@gmod/cram 2.0.3 → 3.0.0
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 +10 -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/byteArrayLength.js +1 -1
- package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
- package/dist/cramFile/codecs/byteArrayStop.d.ts +0 -1
- package/dist/cramFile/codecs/external.js +1 -1
- package/dist/cramFile/codecs/external.js.map +1 -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/huffman.js +2 -1
- package/dist/cramFile/codecs/huffman.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/compressionScheme.d.ts +0 -3
- package/dist/cramFile/container/compressionScheme.js +0 -4
- package/dist/cramFile/container/compressionScheme.js.map +1 -1
- package/dist/cramFile/container/index.d.ts +57 -5
- package/dist/cramFile/container/index.js +15 -9
- package/dist/cramFile/container/index.js.map +1 -1
- package/dist/cramFile/file.d.ts +24 -61
- package/dist/cramFile/file.js +23 -28
- package/dist/cramFile/file.js.map +1 -1
- package/dist/cramFile/record.d.ts +1 -1
- package/dist/cramFile/sectionParsers.d.ts +195 -49
- package/dist/cramFile/sectionParsers.js +622 -304
- 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/slice/index.d.ts +23 -1
- package/dist/cramFile/slice/index.js +9 -6
- package/dist/cramFile/slice/index.js.map +1 -1
- package/dist/cramFile/util.d.ts +6 -6
- package/dist/cramFile/util.js +93 -12
- 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.js +1 -2
- 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/byteArrayLength.js +1 -1
- package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayStop.d.ts +0 -1
- package/esm/cramFile/codecs/external.js +1 -1
- package/esm/cramFile/codecs/external.js.map +1 -1
- package/esm/cramFile/codecs/getBits.d.ts +0 -1
- package/esm/cramFile/codecs/huffman.js +2 -1
- package/esm/cramFile/codecs/huffman.js.map +1 -1
- package/esm/cramFile/container/compressionScheme.d.ts +0 -3
- package/esm/cramFile/container/compressionScheme.js +0 -4
- package/esm/cramFile/container/compressionScheme.js.map +1 -1
- package/esm/cramFile/container/index.d.ts +57 -5
- package/esm/cramFile/container/index.js +15 -9
- package/esm/cramFile/container/index.js.map +1 -1
- package/esm/cramFile/file.d.ts +24 -61
- package/esm/cramFile/file.js +22 -25
- package/esm/cramFile/file.js.map +1 -1
- package/esm/cramFile/record.d.ts +1 -1
- package/esm/cramFile/sectionParsers.d.ts +195 -49
- package/esm/cramFile/sectionParsers.js +620 -303
- package/esm/cramFile/sectionParsers.js.map +1 -1
- package/esm/cramFile/slice/index.d.ts +23 -1
- package/esm/cramFile/slice/index.js +10 -7
- package/esm/cramFile/slice/index.js.map +1 -1
- package/esm/cramFile/util.d.ts +6 -6
- package/esm/cramFile/util.js +87 -6
- package/esm/cramFile/util.js.map +1 -1
- 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/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 +9 -15
- package/src/craiIndex.ts +1 -1
- package/src/cramFile/codecs/byteArrayLength.ts +1 -2
- package/src/cramFile/codecs/external.ts +1 -1
- package/src/cramFile/codecs/huffman.ts +2 -1
- package/src/cramFile/container/compressionScheme.ts +1 -8
- package/src/cramFile/container/index.ts +21 -10
- package/src/cramFile/file.ts +28 -43
- package/src/cramFile/record.ts +1 -1
- package/src/cramFile/sectionParsers.ts +668 -390
- package/src/cramFile/slice/index.ts +11 -5
- package/src/cramFile/util.ts +90 -91
- package/src/indexedCramFile.ts +3 -25
- package/src/io/index.ts +2 -12
- package/src/typescript.ts +0 -7
- package/src/typings/binary-parser.d.ts +0 -44
package/CHANGELOG.md
CHANGED
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@@ -1,3 +1,13 @@
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1
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# v3.0.0
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2
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+
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3
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- Remove @gmod/binary-parser to avoid CSP violation for use of 'eval'/'new
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Function'
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# v2.0.4
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8
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- Remove `fetchSizeLimit`
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- Remove usage of `url` module
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1
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# v2.0.3
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3
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- Update sam header parsing to avoid breaking 'type contract'
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package/README.md
CHANGED
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@@ -344,10 +344,6 @@ that show insertions, deletions, substitutions, etc.
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344
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- `args.cacheSize`
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?**
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optional maximum number of CRAM records to cache. default 20,000
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- `args.fetchSizeLimit`
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**[number](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Number)?**
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optional maximum number of bytes to fetch in a single getRecordsForRange
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call. Default 3 MiB.
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- `args.checkSequenceMD5`
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**[boolean](https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Boolean)?**
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default true. if false, disables verifying the MD5 checksum of the reference
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package/dist/craiIndex.js
CHANGED
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@@ -12,7 +12,7 @@ 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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const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
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const abortable_promise_cache_1 = __importDefault(require("@gmod/abortable-promise-cache"));
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const quick_lru_1 = __importDefault(require("quick-lru"));
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const unzip_1 = require("./unzip");
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const io_1 = require("./io");
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package/dist/craiIndex.js.map
CHANGED
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,
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1
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+
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