@gmod/cram 2.0.2 → 2.0.4
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 +9 -0
- package/README.md +0 -4
- package/dist/craiIndex.js +1 -1
- package/dist/craiIndex.js.map +1 -1
- package/dist/cram-bundle.js +1 -1
- package/dist/cram-bundle.js.LICENSE.txt +0 -2
- package/dist/cramFile/codecs/byteArrayStop.d.ts +0 -1
- package/dist/cramFile/codecs/getBits.d.ts +0 -1
- package/dist/cramFile/codecs/getBits.js +2 -2
- package/dist/cramFile/codecs/getBits.js.map +1 -1
- package/dist/cramFile/codecs/index.js +1 -2
- package/dist/cramFile/codecs/index.js.map +1 -1
- package/dist/cramFile/container/index.d.ts +1 -2
- package/dist/cramFile/file.d.ts +1 -3
- package/dist/cramFile/file.js +2 -2
- package/dist/cramFile/file.js.map +1 -1
- package/dist/cramFile/sectionParsers.d.ts +0 -1
- package/dist/cramFile/sectionParsers.js +3 -3
- package/dist/cramFile/sectionParsers.js.map +1 -1
- package/dist/cramFile/slice/decodeRecord.js +1 -1
- package/dist/cramFile/slice/decodeRecord.js.map +1 -1
- package/dist/cramFile/util.d.ts +0 -2
- package/dist/cramFile/util.js +5 -6
- package/dist/cramFile/util.js.map +1 -1
- package/dist/indexedCramFile.d.ts +0 -3
- package/dist/indexedCramFile.js +4 -16
- package/dist/indexedCramFile.js.map +1 -1
- package/dist/io/index.d.ts +1 -3
- package/dist/io/index.js +3 -16
- package/dist/io/index.js.map +1 -1
- package/dist/rans/d04.js +1 -1
- package/dist/rans/d04.js.map +1 -1
- package/dist/rans/d14.js +1 -1
- package/dist/rans/d14.js.map +1 -1
- package/dist/rans/frequencies.js +2 -3
- package/dist/rans/frequencies.js.map +1 -1
- package/dist/rans/index.js +1 -1
- package/dist/rans/index.js.map +1 -1
- package/dist/sam.d.ts +1 -1
- package/dist/sam.js +3 -4
- package/dist/sam.js.map +1 -1
- package/dist/typescript.d.ts +0 -1
- package/dist/typescript.js +0 -8
- package/dist/typescript.js.map +1 -1
- package/dist/unzip-pako.d.ts +0 -1
- package/dist/unzip-pako.js +1 -2
- package/dist/unzip-pako.js.map +1 -1
- package/dist/unzip.d.ts +0 -1
- package/esm/craiIndex.js +1 -1
- package/esm/craiIndex.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayStop.d.ts +0 -1
- package/esm/cramFile/codecs/getBits.d.ts +0 -1
- package/esm/cramFile/container/index.d.ts +1 -2
- package/esm/cramFile/file.d.ts +1 -3
- package/esm/cramFile/sectionParsers.d.ts +0 -1
- package/esm/cramFile/util.d.ts +0 -2
- package/esm/indexedCramFile.d.ts +0 -3
- package/esm/indexedCramFile.js +3 -15
- package/esm/indexedCramFile.js.map +1 -1
- package/esm/io/index.d.ts +1 -3
- package/esm/io/index.js +2 -11
- package/esm/io/index.js.map +1 -1
- package/esm/sam.d.ts +1 -1
- package/esm/sam.js +2 -2
- package/esm/sam.js.map +1 -1
- package/esm/typescript.d.ts +0 -1
- package/esm/typescript.js +1 -6
- package/esm/typescript.js.map +1 -1
- package/esm/unzip-pako.d.ts +0 -1
- package/esm/unzip.d.ts +0 -1
- package/package.json +5 -10
- package/src/craiIndex.ts +1 -1
- package/src/indexedCramFile.ts +3 -25
- package/src/io/index.ts +2 -12
- package/src/sam.ts +3 -3
- package/src/typescript.ts +0 -7
package/dist/rans/d14.js.map
CHANGED
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@@ -1 +1 @@
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{"version":3,"file":"d14.js","sourceRoot":"","sources":["../../src/rans/d14.ts"],"names":[],"mappings":";;;;;
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{"version":3,"file":"d14.js","sourceRoot":"","sources":["../../src/rans/d14.ts"],"names":[],"mappings":";;;;;AAIA,6BAuDC;AA3DD,aAAa;AACb,2CAAsC;AACtC,0DAAiC;AAEjC,SAAwB,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,CAAC;QACrD,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,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,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACjE,KAAK,GAAG,kBAAQ,CAAC,iBAAiB,CAAC,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QAEjE,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,kBAAQ,CAAC,WAAW,CAAC,KAAK,EAAE,KAAK,CAAC,CAAA;QAC1C,KAAK,GAAG,kBAAQ,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;IACT,CAAC;IAED,YAAY;IACZ,OAAO,EAAE,GAAG,UAAU,EAAE,EAAE,IAAI,CAAC,EAAE,CAAC;QAChC,MAAM,SAAS,CAAC,EAAE,GAAG,IAAI,GAAG,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,kBAAQ,CAAC,GAAG,CAAC,KAAK,EAAE,oBAAQ,CAAC,CAAC,CAAA;QAClE,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,CAAC,CAAA;QACpB,KAAK,GAAG,kBAAQ,CAAC,aAAa,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,CAAC,EAAE,CAAC,CAAC,EAAE,CAAC,EAAE,oBAAQ,CAAC,CAAA;QACpE,EAAE,GAAG,EAAE,CAAA;IACT,CAAC;AACH,CAAC"}
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package/dist/rans/frequencies.js
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@@ -3,7 +3,8 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
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return (mod && mod.__esModule) ? mod : { "default": mod };
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};
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Object.defineProperty(exports, "__esModule", { value: true });
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exports.
