@gmod/cram 1.7.3 → 2.0.0
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 +13 -2
- package/README.md +343 -24
- package/dist/cram-bundle.js +1 -1
- package/dist/cram-bundle.js.LICENSE.txt +7 -1
- package/dist/cramFile/container/index.js.map +1 -1
- package/dist/cramFile/file.d.ts +2 -2
- package/dist/cramFile/file.js +58 -50
- package/dist/cramFile/file.js.map +1 -1
- package/dist/cramFile/record.d.ts +1 -1
- package/dist/cramFile/record.js +1 -1
- package/dist/rans/constants.d.ts +4 -3
- package/dist/rans/constants.js.map +1 -1
- package/dist/rans/d04.js +1 -0
- package/dist/rans/d04.js.map +1 -1
- package/dist/rans/d14.js +1 -0
- package/dist/rans/d14.js.map +1 -1
- package/dist/rans/decoding.d.ts +16 -19
- package/dist/rans/decoding.js +1 -0
- package/dist/rans/decoding.js.map +1 -1
- package/dist/rans/frequencies.d.ts +2 -2
- package/dist/rans/frequencies.js +1 -0
- package/dist/rans/frequencies.js.map +1 -1
- package/dist/rans/index.js +1 -0
- package/dist/rans/index.js.map +1 -1
- package/esm/cramFile/container/index.js.map +1 -1
- package/esm/cramFile/file.d.ts +2 -2
- package/esm/cramFile/file.js +19 -13
- package/esm/cramFile/file.js.map +1 -1
- package/esm/cramFile/record.d.ts +1 -1
- package/esm/cramFile/record.js +1 -1
- package/esm/rans/constants.d.ts +4 -3
- package/esm/rans/constants.js.map +1 -1
- package/esm/rans/d04.js +1 -0
- package/esm/rans/d04.js.map +1 -1
- package/esm/rans/d14.js +1 -0
- package/esm/rans/d14.js.map +1 -1
- package/esm/rans/decoding.d.ts +16 -19
- package/esm/rans/decoding.js +1 -0
- package/esm/rans/decoding.js.map +1 -1
- package/esm/rans/frequencies.d.ts +2 -2
- package/esm/rans/frequencies.js +1 -0
- package/esm/rans/frequencies.js.map +1 -1
- package/esm/rans/index.js +1 -0
- package/esm/rans/index.js.map +1 -1
- package/package.json +14 -14
- package/src/cramFile/container/index.ts +4 -1
- package/src/cramFile/file.ts +25 -19
- package/src/cramFile/record.ts +1 -1
- package/src/rans/{d04.js → d04.ts} +1 -0
- package/src/rans/{d14.js → d14.ts} +1 -0
- package/src/rans/{decoding.js → decoding.ts} +1 -0
- package/src/rans/{frequencies.js → frequencies.ts} +1 -0
- package/src/rans/{index.js → index.ts} +1 -0
- package/src/typings/bzip2.d.ts +0 -7
- /package/src/rans/{constants.js → constants.ts} +0 -0
package/esm/cramFile/file.js.map
CHANGED
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1
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-
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1
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+
{"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,OAAO,SAAS,MAAM,uBAAuB,CAAA;AAE7C,mBAAmB;AACnB,OAAO,KAAK,MAAM,OAAO,CAAA;AACzB,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAA;AAChD,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;AAEzB,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;AAIxC,SAAS,cAAc,CAAC,GAAW;IACjC,OAAO,IAAI,cAAc,CAAC;QACxB,KAAK,CAAC,UAAU;YACd,UAAU,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;YACvB,UAAU,CAAC,KAAK,EAAE,CAAA;QACpB,CAAC;KACF,CAAC,CAAA;AACJ,CAAC;AAED,+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,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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|
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/esm/rans/constants.d.ts
CHANGED
|
@@ -1,3 +1,4 @@
|
|
|
1
|
-
|
|
2
|
-
|
|
3
|
-
|
|
1
|
+
declare const TF_SHIFT = 12;
|
|
2
|
+
declare const TOTFREQ: number;
|
|
3
|
+
declare const RANS_BYTE_L: number;
|
|
4
|
+
export { TF_SHIFT, TOTFREQ, RANS_BYTE_L };
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../src/rans/constants.
|
|
1
|
+
{"version":3,"file":"constants.js","sourceRoot":"","sources":["../../src/rans/constants.ts"],"names":[],"mappings":"AAAA,MAAM,QAAQ,GAAG,EAAE,CAAA;AACnB,MAAM,OAAO,GAAG,CAAC,IAAI,QAAQ,CAAA;AAC7B,MAAM,WAAW,GAAG,CAAC,IAAI,EAAE,CAAA;AAE3B,OAAO,EAAE,QAAQ,EAAE,OAAO,EAAE,WAAW,EAAE,CAAA"}
|
package/esm/rans/d04.js
CHANGED
package/esm/rans/d04.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"d04.js","sourceRoot":"","sources":["../../src/rans/d04.
