CAAA;IAC5C,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,MAAM,CAAC,MAAM,CAAC,CAAA;IAE3C,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;QACrB,OAAO,CAAC,CAAA,CAAC,eAAe;KACzB;SAAM,IAAI,KAAK,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE;QAC5B,OAAO,CAAC,CAAA,CAAC,YAAY;KACtB;SAAM;QACL,OAAO,CAAC,CAAA,CAAC,eAAe;KACzB;AACH,CAAC;AAiCD,MAAM,CAAC,OAAO,OAAO,QAAQ;IAW3B,YAAY,IAAkB;;QAC5B,IAAI,CAAC,IAAI,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QACtD,IAAI,CAAC,iBAAiB,GAAG,IAAI,CAAA;QAC7B,IAAI,CAAC,8BAA8B,GAAG,IAAI,CAAC,QAAQ,CAAA;QACnD,IAAI,CAAC,OAAO,GAAG;YACb,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;YACvC,SAAS,EAAE,MAAA,IAAI,CAAC,SAAS,mCAAI,KAAK;SACnC,CAAA;QAED,6CAA6C;QAC7C,gEAAgE;QAChE,4DAA4D;QAC5D,qCAAqC;QACrC,IAAI,CAAC,YAAY,GAAG,IAAI,QAAQ,CAAC;YAC/B,OAAO,EAAE,IAAI,CAAC,OAAO,CAAC,SAAS;SAChC,CAAC,CAAA;QACF,IAAI,aAAa,EAAE,GAAG,CAAC,EAAE;YACvB,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;SACrE;IACH,CAAC;IAED,eAAe;IACf,8BAA8B;IAC9B,gCAAgC;IAChC,MAAM;IACN,yBAAyB;IACzB,2BAA2B;IAC3B,MAAM;IACN,EAAE;IACF,yBAAyB;IACzB,IAAI;IAEJ,8CAA8C;IAC9C,IAAI,CACF,MAAc,EACd,MAAc,EACd,MAAc,EACd,QAAgB;QAKhB,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;IACzD,CAAC;IAED,8CAA8C;IAC9C,IAAI;QACF,OAAO,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;IACzB,CAAC;IAED,WAAW;IACX,KAAK,CAAC,aAAa;QACjB,MAAM,SAAS,GAAG,MAAM,CAAC,WAAW,CAAC,wBAAwB,CAAC,SAAS,CAAC,CAAA;QACxE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,SAAS,EAAE,CAAC,EAAE,wBAAwB,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QACzE,MAAM,UAAU,GAAG,wBAAwB,CAAC,MAAM,CAAC,KAAK,CAAC,SAAS,CAAC;aAChE,MAAa,CAAA;QAChB,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,IAAI,UAAU,CAAC,YAAY,KAAK,CAAC,EAAE;YAClE,MAAM,IAAI,sBAAsB,CAC9B,gBAAgB,UAAU,CAAC,YAAY,gBAAgB,CACxD,CAAA;SACF;QACD,OAAO,UAAU,CAAA;IACnB,CAAC;IAED,UAAU;IACV,KAAK,CAAC,YAAY;QAChB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAA;QACrD,IAAI,CAAC,cAAc,EAAE;YACnB,MAAM,IAAI,kBAAkB,CAAC,6BAA6B,CAAC,CAAA;SAC5D;QAED,MAAM,UAAU,GAAG,MAAM,cAAc,CAAC,aAAa,EAAE,CAAA;QACvD,IAAI,UAAU,KAAK,SAAS,EAAE;YAC5B,OAAO,eAAe,CAAC,EAAE,CAAC,CAAA;SAC3B;QACD,MAAM,OAAO,GAAG,UAAU,CAAC,OAAO,CAAA;QAClC,wDAAwD;QACxD,MAAM,YAAY,GAAG,OAAO,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;QAC3C,MAAM,SAAS,GAAG,CAAC,CAAA;QACnB,mCAAmC;QACnC,iEAAiE;QACjE,8BAA8B;QAC9B,MAAM,IAAI,GAAG,OAAO,CAAC,QAAQ,CAAC,MAAM,EAAE,SAAS,EAAE,SAAS,GAAG,YAAY,CAAC,CAAA;QAC1E,IAAI,CAAC,MAAM,GAAG,IAAI,CAAA;QAClB,OAAO,eAAe,CAAC,IAAI,CAAC,CAAA;IAC9B,CAAC;IAED,KAAK,CAAC,aAAa;QACjB,MAAM,IAAI,CAAC,YAAY,EAAE,CAAA;QACzB,OAAO,IAAI,CAAC,MAAM,CAAA;IACpB,CAAC;IAED,UAAU;IACV,KAAK,CAAC,iBAAiB;QACrB,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACnD,OAAO,iBAAiB,CAAC,YAAY,CAAC,CAAA;IACxC,CAAC;IAED,KAAK,CAAC,gBAAgB,CAAC,eAAuB;QAC5C,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,IAAI,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;QAC1D,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QACjD,MAAM,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QAE/C,sDAAsD;QACtD,IAAI,gBAAgB,CAAA;QACpB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,eAAe,EAAE,CAAC,IAAI,CAAC,EAAE;YAC5C,gDAAgD;YAChD,uDAAuD;YACvD,IAAI,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,IAAI,QAAQ,EAAE;gBAC7D,OAAO,SAAS,CAAA;aACjB;YAED,gBAAgB,GAAG,IAAI,CAAC,sBAAsB,CAAC,QAAQ,CAAC,CAAA;YACxD,MAAM,aAAa,GAAG,MAAM,gBAAgB,CAAC,SAAS,EAAE,CAAA;YACxD,IAAI,CAAC,aAAa,EAAE;gBAClB,MAAM,IAAI,kBAAkB,CAC1B,aAAa,eAAe,oBAAoB,CACjD,CAAA;aACF;YACD,6DAA6D;YAC7D,6DAA6D;YAC7D,6DAA6D;YAC7D,YAAY;YACZ,IAAI,CAAC,KAAK,CAAC,EAAE;gBACX,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;gBACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;oBACnD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;oBAC5C,IAAI,KAAK,KAAK,SAAS,EAAE;wBACvB,OAAO,SAAS,CAAA;qBACjB;oBACD,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;iBAC9B;aACF;iBAAM;gBACL,8EAA8E;gBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;aACvD;SACF;QAED,OAAO,gBAAgB,CAAA;IACzB,CAAC;IAED,KAAK,CAAC,UAAU,CACd,QAAgB,EAChB,MAAc,EACd,aAAqB,EACrB,WAAmB;QAEnB,MAAM,CAAC,GAAG,MAAM,CAAC,WAAW,CAAC,MAAM,CAAC,CAAA;QACpC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,MAAM,EAAE,QAAQ,CAAC,CAAA;QAC5C,MAAM,eAAe,GAAG,KAAK,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;QACzC,IAAI,eAAe,KAAK,aAAa,EAAE;YACrC,MAAM,IAAI,kBAAkB,CAC1B,mBAAmB,WAAW,sBAAsB,aAAa,4BAA4B,eAAe,EAAE,CAC/G,CAAA;SACF;IACH,CAAC;IAED;;OAEG;IACH,KAAK,CAAC,cAAc;QAClB,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QACjD,MAAM,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;QAE/C,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,IAAI,QAAQ,GAAG,cAAc,CAAC,kBAAkB,CAAC,SAAS,CAAA;QAC1D,OAAO,QAAQ,GAAG,oBAAoB,CAAC,SAAS,GAAG,CAAC,GAAG,QAAQ,EAAE;YAC/D,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,sBAAsB,CACrD,QAAQ,CACT,CAAC,SAAS,EAAE,CAAA;YACb,IAAI,CAAC,aAAa,EAAE;gBAClB,MAAK;aACN;YACD,6DAA6D;YAC7D,mDAAmD;YACnD,yDAAyD;YACzD,IAAI,cAAc,KAAK,CAAC,EAAE;gBACxB,QAAQ,GAAG,aAAa,CAAC,YAAY,CAAA;gBACrC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,CAAC,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;oBACnD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAA;oBAC5C,IAAI,KAAK,KAAK,SAAS,EAAE;wBACvB,OAAO,SAAS,CAAA;qBACjB;oBACD,QAAQ,GAAG,KAAK,CAAC,YAAY,CAAA;iBAC9B;aACF;iBAAM;gBACL,8EAA8E;gBAC9E,QAAQ,IAAI,aAAa,CAAC,KAAK,GAAG,aAAa,CAAC,MAAM,CAAA;aACvD;YACD,cAAc,IAAI,CAAC,CAAA;SACpB;QAED,OAAO,cAAc,CAAA;IACvB,CAAC;IAED,sBAAsB,CAAC,QAAgB;QACrC,OAAO,IAAI,aAAa,CAAC,IAAI,EAAE,QAAQ,CAAC,CAAA;IAC1C,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,QAAgB;QACpC,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,MAAM,EAAE,eAAe,EAAE,GAAG,cAAc,CAAA;QAC1C,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;QAEjD,IAAI,QAAQ,GAAG,eAAe,CAAC,SAAS,IAAI,QAAQ,EAAE;YACpD,OAAO,SAAS,CAAA;SACjB;QAED,MAAM,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,eAAe,CAAC,SAAS,CAAC,CAAA;QAC5D,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,eAAe,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;QACpE,OAAO,SAAS,CAAC,MAAM,EAAE,eAAe,CAAC,MAAM,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;IAC/D,CAAC;IAED,KAAK,CAAC,aAAa,CACjB,OAAiD,EACjD,QAAgB,EAChB,IAAI,GAAG,OAAO,CAAC,SAAS,EACxB,aAAa,GAAG,SAAS;QAEzB,IAAI,MAAM,CAAA;QACV,IAAI,aAAa,EAAE;YACjB,MAAM,GAAG,aAAa,CAAA;SACvB;aAAM;YACL,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;YACjD,IAAI,QAAQ,GAAG,IAAI,IAAI,QAAQ,EAAE;gBAC/B,OAAO,SAAS,CAAA;aACjB;YACD,MAAM,GAAG,MAAM,CAAC,WAAW,CAAC,IAAI,CAAC,CAAA;YACjC,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,IAAI,EAAE,QAAQ,CAAC,CAAA;SAChD;QACD,MAAM,IAAI,GAAG,SAAS,CAAC,MAAM,EAAE,OAAO,CAAC,MAAM,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QAC3D,IAAI,IAAI,CAAC,KAAK,KAAK,IAAI,EAAE;YACvB,MAAM,IAAI,kBAAkB,CAC1B,sCAAsC,IAAI,+BAA+B,IAAI,CAAC,KAAK,EAAE,CACtF,CAAA;SACF;QACD,OAAO,IAAI,CAAA;IACb,CAAC;IAED,WAAW,CACT,iBAAoC,EACpC,WAAmB,EACnB,YAAoB;QAEpB,IAAI,iBAAiB,KAAK,MAAM,EAAE;YAChC,MAAM,MAAM,GAAG,KAAK,CAAC,WAAW,CAAC,CAAA;YACjC,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;SAC1B;aAAM,IAAI,iBAAiB,KAAK,OAAO,EAAE;YACxC,MAAM,IAAI,GAAG,KAAK,CAAC,KAAK,CAAC,WAAW,CAAC,CAAA;YACrC,IAAI,IAAI,GAAG,KAAK,CAAC,MAAM,CAAC,IAAI,CAAC,CAAA;YAC7B,IAAI,CAAC,GAAG,CAAC,CAAA;YACT,IAAI,KAAK,CAAA;YACT,GAAG;gBACD,KAAK,GAAG,KAAK,CAAC,UAAU,CAAC,IAAI,EAAE,IAAI,CAAC,CAAA;gBACpC,IAAI,KAAK,IAAI,CAAC,CAAC,EAAE;oBACf,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC,YAAY,EAAE,CAAC,CAAC,CAAA;oBACxC,CAAC,IAAI,KAAK,CAAC,MAAM,CAAA;oBACjB,IAAI,IAAI,KAAK,CAAC,MAAM,CAAA;iBACrB;aACF,QAAQ,KAAK,IAAI,CAAC,CAAC,EAAC;SACtB;aAAM,IAAI,iBAAiB,KAAK,MAAM,EAAE;YACvC,cAAc,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;YACzC,2CAA2C;YAC3C,uDAAuD;SACxD;aAAM,IAAI,iBAAiB,KAAK,UAAU,EAAE;YAC3C,SAAS,CAAC,gBAAgB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACtD;aAAM,IAAI,iBAAiB,KAAK,OAAO