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exports.readStatsO0 = readStatsO0;
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exports.readStatsO1 = readStatsO1;
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//@ts-nocheck
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const errors_1 = require("../errors");
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const constants_1 = require("./constants");
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} while (j !== 0);
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assert(x < constants_1.TOTFREQ);
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}
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exports.readStatsO0 = readStatsO0;
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function readStatsO1(
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}
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} while (i !== 0);
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}
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exports.readStatsO1 = readStatsO1;
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//# sourceMappingURL=frequencies.js.map
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{"version":3,"file":"frequencies.js","sourceRoot":"","sources":["../../src/rans/frequencies.ts"],"names":[],"mappings":"
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{"version":3,"file":"frequencies.js","sourceRoot":"","sources":["../../src/rans/frequencies.ts"],"names":[],"mappings":";;;;;AAYA,kCA0CC;AAED,kCAiEC;AAzHD,aAAa;AACb,sCAA8C;AAE9C,2CAAqC;AACrC,0DAAiC;AAEjC,SAAS,MAAM,CAAC,MAAM;IACpB,IAAI,CAAC,MAAM,EAAE,CAAC;QACZ,MAAM,IAAI,2BAAkB,CAAC,kBAAkB,CAAC,CAAA;IAClD,CAAC;AACH,CAAC;AAED,SAAgB,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,CAAC;QACF,IAAI,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;YAC1B,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,EAAE,EAAE,CAAA;QACnC,CAAC;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,CAAC;YAC3B,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;QACtE,CAAC;QACD,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAA;QAEnB,kBAAQ,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,CAAC;YACf,OAAO,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,mBAAO,CAAC,CAAA;QAChC,CAAC;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,CAAC;YAChE,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;YACnB,GAAG,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;QACvB,CAAC;aAAM,IAAI,GAAG,KAAK,CAAC,EAAE,CAAC;YACrB,GAAG,IAAI,CAAC,CAAA;YACR,CAAC,IAAI,CAAC,CAAA;QACR,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,EAAE,CAAC,GAAG,EAAE,GAAG,IAAI,CAAA;QACrB,CAAC;IACH,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAC;IAEjB,MAAM,CAAC,CAAC,GAAG,mBAAO,CAAC,CAAA;AACrB,CAAC;AAED,SAAgB,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,CAAC;QACF,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,CAAC;YACjB,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,UAAU,EAAE,CAAA;QAClC,CAAC;QACD,GAAG,CAAC;YACF,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;gBACvB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,EAAE,EAAE,CAAA;YAChC,CAAC;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,CAAC;gBACxB,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;YAChE,CAAC;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,CAAC;gBACvB,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,mBAAO,CAAA;YACxB,CAAC;YAED,IAAI,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,CAAC;gBACvB,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,aAAa,EAAE,CAAA;YAC3C,CAAC;YAED,kBAAQ,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,CAAC;gBACnB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,KAAK,CAAC,mBAAO,CAAC,CAAA;YAC7B,CAAC;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,mBAAO,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,CAAC;gBACjE,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;gBACnB,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YACxB,CAAC;iBAAM,IAAI,IAAI,KAAK,CAAC,EAAE,CAAC;gBACtB,IAAI,IAAI,CAAC,CAAA;gBACT,CAAC,IAAI,CAAC,CAAA;YACR,CAAC;iBAAM,CAAC;gBACN,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YACrB,CAAC;QACH,CAAC,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,CAAC;YACjE,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;YACnB,IAAI,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;QACxB,CAAC;aAAM,IAAI,IAAI,KAAK,CAAC,EAAE,CAAC;YACtB,IAAI,IAAI,CAAC,CAAA;YACT,CAAC,IAAI,CAAC,CAAA;QACR,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,IAAI,GAAG,EAAE,CAAC,GAAG,EAAE,CAAA;QACrB,CAAC;IACH,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAC;AACnB,CAAC"}
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package/dist/rans/index.js
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//# sourceMappingURL=index.js.map
|
package/dist/rans/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/rans/index.ts"],"names":[],"mappings":";;;;;
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/rans/index.ts"],"names":[],"mappings":";;;;;AA8MA,6BA2CC;AAzPD,aAAa;AACb,sCAA8C;AAE9C,0DAAiC;AACjC,+CAAwD;AAExD,gDAAuB;AACvB,gDAAuB;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,kBAAQ,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,CAAC;QACxC,IAAI,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,MAAM,EAAE,CAAA;IACjC,CAAC;IAED,IAAA,yBAAW,EAAC,KAAK,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,IAAA,aAAG,EAAC,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,CAAC;QACrC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,UAAU,EAAE,CAAA;IAClC,CAAC;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,CAAC;QACxC,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,CAAC;YAC3C,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,IAAI,kBAAQ,CAAC,MAAM,EAAE,CAAA;QACpC,CAAC;IACH,CAAC;IACD,IAAA,yBAAW,EAAC,KAAK,EAAE,CAAC,EAAE,IAAI,CAAC,CAAA;IAE3B,IAAA,aAAG,EAAC,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,SAAwB,UAAU,CAChC,WAAW,EACX,YAAY,EACZ,oBAAoB,GAAG,CAAC;IAExB,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;QAC7B,YAAY,CAAC,IAAI,CAAC,CAAC,CAAC,CAAA;QACpB,OAAO,YAAY,CAAA;IACrB,CAAC;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,CAAC;QAC/B,MAAM,IAAI,2BAAkB,CAAC,sBAAsB,KAAK,EAAE,CAAC,CAAA;IAC7D,CAAC;IAED,MAAM,SAAS,CAAC,SAAS,GAAG,KAAK,CAAC,MAAM,EAAE,CAAA;IAC1C,IAAI,SAAS,KAAK,KAAK,CAAC,SAAS,EAAE,GAAG,eAAe,EAAE,CAAC;QACtD,MAAM,IAAI,2BAAkB,CAAC,yBAAyB,CAAC,CAAA;IACzD,CAAC;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,CAAC;QAC/B,MAAM,IAAI,2BAAkB,CAC1B,kCAAkC,UAAU,SAAS,CACtD,CAAA;IACH,CAAC;IAED,QAAQ,KAAK,EAAE,CAAC;QACd,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,2BAAkB,CAAC,uBAAuB,KAAK,EAAE,CAAC,CAAA;IAChE,CAAC;AACH,CAAC"}
|
package/dist/sam.d.ts
CHANGED
package/dist/sam.js
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.parseHeaderText =
|
|
3
|
+
exports.parseHeaderText = parseHeaderText;
|
|
4
4
|
function parseHeaderText(text) {
|
|
5
5
|
const lines = text.split(/\r?\n/);
|
|
6
6
|
const data = [];
|
|
@@ -18,10 +18,10 @@ function parseHeaderText(text) {
|
|
|
18
18
|
}
|
|
19
19
|
: // @CO lines are not comma separated.