|
|
1
|
+
{"version":3,"file":"d04.js","sourceRoot":"","sources":["../../src/rans/d04.ts"],"names":[],"mappings":"AAAA,aAAa;AACb,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAA;AACtC,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,MAAM,CAAC,OAAO,UAAU,UAAU;AAChC,gBAAgB,CAAC,KAAK;AACtB,yBAAyB,CAAC,CAAC;AAC3B,uBAAuB,CAAC,IAAI;AAC5B,gBAAgB,CAAC,GAAG;IAEpB,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAE1B,MAAM,SAAS,CAAC,UAAU,GAAG,GAAG,CAAC,SAAS,EAAE,CAAA;IAC5C,MAAM,SAAS,CAAC,SAAS,GAAG,UAAU,GAAG,CAAC,CAAC,CAAA;IAC3C,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,SAAS,EAAE,CAAC,IAAI,CAAC,EAAE;QACrC,MAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QACxD,MAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QACxD,MAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QACxD,MAAM,UAAU,CAAC,EAAE,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAExD,GAAG,CAAC,KAAK,CAAC,CAAC,EAAE,EAAE,CAAC,CAAA;QAChB,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;QACpB,GAAG,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,EAAE,EAAE,CAAC,CAAA;QAEpB,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACpE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACpE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACpE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QAEpE,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;KAC3C;IAED,GAAG,CAAC,WAAW,CAAC,SAAS,CAAC,CAAA;IAC1B,IAAI,UAAU,CAAC,CAAC,CAAA;IAChB,QAAQ,UAAU,GAAG,CAAC,EAAE;QACtB,KAAK,CAAC;YACJ,MAAK;QACP,KAAK,CAAC;YACJ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;YACtC,QAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACV,MAAK;QAEP,KAAK,CAAC;YACJ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;YACtC,QAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAEV,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;YACtC,QAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACV,MAAK;QAEP,KAAK,CAAC;YACJ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;YACtC,QAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAEV,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;YACtC,QAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YAEV,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;YACtC,QAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,IAAI,GAAG,CAAC,CAAC,EAAE,QAAQ,CAAC,CAAA;YAC9D,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,CAAA;YACV,MAAK;QAEP;YACE,MAAM,IAAI,kBAAkB,CAC1B,sDAAsD,CACvD,CAAA;KACJ;IAED,GAAG,CAAC,WAAW,CAAC,CAAC,CAAC,CAAA;AACpB,CAAC"}
|
package/esm/rans/d14.js
CHANGED
package/esm/rans/d14.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"d14.js","sourceRoot":"","sources":["../../src/rans/d14.
|
|
1
|
+
{"version":3,"file":"d14.js","sourceRoot":"","sources":["../../src/rans/d14.ts"],"names":[],"mappings":"AAAA,aAAa;AACb,OAAO,EAAE,QAAQ,EAAE,MAAM,aAAa,CAAA;AACtC,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,MAAM,CAAC,OAAO,UAAU,UAAU;AAChC,gBAAgB,CAAC,KAAK;AACtB,gBAAgB,CAAC,MAAM;AACvB,2BAA2B,CAAC,CAAC;AAC7B,yBAAyB,CAAC,IAAI;IAE9B,MAAM,SAAS,CAAC,UAAU,GAAG,MAAM,CAAC,SAAS,EAAE,CAAA;IAC/C,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1B,IAAI,KAAK,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAE1B,MAAM,SAAS,CAAC,IAAI,GAAG,UAAU,IAAI,CAAC,CAAA;IACtC,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,IAAI,CAAA;IACvB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,CAAA;IAC3B,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,GAAG,IAAI,CAAA;IAC3B,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,IAAI,SAAS,CAAC,EAAE,GAAG,CAAC,CAAA;IACpB,OAAO,EAAE,GAAG,IAAI,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE,EAAE,IAAI,CAAC,EAAE;QACpD,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAElE,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QAEpB,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,QAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QAEjE,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,QAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAE1C,EAAE,GAAG,EAAE,CAAA;QACP,EAAE,GAAG,EAAE,CAAA;QACP,EAAE,GAAG,EAAE,CAAA;QACP,EAAE,GAAG,EAAE,CAAA;KACR;IAED,YAAY;IACZ,OAAO,EAAE,GAAG,UAAU,EAAE,EAAE,IAAI,CAAC,EAAE;QAC/B,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,QAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,KAAK,GAAG,QAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,QAAQ,CAAC,CAAA;QACpE,EAAE,GAAG,EAAE,CAAA;KACR;AACH,CAAC"}