,EAAE;YACxC,SAAS,CAAC,gBAAgB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACtD;aAAM,IAAI,iBAAiB,KAAK,SAAS,EAAE;YAC1C,SAAS,CAAC,kBAAkB,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACxD;aAAM,IAAI,iBAAiB,KAAK,MAAM,EAAE;YACvC,SAAS,CAAC,eAAe,CAAC,WAAW,EAAE,YAAY,CAAC,CAAA;SACrD;aAAM;YACL,MAAM,IAAI,sBAAsB,CAC9B,GAAG,iBAAiB,oCAAoC,CACzD,CAAA;SACF;IACH,CAAC;IAED,KAAK,CAAC,SAAS,CAAC,QAAgB;QAC9B,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;QACnD,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,iBAAiB,EAAE,CAAA;QACrD,MAAM,WAAW,GAAG,MAAM,IAAI,CAAC,eAAe,CAAC,QAAQ,CAAC,CAAA;QACxD,IAAI,WAAW,KAAK,SAAS,EAAE;YAC7B,OAAO,SAAS,CAAA;SACjB;QACD,MAAM,oBAAoB,GAAG,WAAW,CAAC,YAAY,CAAA;QAErD,MAAM,gBAAgB,GAAG,MAAM,CAAC,WAAW,CAAC,WAAW,CAAC,gBAAgB,CAAC,CAAA;QAEzE,MAAM,KAAK,GAAkB;YAC3B,GAAG,WAAW;YACd,YAAY,EAAE,oBAAoB;YAClC,eAAe,EAAE,oBAAoB;YACrC,OAAO,EAAE,gBAAgB;SAC1B,CAAA;QAED,IAAI,WAAW,CAAC,iBAAiB,KAAK,KAAK,EAAE;YAC3C,MAAM,cAAc,GAAG,MAAM,CAAC,WAAW,CAAC,WAAW,CAAC,cAAc,CAAC,CAAA;YACrE,MAAM,IAAI,CAAC,IAAI,CACb,cAAc,EACd,CAAC,EACD,WAAW,CAAC,cAAc,EAC1B,oBAAoB,CACrB,CAAA;YAED,IAAI,CAAC,WAAW,CACd,WAAW,CAAC,iBAAiB,EAC7B,cAAc,EACd,gBAAgB,CACjB,CAAA;SACF;aAAM;YACL,MAAM,IAAI,CAAC,IAAI,CACb,gBAAgB,EAChB,CAAC,EACD,WAAW,CAAC,gBAAgB,EAC5B,oBAAoB,CACrB,CAAA;SACF;QAED,IAAI,YAAY,IAAI,CAAC,EAAE;YACrB,kBAAkB;YAClB,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,aAAa,CAClC,cAAc,CAAC,cAAc,EAC7B,oBAAoB,GAAG,WAAW,CAAC,cAAc,CAClD,CAAA;YACD,IAAI,GAAG,KAAK,SAAS,EAAE;gBACrB,OAAO,SAAS,CAAA;aACjB;YACD,KAAK,CAAC,KAAK,GAAG,GAAG,CAAC,KAAK,CAAA;YAEvB,6BAA6B;YAC7B,IAAI,IAAI,CAAC,iBAAiB,EAAE;gBAC1B,MAAM,IAAI,CAAC,UAAU,CACnB,QAAQ,EACR,WAAW,CAAC,KAAK,GAAG,WAAW,CAAC,cAAc,EAC9C,GAAG,CAAC,KAAK,EACT,YAAY,CACb,CAAA;aACF;YAED,wDAAwD;YACxD,KAAK,CAAC,YAAY,GAAG,GAAG,CAAC,YAAY,CAAA;YACrC,KAAK,CAAC,KAAK;gBACT,KAAK,CAAC,cAAc,GAAG,cAAc,CAAC,cAAc,CAAC,SAAS,CAAA;SACjE;aAAM;YACL,KAAK,CAAC,YAAY,GAAG,oBAAoB,GAAG,KAAK,CAAC,cAAc,CAAA;YAChE,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,cAAc,CAAA;SACnC;QAED,OAAO,KAAK,CAAA;IACd,CAAC;CACF;AAED,8CAA8C;KAC3C,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,QAAQ,EAAE,MAAM,CAAC,CAAC,CAAA"}
|
package/esm/cramFile/record.d.ts
CHANGED
|
@@ -107,7 +107,7 @@ export default class CramRecord {
|
|
|
107
107
|
/**
|
|
108
108
|
* Annotates this feature with the given reference sequence basepair
|
|
109
109
|
* information. This will add a `sub` and a `ref` item to base
|
|
110
|
-
*
|
|
110
|
+
* substitution read features given the actual substituted and reference
|
|
111
111
|
* base pairs, and will make the `getReadSequence()` method work.