|
|
20
20
|
// See "samtools view -H c2\#pad.3.0.cram"
|
|
21
|
-
// so, just store value tag itself
|
|
21
|
+
// so, just store value tag and value itself
|
|
22
22
|
{
|
|
23
23
|
tag: f,
|
|
24
|
-
value:
|
|
24
|
+
value: '',
|
|
25
25
|
};
|
|
26
26
|
}),
|
|
27
27
|
});
|
|
@@ -29,5 +29,4 @@ function parseHeaderText(text) {
|
|
|
29
29
|
}
|
|
30
30
|
return data;
|
|
31
31
|
}
|
|
32
|
-
exports.parseHeaderText = parseHeaderText;
|
|
33
32
|
//# sourceMappingURL=sam.js.map
|
package/dist/sam.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":";;AAAA,0CAiCC;AAjCD,SAAgB,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAMJ,EAAE,CAAA;IACR,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,OAAO,CAAC,KAAK,CAAC,CAAC;wBACb,CAAC,CAAC;4BACE,GAAG,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC;4BAClB,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC;yBACtB;wBACH,CAAC,CAAC,qCAAqC;4BACrC,0CAA0C;4BAC1C,4CAA4C;4BAC5C;gCACE,GAAG,EAAE,CAAC;gCACN,KAAK,EAAE,EAAE;6BACV,CAAA;gBACP,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
|
package/dist/typescript.d.ts
CHANGED
|
@@ -1,3 +1,2 @@
|
|
|
1
|
-
export declare function ensureNotNullish<T>(x: T | null | undefined): T;
|
|
2
1
|
export type TupleOf<T, N extends number> = N extends N ? number extends N ? T[] : _TupleOf<T, N, []> : never;
|
|
3
2
|
export type _TupleOf<T, N extends number, R extends unknown[]> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>;
|
package/dist/typescript.js
CHANGED
|
@@ -1,11 +1,3 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.ensureNotNullish = void 0;
|
|
4
|
-
function ensureNotNullish(x) {
|
|
5
|
-
if (x === null || x === undefined) {
|
|
6
|
-
throw new Error('Value must not be nullish.');
|
|
7
|
-
}
|
|
8
|
-
return x;
|
|
9
|
-
}
|
|
10
|
-
exports.ensureNotNullish = ensureNotNullish;
|
|
11
3
|
//# sourceMappingURL=typescript.js.map
|
package/dist/typescript.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":""}
|
package/dist/unzip-pako.d.ts
CHANGED
package/dist/unzip-pako.js
CHANGED
|
@@ -1,9 +1,8 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.unzip =
|
|
3
|
+
exports.unzip = unzip;
|
|
4
4
|
const pako_1 = require("pako");
|
|
5
5
|
function unzip(input) {
|
|
6
6
|
return Buffer.from((0, pako_1.inflate)(input));
|
|
7
7
|
}
|
|
8
|
-
exports.unzip = unzip;
|
|
9
8
|
//# sourceMappingURL=unzip-pako.js.map
|
package/dist/unzip-pako.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"unzip-pako.js","sourceRoot":"","sources":["../src/unzip-pako.ts"],"names":[],"mappings":";;AAEA,sBAEC;AAJD,+BAA8B;AAE9B,SAAgB,KAAK,CAAC,KAAa;IACjC,OAAO,MAAM,CAAC,IAAI,CAAC,IAAA,cAAO,EAAC,KAAK,CAAC,CAAC,CAAA;AACpC,CAAC"}
|
package/dist/unzip.d.ts
CHANGED
package/esm/craiIndex.js
CHANGED
package/esm/craiIndex.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.ts"],"names":[],"mappings":"AAAA,OAAO,qBAAqB,MAAM,
|
|
1
|
+
{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.ts"],"names":[],"mappings":"AAAA,OAAO,qBAAqB,MAAM,+BAA+B,CAAA;AACjE,OAAO,QAAQ,MAAM,WAAW,CAAA;AAChC,OAAO,EAAE,KAAK,EAAE,MAAM,SAAS,CAAA;AAC/B,OAAO,EAAE,IAAI,EAAE,MAAM,MAAM,CAAA;AAC3B,OAAO,EAAE,kBAAkB,EAAE,MAAM,UAAU,CAAA;AAI7C,MAAM,SAAS,GAAG,QAAQ,CAAA,CAAC,QAAQ;AAYnC,SAAS,gBAAgB,CAAC,KAAkB,EAAE,MAAgB;IAC5D,MAAM,CAAC,KAAK,EAAE,KAAK,EAAE,IAAI,EAAE,cAAc,EAAE,UAAU,EAAE,UAAU,CAAC,GAAG,MAAM,CAAA;IAE3E,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;QAClB,KAAK,CAAC,KAAK,CAAC,GAAG,EAAE,CAAA;IACnB,CAAC;IAED,KAAK,CAAC,KAAK,CAAC,CAAC,IAAI,CAAC;QAChB,KAAK;QACL,IAAI;QACJ,cAAc;QACd,UAAU;QACV,UAAU;KACX,CAAC,CAAA;AACJ,CAAC;AAED,MAAM,CAAC,OAAO,OAAO,SAAS;IAY5B;;;;;;OAMG;IACH,YAAY,IAAoB;QAC9B,IAAI,CAAC,UAAU,GAAG,IAAI,CAAC,IAAI,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,EAAE,IAAI,CAAC,UAAU,CAAC,CAAA;QAC5D,IAAI,CAAC,WAAW,GAAG,IAAI,qBAAqB,CAAuB;YACjE,KAAK,EAAE,IAAI,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;YACnC,IAAI,EAAE,CAAC,KAAK,EAAE,OAAO,EAAE,EAAE,CAAC,IAAI,CAAC,UAAU,EAAE;SAC5C,CAAC,CAAA;IACJ,CAAC;