|
package/esm/rans/decoding.d.ts
CHANGED
|
@@ -1,30 +1,27 @@
|
|
|
1
|
-
export default Decode;
|
|
2
|
-
declare namespace Decode {
|
|
3
|
-
export { FC };
|
|
4
|
-
export { AriDecoder };
|
|
5
|
-
export { Symbol };
|
|
6
|
-
export { symbolInit };
|
|
7
|
-
export { advanceStep };
|
|
8
|
-
export { advanceSymbolStep };
|
|
9
|
-
export { get };
|
|
10
|
-
export { advanceSymbol };
|
|
11
|
-
export { renormalize };
|
|
12
|
-
}
|
|
13
1
|
declare class FC {
|
|
14
|
-
|
|
15
|
-
C: any;
|
|
2
|
+
constructor();
|
|
16
3
|
}
|
|
17
4
|
declare class AriDecoder {
|
|
18
|
-
|
|
19
|
-
R: any;
|
|
5
|
+
constructor();
|
|
20
6
|
}
|
|
21
7
|
declare class Symbol {
|
|
22
|
-
|
|
23
|
-
freq: any;
|
|
8
|
+
constructor();
|
|
24
9
|
}
|
|
25
10
|
declare function symbolInit(sym: any, start: any, freq: any): void;
|
|
26
11
|
declare function advanceStep(r: any, start: any, freq: any, scaleBits: any): number;
|
|
27
12
|
declare function advanceSymbolStep(r: any, sym: any, scaleBits: any): number;
|
|
28
|
-
declare function get(r: any, scaleBits: any): number;
|
|
13
|
+
declare function get(/* final int */ r: any, /* final int */ scaleBits: any): number;
|
|
29
14
|
declare function advanceSymbol(r: any, pptr: any, sym: any, scaleBits: any): any;
|
|
30
15
|
declare function renormalize(r: any, pptr: any): any;
|
|
16
|
+
declare const Decode: {
|
|
17
|
+
FC: typeof FC;
|
|
18
|
+
AriDecoder: typeof AriDecoder;
|
|
19
|
+
Symbol: typeof Symbol;
|
|
20
|
+
symbolInit: typeof symbolInit;
|
|
21
|
+
advanceStep: typeof advanceStep;
|
|
22
|
+
advanceSymbolStep: typeof advanceSymbolStep;
|
|
23
|
+
get: typeof get;
|
|
24
|
+
advanceSymbol: typeof advanceSymbol;
|
|
25
|
+
renormalize: typeof renormalize;
|
|
26
|
+
};
|
|
27
|
+
export default Decode;
|
package/esm/rans/decoding.js
CHANGED
package/esm/rans/decoding.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"decoding.js","sourceRoot":"","sources":["../../src/rans/decoding.
|
|
1
|
+
{"version":3,"file":"decoding.js","sourceRoot":"","sources":["../../src/rans/decoding.ts"],"names":[],"mappings":"AAAA,aAAa;AACb,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,EAAE,WAAW,EAAE,MAAM,aAAa,CAAA;AAEzC,MAAM,EAAE;IACN,YAAY;IACZ;QACE,IAAI,CAAC,CAAC,GAAG,SAAS,CAAA;QAClB,IAAI,CAAC,CAAC,GAAG,SAAS,CAAA;IACpB,CAAC;CACF;AAED,MAAM,UAAU;IACd,+BAA+B;IAC/B,YAAY;IAEZ;QACE,IAAI,CAAC,EAAE,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,EAAE,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC1C,IAAI,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,EAAE,EAAE,CAAA;SACtB;QACD,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;IACf,CAAC;CACF;AAED,MAAM,MAAM;IACV,gCAAgC;IAChC,iCAAiC;IACjC;QACE,IAAI,CAAC,KAAK,GAAG,SAAS,CAAA;QACtB,IAAI,CAAC,IAAI,GAAG,SAAS,CAAA;IACvB,CAAC;CACF;AAED,oEAAoE;AACpE,SAAS,UAAU,CAAC,GAAG,EAAE,KAAK,EAAE,IAAI;IAClC,IAAI,CAAC,CAAC,KAAK,IAAI,CAAC,IAAI,EAAE,CAAC,EAAE;QACvB,MAAM,IAAI,kBAAkB,CAAC,kCAAkC,CAAC,CAAA;KACjE;IACD,IAAI,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,IAAI,EAAE,CAAC,GAAG,KAAK,CAAC,EAAE;QAChC,MAAM,IAAI,kBAAkB,CAAC,iCAAiC,CAAC,CAAA;KAChE;IACD,GAAG,CAAC,KAAK,GAAG,KAAK,CAAA;IACjB,GAAG,CAAC,IAAI,GAAG,IAAI,CAAA;AACjB,CAAC;AAED,2EAA2E;AAC3E,sEAAsE;AACtE,oBAAoB;AACpB,wCAAwC;AACxC,wBAAwB,CAAC,SAAS,WAAW;AAC3C,eAAe,CAAC,CAAC;AACjB,eAAe,CAAC,KAAK;AACrB,eAAe,CAAC,IAAI;AACpB,eAAe,CAAC,SAAS;IAEzB,eAAe,CAAC,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAA;IAEjD,cAAc;IACd,OAAO,IAAI,GAAG,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,KAAK,CAAA;AACrD,CAAC;AAED,wDAAwD;AACxD,iBAAiB,CAAC,SAAS,iBAAiB;AAC1C,eAAe,CAAC,CAAC;AACjB,yBAAyB,CAAC,GAAG;AAC7B,eAAe,CAAC,SAAS;IAEzB,OAAO,WAAW,CAAC,CAAC,EAAE,