|
|
112
112
|
*
|
|
113
113
|
* @param {object} refRegion
|
package/esm/cramFile/record.js
CHANGED
|
@@ -330,7 +330,7 @@ export default class CramRecord {
|
|
|
330
330
|
/**
|
|
331
331
|
* Annotates this feature with the given reference sequence basepair
|
|
332
332
|
* information. This will add a `sub` and a `ref` item to base
|
|
333
|
-
*
|
|
333
|
+
* substitution read features given the actual substituted and reference
|
|
334
334
|
* base pairs, and will make the `getReadSequence()` method work.
|
|
335
335
|
*
|
|
336
336
|
* @param {object} refRegion
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/cram",
|
|
3
|
-
"version": "1.7.
|
|
3
|
+
"version": "1.7.4",
|
|
4
4
|
"description": "read CRAM files with pure Javascript",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/cram-js",
|
|
@@ -47,7 +47,6 @@
|
|
|
47
47
|
"abortable-promise-cache": "^1.2.0",
|
|
48
48
|
"buffer-crc32": "^0.2.13",
|
|
49
49
|
"bzip2": "^0.1.1",
|
|
50
|
-
"cross-fetch": "^3.0.0",
|
|
51
50
|
"long": "^4.0.0",
|
|
52
51
|
"md5": "^2.2.1",
|
|
53
52
|
"pako": "^1.0.4",
|
|
@@ -70,15 +69,15 @@
|
|
|
70
69
|
"eslint-config-prettier": "^8.5.0",
|
|
71
70
|
"eslint-plugin-import": "^2.25.4",
|
|
72
71
|
"eslint-plugin-prettier": "^4.0.0",
|
|
73
|
-
"glob": "^
|
|
72
|
+
"glob": "^10.3.1",
|
|
74
73
|
"jest": "^29.3.1",
|
|
75
74
|
"mock-fs": "^5.2.0",
|
|
76
75
|
"prettier": "^2.8.1",
|
|
77
|
-
"rimraf": "^
|
|
76
|
+
"rimraf": "^5.0.1",
|
|
78
77
|
"ts-jest": "^29.0.3",
|
|
79
|
-
"typescript": "^
|
|
78
|
+
"typescript": "^5.0.3",
|
|
80
79
|
"url": "^0.11.0",
|
|
81
|
-
"webpack": "5.
|
|
80
|
+
"webpack": "5.88.1",
|
|
82
81
|
"webpack-cli": "^5.0.1"
|
|
83
82
|
},
|
|
84
83
|
"publishConfig": {
|
package/src/cramFile/file.ts
CHANGED
|
@@ -1,6 +1,8 @@
|
|
|
1
1
|
import { unzip } from '../unzip'
|
|
2
2
|
import crc32 from 'buffer-crc32'
|
|
3
3
|
import QuickLRU from 'quick-lru'
|
|
4
|
+
// @ts-expect-error
|
|
5
|
+
import bzip2 from 'bzip2'
|
|
4
6
|
|
|
5
7
|
import { CramMalformedError, CramUnimplementedError } from '../errors'
|
|
6
8
|
import ransuncompress from '../rans'
|
package/src/cramFile/record.ts
CHANGED
|
@@ -450,7 +450,7 @@ export default class CramRecord {
|
|
|
450
450
|
/**
|
|
451
451
|
* Annotates this feature with the given reference sequence basepair
|
|
452
452
|
* information. This will add a `sub` and a `ref` item to base
|
|
453
|
-
*
|
|
453
|
+
* substitution read features given the actual substituted and reference
|
|
454
454
|
* base pairs, and will make the `getReadSequence()` method work.
|
|
455
455
|
*
|
|
456
456
|
* @param {object} refRegion
|
package/src/typings/bzip2.d.ts
DELETED