IAED,UAAU;QACR,MAAM,KAAK,GAAgB,EAAE,CAAA;QAC7B,OAAO,IAAI,CAAC,UAAU;aACnB,QAAQ,EAAE;aACV,IAAI,CAAC,IAAI,CAAC,EAAE;YACX,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,EAAE,IAAI,IAAI,CAAC,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;gBACtC,OAAO,KAAK,CAAC,IAAI,CAAC,CAAA;YACpB,CAAC;YACD,OAAO,IAAI,CAAA;QACb,CAAC,CAAC;aACD,IAAI,CAAC,kBAAkB,CAAC,EAAE;YACzB,IACE,kBAAkB,CAAC,MAAM,GAAG,CAAC;gBAC7B,kBAAkB,CAAC,YAAY,CAAC,CAAC,CAAC,KAAK,SAAS,EAChD,CAAC;gBACD,MAAM,IAAI,kBAAkB,CAC1B,+IAA+I,CAChJ,CAAA;YACH,CAAC;YACD,mDAAmD;YACnD,uDAAuD;YACvD,uEAAuE;YACvE,gDAAgD;YAChD,IAAI,aAAa,GAAa,EAAE,CAAA;YAChC,IAAI,aAAa,GAAG,EAAE,CAAA;YACtB,KAAK,MAAM,QAAQ,IAAI,kBAAkB,EAAE,CAAC;gBAC1C,IACE,CAAC,QAAQ,IAAI,EAAE,IAAI,QAAQ,IAAI,EAAE,CAAC,CAAC,SAAS;oBAC5C,CAAC,CAAC,aAAa,IAAI,QAAQ,KAAK,EAAE,CAAC,CAAC,eAAe,EACnD,CAAC;oBACD,aAAa,IAAI,MAAM,CAAC,YAAY,CAAC,QAAQ,CAAC,CAAA;gBAChD,CAAC;qBAAM,IAAI,QAAQ,KAAK,CAAC,CAAC,QAAQ,EAAE,CAAC;oBACnC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;oBACtD,aAAa,GAAG,EAAE,CAAA;gBACpB,CAAC;qBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,EAAE,CAAC;oBACpC,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;oBACtD,aAAa,GAAG,EAAE,CAAA;oBAClB,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;oBACtC,aAAa,GAAG,EAAE,CAAA;gBACpB,CAAC;qBAAM,IAAI,QAAQ,KAAK,EAAE,CAAC,QAAQ,IAAI,QAAQ,KAAK,EAAE,CAAC,WAAW,EAAE,CAAC;oBACnE,oDAAoD;oBACpD,oCAAoC;oBACpC,MAAM,IAAI,kBAAkB,CAAC,0BAA0B,CAAC,CAAA;gBAC1D,CAAC;YACH,CAAC;YAED,8DAA8D;YAC9D,IAAI,aAAa,EAAE,CAAC;gBAClB,aAAa,CAAC,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,aAAa,EAAE,EAAE,CAAC,CAAC,CAAA;YACxD,CAAC;YACD,IAAI,aAAa,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;gBAC/B,gBAAgB,CAAC,KAAK,EAAE,aAAa,CAAC,CAAA;YACxC,CAAC;YAED,6BAA6B;YAC7B,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK,EAAE,GAAG,CAAC,EAAE,EAAE;gBAC7C,KAAK,CAAC,KAAK,CAAC,GAAG,GAAG,CAAC,IAAI,CACrB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,GAAG,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,GAAG,CAAC,CAAC,IAAI,CAC/C,CAAA;YACH,CAAC,CAAC,CAAA;YACF,OAAO,KAAK,CAAA;QACd,CAAC,CAAC,CAAA;IACN,CAAC;IAED,QAAQ,CAAC,OAAiC,EAAE;QAC1C,OAAO,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,OAAO,EAAE,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,CAAA;IACzD,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,2BAA2B,CAAC,KAAa;QAC7C,OAAO,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;IACzC,CAAC;IAED;;;;;;;;;;OAUG;IACH,KAAK,CAAC,kBAAkB,CACtB,KAAa,EACb,UAAkB,EAClB,QAAgB;QAEhB,MAAM,UAAU,GAAG,CAAC,MAAM,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAA;QACjD,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,OAAO,EAAE,CAAA;QACX,CAAC;QAED,MAAM,OAAO,GAAG,CAAC,KAAY,EAAE,EAAE;YAC/B,MAAM,UAAU,GAAG,KAAK,CAAC,KAAK,CAAA;YAC9B,MAAM,QAAQ,GAAG,KAAK,CAAC,KAAK,GAAG,KAAK,CAAC,IAAI,CAAA;YACzC,IAAI,UAAU,GAAG,QAAQ,EAAE,CAAC;gBAC1B,OAAO,CAAC,CAAC,CAAA;YACX,CAAC,CAAC,0BAA0B;YAC5B,IAAI,QAAQ,IAAI,UAAU,EAAE,CAAC;gBAC3B,OAAO,CAAC,CAAA;YACV,CAAC,CAAC,wBAAwB;YAC1B,OAAO,CAAC,CAAA,CAAC,uBAAuB;QAClC,CAAC,CAAA;QACD,MAAM,IAAI,GAAG,EAAa,CAAA;QAC1B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;YAC/B,IAAI,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;gBACzB,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,CAAA;YAClB,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAA;IACb,CAAC;CACF"}
|
|
@@ -1,4 +1,3 @@
|
|
|
1
|
-
/// <reference types="node" />
|
|
2
1
|
import CramSlice from '../slice';
|
|
3
2
|
import CramContainerCompressionScheme from './compressionScheme';
|
|
4
3
|
import CramFile from '../file';
|
|
@@ -18,7 +17,7 @@ export default class CramContainer {
|
|
|
18
17
|
contentPosition: number;
|
|
19
18
|
_size: number;
|
|
20
19
|
content: Buffer;
|
|
21
|
-
crc32?: number
|
|
20
|
+
crc32?: number;
|
|
22
21
|
} | null | undefined>;
|
|
23
22
|
getFirstBlock(): Promise<import("../file").CramFileBlock | undefined>;
|
|
24
23
|
getCompressionScheme(): Promise<CramContainerCompressionScheme | undefined>;
|
package/esm/cramFile/file.d.ts