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;AACvD,CAAC;AAED,0EAA0E;AAC1E,gBAAgB,CAAC,SAAS,GAAG,CAAC,eAAe,CAAC,CAAC,EAAE,eAAe,CAAC,SAAS;IACxE,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAC,CAAA;AACnC,CAAC;AAED,2EAA2E;AAC3E,sEAAsE;AACtE,oBAAoB;AACpB,iEAAiE;AACjE,wBAAwB,CAAC,SAAS,OAAO;AACvC,SAAS,CAAC,CAAC;AACX,sBAAsB,CAAC,IAAI;AAC3B,eAAe,CAAC,KAAK;AACrB,eAAe,CAAC,IAAI;AACpB,eAAe,CAAC,SAAS;IAEzB,eAAe,CAAC,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAA;IAEjD,cAAc;IACd,CAAC,GAAG,IAAI,GAAG,CAAC,CAAC,IAAI,SAAS,CAAC,GAAG,CAAC,CAAC,GAAG,IAAI,CAAC,GAAG,KAAK,CAAA;IAEhD,eAAe;IACf,IAAI,CAAC,GAAG,WAAW,EAAE;QACnB,GAAG;YACD,eAAe,CAAC,MAAM,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,GAAG,EAAE,CAAA;YAC3C,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAA;SACjB,QAAQ,CAAC,GAAG,WAAW,EAAC;KAC1B;IAED,OAAO,CAAC,CAAA;AACV,CAAC;AAED,oDAAoD;AACpD,iBAAiB,CAAC,SAAS,aAAa;AACtC,eAAe,CAAC,CAAC;AACjB,sBAAsB,CAAC,IAAI;AAC3B,yBAAyB,CAAC,GAAG;AAC7B,eAAe,CAAC,SAAS;IAEzB,OAAO,OAAO,CAAC,CAAC,EAAE,IAAI,EAAE,GAAG,CAAC,KAAK,EAAE,GAAG,CAAC,IAAI,EAAE,SAAS,CAAC,CAAA;AACzD,CAAC;AAED,gBAAgB;AAChB,iBAAiB,CAAC,SAAS,WAAW;AACpC,SAAS,CAAC,CAAC;AACX,sBAAsB,CAAC,IAAI;IAE3B,eAAe;IACf,IAAI,CAAC,GAAG,WAAW,EAAE;QACnB,GAAG;YACD,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,GAAG,IAAI,CAAC,GAAG,EAAE,CAAC,CAAA;SACnC,QAAQ,CAAC,GAAG,WAAW,EAAC;KAC1B;IAED,OAAO,CAAC,CAAA;AACV,CAAC;AAED,MAAM,MAAM,GAAG;IACb,EAAE;IACF,UAAU;IACV,MAAM;IACN,UAAU;IACV,WAAW;IACX,iBAAiB;IACjB,GAAG;IACH,aAAa;IACb,WAAW;CACZ,CAAA;AAED,eAAe,MAAM,CAAA"}
|
|
@@ -1,2 +1,2 @@
|
|
|
1
|
-
export function readStatsO0(cp: any, decoder: any, syms: any): void;
|
|
2
|
-
export function readStatsO1(cp: any, D: any, syms: any): void;
|
|
1
|
+
export declare function readStatsO0(cp: any, decoder: any, syms: any): void;
|
|
2
|
+
export declare function readStatsO1(cp: any, D: any, syms: any): void;
|
package/esm/rans/frequencies.js
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"frequencies.js","sourceRoot":"","sources":["../../src/rans/frequencies.
|
|
1
|
+
{"version":3,"file":"frequencies.js","sourceRoot":"","sources":["../../src/rans/frequencies.ts"],"names":[],"mappings":"AAAA,aAAa;AACb,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,EAAE,OAAO,EAAE,MAAM,aAAa,CAAA;AACrC,OAAO,QAAQ,MAAM,YAAY,CAAA;AAEjC,SAAS,MAAM,CAAC,MAAM;IACpB,IAAI,CAAC,MAAM,EAAE;QACX,MAAM,IAAI,kBAAkB,CAAC,kBAAkB,CAAC,CAAA;KACjD;AACH,CAAC;AAED,MAAM,UAAU,WAAW;AACzB,gBAAgB,CAAC,EAAE;AACnB,yBAAyB,CAAC,OAAO;AACjC,8BAA8B,CAAC,IAAI;IAEnC,2CAA2C;IAC3C,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IAAI,CAAC,GAAG,CAAC,CAAA;IACT,IAAI,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;IACvB,GAAG;QACD,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;YACzB,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,EAAE,EAAE,CAAA;SAClC;QACD,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;QACjC,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE;YAC1B,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAA;YACvB,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAC,CAAA;SACrE;QACD,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnB,QAAQ,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAE9D,gCAAgC;QAChC,IAAI,CAAC,OAAO,CAAC,CAAC,EAAE;YACd,OAAO,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,OAAO,CAAC,CAAA;SAC/B;QACD,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,GAAG,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEzC,CAAC,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;QAEpB,IAAI,GAAG,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE;YAC/D,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;YACnB,GAAG,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;SACtB;aAAM,IAAI,GAAG,KAAK,CAAC,EAAE;YACpB,GAAG,IAAI,CAAC,CAAA;YACR,CAAC,IAAI,CAAC,CAAA;SACP;aAAM;YACL,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;SACpB;KACF,QAAQ,CAAC,KAAK,CAAC,EAAC;IAEjB,MAAM,CAAC,CAAC,GAAG,OAAO,CAAC,CAAA;AACrB,CAAC;AAED,MAAM,UAAU,WAAW;AACzB,gBAAgB,CAAC,EAAE;AACnB,4BAA4B,CAAC,CAAC;AAC9B,gCAAgC,CAAC,IAAI;IAErC,IAAI,IAAI,GAAG,CAAC,CAAA;IACZ,IAAI,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;IACvB,GAAG;QACD,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,CAAC,GAAG,CAAC,CAAA;QACT,IAAI,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;QACvB,IAAI,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;YAChB,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAA;SACjC;QACD,GAAG;YACD,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;gBACtB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,EAAE,EAAE,CAAA;aAC/B;YACD,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YAC9B,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,GAAG,EAAE;gBACvB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,GAAG,CAAA;gBACpB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,GAAG,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAC,CAAA;aAC/D;YACD,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;YAEhB,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE;gBACtB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,OAAO,CAAA;aACvB;YAED,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;gBACtB,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,aAAa,EAAE,CAAA;aAC1C;YAED,QAAQ,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAE3D,gCAAgC;YAChC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE;gBAClB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,OAAO,CAAC,CAAA;aAC5B;YACD,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,EAAE,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YAEnC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;YACjB,MAAM,CAAC,CAAC,IAAI,OAAO,CAAC,CAAA;YAEpB,IAAI,IAAI,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE;gBAChE,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;gBACnB,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;aACvB;iBAAM,IAAI,IAAI,KAAK,CAAC,EAAE;gBACrB,IAAI,IAAI,CAAC,CAAA;gBACT,CAAC,IAAI,CAAC,CAAA;aACP;iBAAM;gBACL,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;aACpB;SACF,QAAQ,CAAC,KAAK,CAAC,EAAC;QAEjB,IAAI,IAAI,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,IAAI,GAAG,EAAE,CAAC,SAAS,CAAC,EAAE,CAAC,QAAQ,EAAE,CAAC,CAAC,EAAE;YAChE,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YACnB,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;SACvB;aAAM,IAAI,IAAI,KAAK,CAAC,EAAE;YACrB,IAAI,IAAI,CAAC,CAAA;YACT,CAAC,IAAI,CAAC,CAAA;SACP;aAAM;YACL,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;SACpB;KACF,QAAQ,CAAC,KAAK,CAAC,EAAC;AACnB,CAAC"}
|
package/esm/rans/index.js
CHANGED
package/esm/rans/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/rans/index.
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/rans/index.ts"],"names":[],"mappings":"AAAA,aAAa;AACb,OAAO,EAAE,kBAAkB,EAAE,MAAM,WAAW,CAAA;AAE9C,OAAO,QAAQ,MAAM,YAAY,CAAA;AACjC,OAAO,EAAE,WAAW,EAAE,WAAW,EAAE,MAAM,eAAe,CAAA;AAExD,OAAO,GAAG,MAAM,OAAO,CAAA;AACvB,OAAO,GAAG,MAAM,OAAO,CAAA;AAEvB,wCAAwC;AACxC,6CAA6C;AAC7C,MAAM,SAAS,CAAC,eAAe,GAAG,CAAC,CAAA;AACnC,uCAAuC;AACvC,iEAAiE;AAEjE,eAAe;AACf,iBAAiB;AAEjB,oDAAoD;AACpD,gBAAgB;AAChB,4CAA4C;AAC5C,6DAA6D;AAC7D,0EAA0E;AAC1E,YAAY;AACZ,QAAQ;AACR,IAAI;AAEJ,gGAAgG;AAChG,kCAAkC;AAClC,+BAA+B;AAE/B,iCAAiC;AACjC,iDAAiD;AAEjD,uBAAuB;AACvB,qBAAqB;AACrB,qDAAqD;AACrD,oBAAoB;AACpB,qDAAqD;AAErD,mBAAmB;AACnB,0EAA0E;AAC1E,QAAQ;AACR,IAAI;AAEJ,oEAAoE;AACpE,+EAA+E;AAC/E,yFAAyF;AACzF,2BAA2B;AAC3B,sDAAsD;AACtD,gDAAgD;AAChD,mEAAmE;AACnE,8CAA8C;AAC9C,sBAAsB;AACtB,IAAI;AAEJ,+DAA+D;AAC/D,qEAAqE;AACrE,mDAAmD;AACnD,oDAAoD;AACpD,2DAA2D;AAC3D,wCAAwC;AAExC,gEAAgE;AAChE,gEAAgE;AAEhE,6CAA6C;AAC7C,oFAAoF;AAEpF,sBAAsB;AACtB,2EAA2E;AAE3E,mEAAmE;AACnE,oCAAoC;AACpC,sBAAsB;AACtB,IAAI;AAEJ,+DAA+D;AAC/D,qEAAqE;AACrE,mDAAmD;AACnD,oDAAoD;AACpD,2DAA2D;AAC3D,wCAAwC;AAExC,kEAAkE;AAClE,kEAAkE;AAElE,6CAA6C;AAC7C,oFAAoF;AAEpF,sBAAsB;AACtB,2EAA2E;AAE3E,mEAAmE;AACnE,oCAAoC;AACpC,sBAAsB;AACtB,IAAI;AAEJ,kFAAkF;AAClF,8IAA8I;AAC9I,6DAA6D;AAC7D,sCAAsC;AACtC,oCAAoC;AACpC,8CAA8C;AAC9C,gEAAgE;AAChE,+DAA+D;AAC/D,sCAAsC;AACtC,kFAAkF;AAClF,8CAA8C;AAC9C,wBAAwB;AACxB,IAAI;AAEJ,SAAiC,oBAAoB;AACnD,uBAAuB,CAAC,KAAK;AAC7B,uBAAuB,CAAC,GAAG;IAE3B,wCAAwC;IACxC,MAAM,CAAC,GAAG,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAA;IACnC,MAAM,IAAI,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IAC3B,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QACvC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,MAAM,EAAE,CAAA;KAChC;IAED,WAAW,CAAC,KAAK,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,GAAG,CAAC,KAAK,EAAE,CAAC,EAAE,IAAI,EAAE,GAAG,CAAC,CAAA;IAExB,OAAO,GAAG,CAAA;AACZ,CAAC;AAED,SAAiC,oBAAoB;AACnD,sBAAsB,CAAC,KAAK;AAC5B,sBAAsB,CAAC,MAAM;IAE7B,MAAM,CAAC,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QACpC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,UAAU,EAAE,CAAA;KACjC;IACD,MAAM,iCAAiC,CAAC,IAAI,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;IAC7D,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;QACvC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,GAAG,CAAC,CAAA;QACxB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE;YAC1C,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,QAAQ,CAAC,MAAM,EAAE,CAAA;SACnC;KACF;IACD,WAAW,CAAC,KAAK,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,GAAG,CAAC,KAAK,EAAE,MAAM,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,OAAO,MAAM,CAAA;AACf,CAAC;AAED,mEAAmE;AACnE,MAAM,UAAU;IACd,YAAY,UAAU,EAAE,oBAAoB,GAAG,CAAC;QAC9C,IAAI,CAAC,OAAO,GAAG,UAAU,CAAA;QACzB,IAAI,CAAC,SAAS,GAAG,oBAAoB,CAAA;QACrC,IAAI,CAAC,MAAM,GAAG,UAAU,CAAC,MAAM,CAAA;IACjC,CAAC;IAED,GAAG;QACD,MAAM,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;QACtC,IAAI,CAAC,SAAS,IAAI,CAAC,CAAA;QACnB,OAAO,CAAC,CAAA;IACV,CAAC;IAED,OAAO;QACL,OAAO,IAAI,CAAC,GAAG,EAAE,CAAA;IACnB,CAAC;IAED,SAAS,CAAC,QAAQ;QAChB,OAAO,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAA;IAC/B,CAAC;IAED,QAAQ;QACN,OAAO,IAAI,CAAC,SAAS,CAAA;IACvB,CAAC;IAED,GAAG,CAAC,GAAG;QACL,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,GAAG,CAAA;QAClC,IAAI,CAAC,SAAS,IAAI,CAAC,CAAA;QACnB,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,KAAK,CAAC,QAAQ,EAAE,GAAG;QACjB,IAAI,CAAC,OAAO,CAAC,QAAQ,CAAC,GAAG,GAAG,CAAA;QAC5B,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,WAAW,CAAC,GAAG;QACb,IAAI,CAAC,SAAS,GAAG,GAAG,CAAA;QACpB,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,MAAM;QACJ,MAAM,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,WAAW,CAAC,IAAI,CAAC,SAAS,CAAC,CAAA;QAClD,IAAI,CAAC,SAAS,IAAI,CAAC,CAAA;QACnB,OAAO,CAAC,CAAA;IACV,CAAC;IAED,SAAS;QACP,OAAO,IAAI,CAAC,OAAO,CAAC,MAAM,GAAG,IAAI,CAAC,SAAS,CAAA;IAC7C,CAAC;CACF;AAED,uEAAuE;AACvE,MAAM,CAAC,OAAO,UAAU,UAAU,CAChC,WAAW,EACX,YAAY,EACZ,oBAAoB,GAAG,CAAC;IAExB,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE;QAC5B,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACpB,OAAO,YAAY,CAAA;KACpB;IAED,MAAM,KAAK,GAAG,IAAI,UAAU,CAAC,WAAW,EAAE,oBAAoB,CAAC,CAAA;IAC/D,wCAAwC;IAExC,MAAM,KAAK,GAAG,KAAK,CAAC,GAAG,EAAE,CAAA;IACzB,IAAI,KAAK,KAAK,CAAC,IAAI,KAAK,KAAK,CAAC,EAAE;QAC9B,MAAM,IAAI,kBAAkB,CAAC,sBAAsB,KAAK,EAAE,CAAC,CAAA;KAC5D;IAED,MAAM,SAAS,CAAC,SAAS,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1C,IAAI,SAAS,KAAK,KAAK,CAAC,SAAS,EAAE,GAAG,eAAe,EAAE;QACrD,MAAM,IAAI,kBAAkB,CAAC,yBAAyB,CAAC,CAAA;KACxD;IAED,MAAM,SAAS,CAAC,UAAU,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC3C,MAAM,MAAM,GAAG,IAAI,UAAU,CAAC,YAAY,IAAI,MAAM,CAAC,WAAW,CAAC,UAAU,CAAC,CAAC,CAAA;IAC7E,gCAAgC;IAEhC,IAAI,MAAM,CAAC,MAAM,GAAG,UAAU,EAAE;QAC9B,MAAM,IAAI,kBAAkB,CAC1B,kCAAkC,UAAU,SAAS,CACtD,CAAA;KACF;IAED,QAAQ,KAAK,EAAE;QACb,KAAK,CAAC;YACJ,OAAO,oBAAoB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAE5C,KAAK,CAAC;YACJ,OAAO,oBAAoB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAA;QAE5C;YACE,MAAM,IAAI,kBAAkB,CAAC,uBAAuB,KAAK,EAAE,CAAC,CAAA;KAC/D;AACH,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/cram",
|
|
3
|
-
"version": "
|
|
3
|
+
"version": "2.0.0",
|
|
4
4
|
"description": "read CRAM files with pure Javascript",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/cram-js",
|
|
@@ -23,7 +23,7 @@
|
|
|
23
23
|
"scripts": {
|
|
24
24
|
"test": "jest",
|
|
25
25
|
"lint": "eslint src test",
|
|
26
|
-
"docs": "documentation readme --shallow src/indexedCramFile.
|
|
26
|
+
"docs": "documentation readme --shallow src/indexedCramFile.ts --section=IndexedCramFile; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/craiIndex.ts --section=CraiIndex; documentation readme --shallow errors.ts '--section=Exception Classes'; documentation readme --shallow src/cramFile/file.ts --section=CramFile; documentation readme --shallow src/cramFile/record.ts --section=CramRecord",
|
|
27
27
|
"prebuild": "npm run clean",
|
|
28
28
|
"clean": "rimraf dist esm",
|
|
29
29
|
"build:esm": "tsc --target es2018 --outDir esm",
|
|
@@ -47,38 +47,38 @@
|
|
|
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",
|
|
54
|
-
"quick-lru": "^4.0.1"
|
|
53
|
+
"quick-lru": "^4.0.1",
|
|
54
|
+
"xz-decompress": "^0.2.1"
|
|
55
55
|
},
|
|
56
56
|
"devDependencies": {
|
|
57
57
|
"@babel/plugin-transform-modules-commonjs": "^7.18.2",
|
|
58
58
|
"@babel/preset-typescript": "^7.17.12",
|
|
59
|
-
"@gmod/indexedfasta": "^2.0
|
|
59
|
+
"@gmod/indexedfasta": "^2.1.0",
|
|
60
60
|
"@types/buffer-crc32": "^0.2.2",
|
|
61
61
|
"@types/jest": "^29.2.4",
|
|
62
62
|
"@types/long": "^4.0.2",
|
|
63
63
|
"@types/md5": "^2.3.2",
|
|
64
64
|
"@types/pako": "^1.0.3",
|
|
65
|
-
"@typescript-eslint/eslint-plugin": "^
|
|
66
|
-
"@typescript-eslint/parser": "^
|
|
65
|
+
"@typescript-eslint/eslint-plugin": "^6.9.1",
|
|
66
|
+
"@typescript-eslint/parser": "^6.9.1",
|
|
67
67
|
"buffer": "^6.0.3",
|
|
68
68
|
"documentation": "^14.0.1",
|
|
69
69
|
"eslint": "^8.30.0",
|
|
70
|
-
"eslint-config-prettier": "^
|
|
70
|
+
"eslint-config-prettier": "^9.0.0",
|
|
71
71
|
"eslint-plugin-import": "^2.25.4",
|
|
72
|
-
"eslint-plugin-prettier": "^
|
|
73
|
-
"glob": "^
|
|
72
|
+
"eslint-plugin-prettier": "^5.0.1",
|
|
73
|
+
"glob": "^10.3.1",
|
|
74
74
|
"jest": "^29.3.1",
|
|
75
75
|
"mock-fs": "^5.2.0",
|
|
76
|
-
"prettier": "^
|
|
77
|
-
"rimraf": "^
|
|
76
|
+
"prettier": "^3.0.3",
|
|
77
|
+
"rimraf": "^5.0.1",
|
|
78
78
|
"ts-jest": "^29.0.3",
|
|
79
|
-
"typescript": "^
|
|
79
|
+
"typescript": "^5.0.3",
|
|
80
80
|
"url": "^0.11.0",
|
|
81
|
-
"webpack": "5.