CHANGED
|
@@ -1,5 +1,3 @@
|
|
|
1
|
-
/// <reference path="../../src/typings/binary-parser.d.ts" />
|
|
2
|
-
/// <reference types="node" />
|
|
3
1
|
import QuickLRU from 'quick-lru';
|
|
4
2
|
import { Parser } from '@gmod/binary-parser';
|
|
5
3
|
import { BlockHeader, CompressionMethod } from './sectionParsers';
|
|
@@ -45,7 +43,7 @@ export default class CramFile {
|
|
|
45
43
|
tag: string;
|
|
46
44
|
data: {
|
|
47
45
|
tag: string;
|
|
48
|
-
value: string
|
|
46
|
+
value: string;
|
|
49
47
|
}[];
|
|
50
48
|
}[]>;
|
|
51
49
|
getHeaderText(): Promise<string | undefined>;
|
package/esm/cramFile/util.d.ts
CHANGED
|
@@ -1,5 +1,3 @@
|
|
|
1
|
-
/// <reference path="../../src/typings/binary-parser.d.ts" />
|
|
2
|
-
/// <reference types="node" />
|
|
3
1
|
import { Parser } from '@gmod/binary-parser';
|
|
4
2
|
export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;
|
|
5
3
|
export declare function parseItf8(buffer: Uint8Array, initialOffset: number): [number, number];
|
package/esm/indexedCramFile.d.ts
CHANGED
|
@@ -15,20 +15,17 @@ export interface CramIndexLike {
|
|
|
15
15
|
export default class IndexedCramFile {
|
|
16
16
|
cram: CramFile;
|
|
17
17
|
index: CramIndexLike;
|
|
18
|
-
private fetchSizeLimit;
|
|
19
18
|
/**
|
|
20
19
|
*
|
|
21
20
|
* @param {object} args
|
|
22
21
|
* @param {CramFile} args.cram
|
|
23
22
|
* @param {Index-like} args.index object that supports getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
|
|
24
23
|
* @param {number} [args.cacheSize] optional maximum number of CRAM records to cache. default 20,000
|
|
25
|
-
* @param {number} [args.fetchSizeLimit] optional maximum number of bytes to fetch in a single getRecordsForRange call. Default 3 MiB.
|
|
26
24
|
* @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
|
|
27
25
|
* checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
|
|
28
26
|
*/
|
|
29
27
|
constructor(args: {
|
|
30
28
|
index: CramIndexLike;
|
|
31
|
-
fetchSizeLimit?: number;
|
|
32
29
|
} & ({
|
|
33
30
|
cram: CramFile;
|
|
34
31
|
} | ({
|
package/esm/indexedCramFile.js
CHANGED
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import {
|
|
1
|
+
import { CramUnimplementedError } from './errors';
|
|
2
2
|
import CramFile from './cramFile';
|
|
3
3
|
export default class IndexedCramFile {
|
|
4
4
|
/**
|
|
@@ -7,7 +7,6 @@ export default class IndexedCramFile {
|
|
|
7
7
|
* @param {CramFile} args.cram
|
|
8
8
|
* @param {Index-like} args.index object that supports getEntriesForRange(seqId,start,end) -> Promise[Array[index entries]]
|
|
9
9
|
* @param {number} [args.cacheSize] optional maximum number of CRAM records to cache. default 20,000
|
|
10
|
-
* @param {number} [args.fetchSizeLimit] optional maximum number of bytes to fetch in a single getRecordsForRange call. Default 3 MiB.
|
|
11
10
|
* @param {boolean} [args.checkSequenceMD5] - default true. if false, disables verifying the MD5
|
|
12
11
|
* checksum of the reference sequence underlying a slice. In some applications, this check can cause an inconvenient amount (many megabases) of sequences to be fetched.
|
|
13
12
|
*/
|
|
@@ -30,7 +29,6 @@ export default class IndexedCramFile {
|
|
|
30
29
|
if (!this.index.getEntriesForRange) {
|
|
31
30
|
throw new Error('invalid arguments: not an index');
|
|
32
31
|
}
|
|
33
|
-
this.fetchSizeLimit = args.fetchSizeLimit || 3000000;
|
|
34
32
|
}
|
|
35
33
|
/**
|
|
36
34
|
*
|
|
@@ -49,10 +47,6 @@ export default class IndexedCramFile {
|
|
|
49
47
|
}
|
|
50
48
|
const seqId = seq;
|
|
51
49
|
const slices = await this.index.getEntriesForRange(seqId, start, end);
|
|
52
|
-
const totalSize = slices.map(s => s.sliceBytes).reduce((a, b) => a + b, 0);
|
|
53
|
-
if (totalSize > this.fetchSizeLimit) {
|
|
54
|
-
throw new CramSizeLimitError(`data size of ${totalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);
|
|
55
|
-
}
|
|
56
50
|
// TODO: do we need to merge or de-duplicate the blocks?