|
|
81
|
+
"webpack": "5.89.0",
|
|
82
82
|
"webpack-cli": "^5.0.1"
|
|
83
83
|
},
|
|
84
84
|
"publishConfig": {
|
|
@@ -6,7 +6,10 @@ import CramContainerCompressionScheme from './compressionScheme'
|
|
|
6
6
|
import CramFile from '../file'
|
|
7
7
|
|
|
8
8
|
export default class CramContainer {
|
|
9
|
-
constructor(
|
|
9
|
+
constructor(
|
|
10
|
+
public file: CramFile,
|
|
11
|
+
public filePosition: number,
|
|
12
|
+
) {}
|
|
10
13
|
|
|
11
14
|
// memoize
|
|
12
15
|
getHeader() {
|
package/src/cramFile/file.ts
CHANGED
|
@@ -1,7 +1,11 @@
|
|
|
1
1
|
import { unzip } from '../unzip'
|
|
2
2
|
import crc32 from 'buffer-crc32'
|
|
3
3
|
import QuickLRU from 'quick-lru'
|
|
4
|
-
|
|
4
|
+
import htscodecs from '@jkbonfield/htscodecs'
|
|
5
|
+
import { Parser } from '@gmod/binary-parser'
|
|
6
|
+
// @ts-expect-error
|
|
7
|
+
import bzip2 from 'bzip2'
|
|
8
|
+
import { XzReadableStream } from 'xz-decompress'
|
|
5
9
|
import { CramMalformedError, CramUnimplementedError } from '../errors'
|
|
6
10
|
import ransuncompress from '../rans'
|
|
7
11
|
import {
|
|
@@ -10,16 +14,24 @@ import {
|
|
|
10
14
|
cramFileDefinition as cramFileDefinitionParser,
|
|
11
15
|
getSectionParsers,
|
|
12
16
|
} from './sectionParsers'
|
|
13
|
-
|
|
17
|
+
|
|
14
18
|
import CramContainer from './container'
|
|
15
19
|
|
|
16
20
|
import { open } from '../io'
|
|
17
21
|
import { parseItem, tinyMemoize } from './util'
|
|
18
22
|
import { parseHeaderText } from '../sam'
|
|
19
|
-
import { Parser } from '@gmod/binary-parser'
|
|
20
23
|
import CramRecord from './record'
|
|
21
24
|
import { Filehandle } from './filehandle'
|
|
22
25
|
|
|
26
|
+
function bufferToStream(buf: Buffer) {
|
|
27
|
+
return new ReadableStream({
|
|
28
|
+
start(controller) {
|
|
29
|
+
controller.enqueue(buf)
|
|
30
|
+
controller.close()
|
|
31
|
+
},
|
|
32
|
+
})
|
|
33
|
+
}
|
|
34
|
+
|
|
23
35
|
//source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
|
|
24
36
|
function getEndianness() {
|
|
25
37
|
const uInt32 = new Uint32Array([0x11223344])
|
|
@@ -97,17 +109,6 @@ export default class CramFile {
|
|
|
97
109
|
}
|
|
98
110
|
}
|
|
99
111
|
|
|
100
|
-
// toString() {
|
|
101
|
-
// if (this.file.filename) {
|
|
102
|
-
// return this.file.filename
|
|
103
|
-
// }
|
|
104
|
-
// if (this.file.url) {
|
|
105
|
-
// return this.file.url
|
|
106
|
-
// }
|
|
107
|
-
//
|
|
108
|
-
// return '(cram file)'
|
|
109
|
-
// }
|
|
110
|
-
|
|
111
112
|
// can just read this object like a filehandle
|
|
112
113
|
read(
|
|
113
114
|
buffer: Buffer,
|
|
@@ -245,9 +246,8 @@ export default class CramFile {
|
|
|
245
246
|
let containerCount = 0
|
|
246
247
|
let position = sectionParsers.cramFileDefinition.maxLength
|
|
247
248
|
while (position + cramContainerHeader1.maxLength + 8 < fileSize) {
|
|
248
|
-
const currentHeader =
|
|
249
|
-
position
|
|
250
|
-
).getHeader()
|
|
249
|
+
const currentHeader =
|
|
250
|
+
await this.getContainerAtPosition(position).getHeader()
|
|
251
251
|
if (!currentHeader) {
|
|
252
252
|
break
|
|
253
253
|
}
|
|
@@ -317,7 +317,7 @@ export default class CramFile {
|
|
|
317
317
|
return data
|
|
318
318
|
}
|
|
319
319
|
|
|
320
|
-
_uncompress(
|
|
320
|
+
async _uncompress(
|
|
321
321
|
compressionMethod: CompressionMethod,
|
|
322
322
|
inputBuffer: Buffer,
|
|
323
323
|
outputBuffer: Buffer,
|
|
@@ -338,6 +338,12 @@ export default class CramFile {
|
|
|
338
338
|
size -= chunk.length
|
|
339
339
|
}
|
|
340
340
|
} while (chunk != -1)
|
|
341
|
+
} else if (compressionMethod === 'lzma') {
|
|
342
|
+
const decompressedResponse = new Response(
|
|
343
|
+
new XzReadableStream(bufferToStream(inputBuffer)),
|
|
344
|
+
)
|
|
345
|
+
const ret = Buffer.from(await decompressedResponse.arrayBuffer())
|
|
346
|
+
ret.copy(outputBuffer)
|
|
341
347
|
} else if (compressionMethod === 'rans') {
|
|
342
348
|
ransuncompress(inputBuffer, outputBuffer)
|
|
343
349
|
//htscodecs r4x8 is slower, but compatible.
|
|
@@ -384,7 +390,7 @@ export default class CramFile {
|
|
|
384
390
|
blockContentPosition,
|
|
385
391
|
)
|
|
386
392
|
|
|
387
|
-
this._uncompress(
|
|
393
|
+
await this._uncompress(
|
|
388
394
|
blockHeader.compressionMethod,
|
|
389
395
|
compressedData,
|
|
390
396
|
uncompressedData,
|
package/src/cramFile/record.ts
CHANGED
|
@@ -450,7 +450,7 @@ export default class CramRecord {
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/**
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* Annotates this feature with the given reference sequence basepair
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* information. This will add a `sub` and a `ref` item to base
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-
*
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453
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+
* substitution read features given the actual substituted and reference
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* base pairs, and will make the `getReadSequence()` method work.
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*
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* @param {object} refRegion
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package/src/typings/bzip2.d.ts
DELETED
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File without changes
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