|
|
57
51
|
// fetch all the slices and parse the feature data
|
|
58
52
|
const filter = (feature) => feature.sequenceId === seq &&
|
|
@@ -108,13 +102,7 @@ export default class IndexedCramFile {
|
|
|
108
102
|
.filter((item, pos, ary) => !pos || item.toString() !== ary[pos - 1].toString());
|
|
109
103
|
const mateRecordPromises = [];
|
|
110
104
|
const mateFeatPromises = [];
|
|
111
|
-
const
|
|
112
|
-
.map(s => s.sliceBytes)
|
|
113
|
-
.reduce((a, b) => a + b, 0);
|
|
114
|
-
if (mateTotalSize > this.fetchSizeLimit) {
|
|
115
|
-
throw new Error(`mate data size of ${mateTotalSize.toLocaleString()} bytes exceeded fetch size limit of ${this.fetchSizeLimit.toLocaleString()} bytes`);
|
|
116
|
-
}
|
|
117
|
-
mateChunks.forEach(c => {
|
|
105
|
+
for (const c of mateChunks) {
|
|
118
106
|
let recordPromise = this.cram.featureCache.get(c.toString());
|
|
119
107
|
if (!recordPromise) {
|
|
120
108
|
recordPromise = this.getRecordsInSlice(c, () => true);
|
|
@@ -134,7 +122,7 @@ export default class IndexedCramFile {
|
|
|
134
122
|
return mateRecs;
|
|
135
123
|
});
|
|
136
124
|
mateFeatPromises.push(featPromise);
|
|
137
|
-
}
|
|
125
|
+
}
|
|
138
126
|
const newMateFeats = await Promise.all(mateFeatPromises);
|
|
139
127
|
if (newMateFeats.length) {
|
|
140
128
|
const newMates = newMateFeats.reduce((result, current) => result.concat(current));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"indexedCramFile.js","sourceRoot":"","sources":["../src/indexedCramFile.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"indexedCramFile.js","sourceRoot":"","sources":["../src/indexedCramFile.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,UAAU,CAAA;AACjD,OAAO,QAAQ,MAAM,YAAY,CAAA;AAqBjC,MAAM,CAAC,OAAO,OAAO,eAAe;IAIlC;;;;;;;;OAQG;IACH,YACE,IAUC;;QAED,uDAAuD;QACvD,IAAI,CAAC,IAAI;YACP,MAAA,IAAI,CAAC,IAAI,mCACT,IAAI,QAAQ,CAAC;gBACX,GAAG,EAAE,IAAI,CAAC,OAAO;gBACjB,IAAI,EAAE,IAAI,CAAC,QAAQ;gBACnB,UAAU,EAAE,IAAI,CAAC,cAAc;gBAC/B,QAAQ,EAAE,IAAI,CAAC,QAAQ;gBACvB,gBAAgB,EAAE,IAAI,CAAC,gBAAgB;gBACvC,SAAS,EAAE,IAAI,CAAC,SAAS;aAC1B,CAAC,CAAA;QAEJ,IAAI,CAAC,CAAC,IAAI,CAAC,IAAI,YAAY,QAAQ,CAAC,EAAE,CAAC;YACrC,MAAM,IAAI,KAAK,CAAC,gCAAgC,CAAC,CAAA;QACnD,CAAC;QAED,IAAI,CAAC,KAAK,GAAG,IAAI,CAAC,KAAK,CAAA;QACvB,IAAI,CAAC,IAAI,CAAC,KAAK,CAAC,kBAAkB,EAAE,CAAC;YACnC,MAAM,IAAI,KAAK,CAAC,iCAAiC,CAAC,CAAA;QACpD,CAAC;IACH,CAAC;IAED;;;;;;OAMG;IACH,KAAK,CAAC,kBAAkB,CACtB,GAAW,EACX,KAAa,EACb,GAAW,EACX,OAII,EAAE;QAEN,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,IAAI,KAAK,CAAA;QAC5C,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,KAAK,CAAA;QAChD,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,MAAM,CAAA;QAEjD,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;YAC5B,wDAAwD;YACxD,MAAM,IAAI,sBAAsB,CAC9B,yCAAyC,CAC1C,CAAA;QACH,CAAC;QACD,MAAM,KAAK,GAAG,GAAG,CAAA;QACjB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;QAErE,wDAAwD;QAExD,kDAAkD;QAClD,MAAM,MAAM,GAAG,CAAC,OAAmB,EAAE,EAAE,CACrC,OAAO,CAAC,UAAU,KAAK,GAAG;YAC1B,OAAO,CAAC,cAAc,IAAI,GAAG;YAC7B,OAAO,CAAC,WAAW,KAAK,SAAS;YACjC,OAAO,CAAC,cAAc,GAAG,OAAO,CAAC,WAAW,GAAG,CAAC,IAAI,KAAK,CAAA;QAC3D,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,MAAM,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC,IAAI,CAAC,iBAAiB,CAAC,KAAK,EAAE,MAAM,CAAC,CAAC,CAC3D,CAAA;QAED,IAAI,GAAG,GAAiB,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,YAAY,CAAC,CAAA;QAC/D,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACrB,MAAM,SAAS,GAA2B,EAAE,CAAA;YAC5C,MAAM,OAAO,GAA2B,EAAE,CAAA;YAC1C,KAAK,MAAM,IAAI,IAAI,GAAG,EAAE,CAAC;gBACvB,MAAM,IAAI,GAAG,IAAI,CAAC,QAAQ,CAAA;gBAC1B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBACvB,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBACvC,CAAC;gBACD,MAAM,EAAE,GAAG,IAAI,CAAC,QAAQ,CAAA;gBACxB,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;oBACrB,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;gBACrB,CAAC;gBACD,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACpB,OAAO,CAAC,EAAE,CAAC,GAAG,CAAC,CAAA;YACjB,CAAC;YACD,MAAM,YAAY,GAA4B,EAAE,CAAA;YAChD,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE;gBAC3C,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;oBACZ,YAAY,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;gBACxB,CAAC;YACH,CAAC,CAAC,CAAA;YACF,MAAM,YAAY,GAAG,EAAE,CAAA;YACvB,KAAK,MAAM,UAAU,IAAI,GAAG,EAAE,CAAC;gBAC7B,MAAM,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;gBAChC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;oBACvB,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;gBACvC,CAAC;gBACD,IACE,YAAY,CAAC,IAAI,CAAC;oBAClB,UAAU,CAAC,IAAI;oBACf,CAAC,UAAU,CAAC,IAAI,CAAC,UAAU,KAAK,KAAK,IAAI,IAAI,CAAC,aAAa,CAAC;oBAC5D,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,cAAc,GAAG,UAAU,CAAC,IAAI,CAAC,cAAc,CAAC;wBAClE,IAAI,CAAC,aAAa,EACpB,CAAC;oBACD,MAAM,UAAU,GAAG,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAC9C,UAAU,CAAC,IAAI,CAAC,UAAU,EAC1B,UAAU,CAAC,IAAI,CAAC,cAAc,EAC9B,UAAU,CAAC,IAAI,CAAC,cAAc,GAAG,CAAC,CACnC,CAAA;oBACD,YAAY,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;gBAC/B,CAAC;YACH,CAAC;YACD,MAAM,UAAU,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;YAClD,IAAI,UAAU,GAAG,EAAa,CAAA;YAC9B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;gBAC/B,UAAU,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,CAAA;YAC3B,CAAC;YACD,wBAAwB;YACxB,UAAU,GAAG,UAAU;iBACpB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;iBACxD,MAAM,CACL,CAAC,IAAI,EAAE,GAAG,EAAE,GAAG,EAAE,EAAE,CACjB,CAAC,GAAG,IAAI,IAAI,CAAC,QAAQ,EAAE,KAAK,GAAG,CAAC,GAAG,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CACtD,CAAA;YAEH,MAAM,kBAAkB,GAAG,EAAE,CAAA;YAC7B,MAAM,gBAAgB,GAA4B,EAAE,CAAA;YACpD,KAAK,MAAM,CAAC,IAAI,UAAU,EAAE,CAAC;gBAC3B,IAAI,aAAa,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAA;gBAC5D,IAAI,CAAC,aAAa,EAAE,CAAC;oBACnB,aAAa,GAAG,IAAI,CAAC,iBAAiB,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,CAAA;oBACrD,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,EAAE,aAAa,CAAC,CAAA;gBACzD,CAAC;gBACD,kBAAkB,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;gBACtC,MAAM,WAAW,GAAG,aAAa,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE;oBAC7C,MAAM,QAAQ,GAAG,EAAE,CAAA;oBACnB,KAAK,MAAM,OAAO,IAAI,KAAK,EAAE,CAAC;wBAC5B,IAAI,OAAO,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;4BACnC,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;wBACvC,CAAC;wBACD,IAAI,YAAY,CAAC,OAAO,CAAC,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,OAAO,CAAC,QAAQ,CAAC,EAAE,CAAC;4BACjE,QAAQ,CAAC,IAAI,CAAC,OAAO,CAAC,CAAA;wBACxB,CAAC;oBACH,CAAC;oBACD,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBACF,gBAAgB,CAAC,IAAI,CAAC,WAAW,CAAC,CAAA;YACpC,CAAC;YACD,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,CAAA;YACxD,IAAI,YAAY,CAAC,MAAM,EAAE,CAAC;gBACxB,MAAM,QAAQ,GAAG,YAAY,CAAC,MAAM,CAAC,CAAC,MAAM,EAAE,OAAO,EAAE,EAAE,CACvD,MAAM,CAAC,MAAM,CAAC,OAAO,CAAC,CACvB,CAAA;gBACD,GAAG,GAAG,GAAG,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAA;YAC5B,CAAC;QACH,CAAC;QACD,OAAO,GAAG,CAAA;IACZ,CAAC;IAED,iBAAiB,CACf,EACE,cAAc,EACd,UAAU,EACV,UAAU,GACyD,EACrE,cAA0C;QAE1C,MAAM,SAAS,GAAG,IAAI,CAAC,IAAI,CAAC,sBAAsB,CAAC,cAAc,CAAC,CAAA;QAClE,MAAM,KAAK,GAAG,SAAS,CAAC,QAAQ,CAAC,UAAU,EAAE,UAAU,CAAC,CAAA;QACxD,OAAO,KAAK,CAAC,UAAU,CAAC,cAAc,CAAC,CAAA;IACzC,CAAC;IAED;;;;;OAKG;IACH,2BAA2B,CAAC,KAAa;QACvC,OAAO,IAAI,CAAC,KAAK,CAAC,2BAA2B,CAAC,KAAK,CAAC,CAAA;IACtD,CAAC;CACF"}
|
package/esm/io/index.d.ts
CHANGED
|
@@ -1,6 +1,4 @@
|
|
|
1
1
|
import { Filehandle } from '../cramFile/filehandle';
|
|
2
|
-
import { LocalFile, RemoteFile } from 'generic-filehandle';
|
|
3
|
-
declare function fromUrl(source: string): LocalFile | RemoteFile;
|
|
4
2
|
declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: Filehandle): Filehandle;
|
|
5
|
-
export {
|
|
3
|
+
export { open };
|
|
6
4
|
export { LocalFile, RemoteFile } from 'generic-filehandle';
|
package/esm/io/index.js
CHANGED
|
@@ -1,25 +1,16 @@
|
|
|
1
|
-
import url from 'url';
|
|
2
|
-
import { ensureNotNullish } from '../typescript';
|
|
3
1
|
import { LocalFile, RemoteFile } from 'generic-filehandle';
|
|
4
|
-
function fromUrl(source) {
|
|
5
|
-
const { protocol, pathname } = url.parse(source);
|
|
6
|
-
if (protocol === 'file:') {
|
|
7
|
-
return new LocalFile(unescape(ensureNotNullish(pathname)));
|
|
8
|
-
}
|
|
9
|
-
return new RemoteFile(source);
|
|
10
|
-
}
|
|
11
2
|
function open(maybeUrl, maybePath, maybeFilehandle) {
|
|
12
3
|
if (maybeFilehandle) {
|
|
13
4
|
return maybeFilehandle;
|
|
14
5
|
}
|
|
15
6
|
if (maybeUrl) {
|
|
16
|
-
return
|
|
7
|
+
return new RemoteFile(maybeUrl);
|
|
17
8
|
}
|
|
18
9
|
if (maybePath) {
|
|
19
10
|
return new LocalFile(maybePath);
|
|
20
11
|
}
|
|
21
12
|
throw new Error('no url, path, or filehandle provided, cannot open');
|
|
22
13
|
}
|
|
23
|
-
export {
|
|
14
|
+
export { open };
|
|
24
15
|
export { LocalFile, RemoteFile } from 'generic-filehandle';
|
|
25
16
|
//# sourceMappingURL=index.js.map
|
package/esm/io/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.ts"],"names":[],"mappings":"AACA,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA;AAE1D,SAAS,IAAI,CACX,QAAiB,EACjB,SAAkB,EAClB,eAA4B;IAE5B,IAAI,eAAe,EAAE,CAAC;QACpB,OAAO,eAAe,CAAA;IACxB,CAAC;IACD,IAAI,QAAQ,EAAE,CAAC;QACb,OAAO,IAAI,UAAU,CAAC,QAAQ,CAAC,CAAA;IACjC,CAAC;IACD,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,IAAI,SAAS,CAAC,SAAS,CAAC,CAAA;IACjC,CAAC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;AAED,OAAO,EAAE,IAAI,EAAE,CAAA;AAEf,OAAO,EAAE,SAAS,EAAE,UAAU,EAAE,MAAM,oBAAoB,CAAA"}
|
package/esm/sam.d.ts
CHANGED
package/esm/sam.js
CHANGED
|
@@ -15,10 +15,10 @@ export function parseHeaderText(text) {
|
|
|
15
15
|
}
|
|
16
16
|
: // @CO lines are not comma separated.
|
|
17
17
|
// See "samtools view -H c2\#pad.3.0.cram"
|
|
18
|
-
// so, just store value tag itself
|
|
18
|
+
// so, just store value tag and value itself
|
|
19
19
|
{
|
|
20
20
|
tag: f,
|
|
21
|
-
value:
|
|
21
|
+
value: '',
|
|
22
22
|
};
|
|
23
23
|
}),
|
|
24
24
|
});
|
package/esm/sam.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAMJ,EAAE,CAAA;IACR,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,OAAO,CAAC,KAAK,CAAC,CAAC;wBACb,CAAC,CAAC;4BACE,GAAG,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC;4BAClB,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC;yBACtB;wBACH,CAAC,CAAC,qCAAqC;4BACrC,0CAA0C;4BAC1C,
|
|
1
|
+
{"version":3,"file":"sam.js","sourceRoot":"","sources":["../src/sam.ts"],"names":[],"mappings":"AAAA,MAAM,UAAU,eAAe,CAAC,IAAY;IAC1C,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;IACjC,MAAM,IAAI,GAMJ,EAAE,CAAA;IACR,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,MAAM,CAAC,GAAG,EAAE,GAAG,MAAM,CAAC,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;QACzC,IAAI,GAAG,EAAE,CAAC;YACR,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG,EAAE,GAAG,CAAC,KAAK,CAAC,CAAC,CAAC;gBACjB,IAAI,EAAE,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE;oBACnB,MAAM,CAAC,GAAG,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;oBACxB,OAAO,CAAC,KAAK,CAAC,CAAC;wBACb,CAAC,CAAC;4BACE,GAAG,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC;4BAClB,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,GAAG,CAAC,CAAC;yBACtB;wBACH,CAAC,CAAC,qCAAqC;4BACrC,0CAA0C;4BAC1C,4CAA4C;4BAC5C;gCACE,GAAG,EAAE,CAAC;gCACN,KAAK,EAAE,EAAE;6BACV,CAAA;gBACP,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC"}
|
package/esm/typescript.d.ts
CHANGED
|
@@ -1,3 +1,2 @@
|
|
|
1
|
-
export declare function ensureNotNullish<T>(x: T | null | undefined): T;
|
|
2
1
|
export type TupleOf<T, N extends number> = N extends N ? number extends N ? T[] : _TupleOf<T, N, []> : never;
|
|
3
2
|
export type _TupleOf<T, N extends number, R extends unknown[]> = R['length'] extends N ? R : _TupleOf<T, N, [T, ...R]>;
|
package/esm/typescript.js
CHANGED
package/esm/typescript.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":"
|
|
1
|
+
{"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":""}
|
package/esm/unzip-pako.d.ts
CHANGED
package/esm/unzip.d.ts
CHANGED
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@gmod/cram",
|
|
3
|
-
"version": "2.0.
|
|
3
|
+
"version": "2.0.4",
|
|
4
4
|
"description": "read CRAM files with pure Javascript",
|
|
5
5
|
"license": "MIT",
|
|
6
6
|
"repository": "GMOD/cram-js",
|
|
@@ -42,9 +42,9 @@
|
|
|
42
42
|
"biojs"
|
|
43
43
|
],
|
|
44
44
|
"dependencies": {
|
|
45
|
+
"@gmod/abortable-promise-cache": "^2.0.0",
|
|
45
46
|
"@gmod/binary-parser": "^1.3.5",
|
|
46
47
|
"@jkbonfield/htscodecs": "^0.5.1",
|
|
47
|
-
"abortable-promise-cache": "^1.2.0",
|
|
48
48
|
"buffer-crc32": "^1.0.0",
|
|
49
49
|
"bzip2": "^0.1.1",
|
|
50
50
|
"long": "^4.0.0",
|
|
@@ -54,30 +54,25 @@
|
|
|
54
54
|
"xz-decompress": "^0.2.1"
|
|
55
55
|
},
|
|
56
56
|
"devDependencies": {
|
|
57
|
-
"@babel/plugin-transform-modules-commonjs": "^7.18.2",
|
|
58
|
-
"@babel/preset-typescript": "^7.17.12",
|
|
59
57
|
"@gmod/indexedfasta": "^2.1.0",
|
|
60
58
|
"@types/jest": "^29.5.12",
|
|
61
|
-
"@types/long": "^4.0.
|
|
59
|
+
"@types/long": "^4.0.0",
|
|
62
60
|
"@types/md5": "^2.3.2",
|
|
63
61
|
"@types/pako": "^1.0.3",
|
|
64
62
|
"@typescript-eslint/eslint-plugin": "^7.0.2",
|
|
65
63
|
"@typescript-eslint/parser": "^7.0.2",
|
|
66
64
|
"buffer": "^6.0.3",
|
|
67
65
|
"documentation": "^14.0.3",
|
|
68
|
-
"eslint": "^
|
|
66
|
+
"eslint": "^9.0.0",
|
|
69
67
|
"eslint-config-prettier": "^9.0.0",
|
|
70
|
-
"eslint-plugin-import": "^2.25.4",
|
|
71
68
|
"eslint-plugin-prettier": "^5.1.3",
|
|
72
|
-
"eslint-plugin-unicorn": "^
|
|
73
|
-
"glob": "^10.3.1",
|
|
69
|
+
"eslint-plugin-unicorn": "^54.0.0",
|
|
74
70
|
"jest": "^29.3.1",
|
|
75
71
|
"mock-fs": "^5.2.0",
|
|
76
72
|
"prettier": "^3.2.5",
|
|
77
73
|
"rimraf": "^5.0.1",
|
|
78
74
|
"ts-jest": "^29.1.2",
|
|
79
75
|
"typescript": "^5.0.3",
|
|
80
|
-
"url": "^0.11.0",
|
|
81
76
|
"webpack": "^5.90.3",
|
|
82
77
|
"webpack-cli": "^5.0.1"
|
|
83
78
|
},
|
package/src/craiIndex.ts
CHANGED