@gmod/cram 1.6.4 → 1.7.1
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/dist/craiIndex.d.ts +19 -12
- package/dist/craiIndex.js +63 -123
- package/dist/craiIndex.js.map +1 -1
- package/dist/cram-bundle.js +2 -17
- package/dist/cram-bundle.js.LICENSE.txt +17 -0
- package/dist/cramFile/codecs/_base.d.ts +26 -5
- package/dist/cramFile/codecs/_base.js +3 -39
- package/dist/cramFile/codecs/_base.js.map +1 -1
- package/dist/cramFile/codecs/beta.d.ts +7 -3
- package/dist/cramFile/codecs/beta.js +13 -31
- package/dist/cramFile/codecs/beta.js.map +1 -1
- package/dist/cramFile/codecs/byteArrayLength.d.ts +13 -7
- package/dist/cramFile/codecs/byteArrayLength.js +22 -41
- package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
- package/dist/cramFile/codecs/byteArrayStop.d.ts +9 -5
- package/dist/cramFile/codecs/byteArrayStop.js +25 -46
- package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
- package/dist/cramFile/codecs/dataSeriesTypes.d.ts +4 -0
- package/dist/cramFile/codecs/dataSeriesTypes.js +3 -0
- package/dist/cramFile/codecs/dataSeriesTypes.js.map +1 -0
- package/dist/cramFile/codecs/external.d.ts +10 -6
- package/dist/cramFile/codecs/external.js +26 -44
- package/dist/cramFile/codecs/external.js.map +1 -1
- package/dist/cramFile/codecs/gamma.d.ts +7 -3
- package/dist/cramFile/codecs/gamma.js +16 -34
- package/dist/cramFile/codecs/gamma.js.map +1 -1
- package/dist/cramFile/codecs/getBits.d.ts +7 -0
- package/dist/cramFile/codecs/getBits.js +26 -0
- package/dist/cramFile/codecs/getBits.js.map +1 -0
- package/dist/cramFile/codecs/huffman.d.ts +17 -13
- package/dist/cramFile/codecs/huffman.js +76 -85
- package/dist/cramFile/codecs/huffman.js.map +1 -1
- package/dist/cramFile/codecs/index.d.ts +4 -2
- package/dist/cramFile/codecs/index.js +12 -13
- package/dist/cramFile/codecs/index.js.map +1 -1
- package/dist/cramFile/codecs/subexp.d.ts +7 -3
- package/dist/cramFile/codecs/subexp.js +19 -36
- package/dist/cramFile/codecs/subexp.js.map +1 -1
- package/dist/cramFile/constants.d.ts +35 -35
- package/dist/cramFile/constants.js +1 -1
- package/dist/cramFile/constants.js.map +1 -1
- package/dist/cramFile/container/compressionScheme.d.ts +57 -11
- package/dist/cramFile/container/compressionScheme.js +37 -32
- package/dist/cramFile/container/compressionScheme.js.map +1 -1
- package/dist/cramFile/container/index.d.ts +23 -9
- package/dist/cramFile/container/index.js +74 -144
- package/dist/cramFile/container/index.js.map +1 -1
- package/dist/cramFile/encoding.d.ts +78 -0
- package/dist/cramFile/encoding.js +3 -0
- package/dist/cramFile/encoding.js.map +1 -0
- package/dist/cramFile/file.d.ts +91 -41
- package/dist/cramFile/file.js +234 -368
- package/dist/cramFile/file.js.map +1 -1
- package/dist/cramFile/filehandle.d.ts +2 -0
- package/dist/cramFile/filehandle.js +3 -0
- package/dist/cramFile/filehandle.js.map +1 -0
- package/dist/cramFile/index.d.ts +2 -1
- package/dist/cramFile/index.js +4 -1
- package/dist/cramFile/index.js.map +1 -1
- package/dist/cramFile/record.d.ts +61 -17
- package/dist/cramFile/record.js +153 -77
- package/dist/cramFile/record.js.map +1 -1
- package/dist/cramFile/sectionParsers.d.ts +99 -8
- package/dist/cramFile/sectionParsers.js +70 -80
- package/dist/cramFile/sectionParsers.js.map +1 -1
- package/dist/cramFile/slice/decodeRecord.d.ts +30 -2
- package/dist/cramFile/slice/decodeRecord.js +148 -118
- package/dist/cramFile/slice/decodeRecord.js.map +1 -1
- package/dist/cramFile/slice/index.d.ts +21 -14
- package/dist/cramFile/slice/index.js +286 -381
- package/dist/cramFile/slice/index.js.map +1 -1
- package/dist/cramFile/util.d.ts +11 -5
- package/dist/cramFile/util.js +19 -97
- package/dist/cramFile/util.js.map +1 -1
- package/dist/errors.d.ts +5 -10
- package/dist/errors.js +11 -62
- package/dist/errors.js.map +1 -1
- package/dist/index.d.ts +4 -4
- package/dist/index.js +28 -4
- package/dist/index.js.map +1 -1
- package/dist/indexedCramFile.d.ts +37 -12
- package/dist/indexedCramFile.js +114 -154
- package/dist/indexedCramFile.js.map +1 -1
- package/dist/io/index.d.ts +5 -5
- package/dist/io/index.js +9 -9
- package/dist/io/index.js.map +1 -1
- package/dist/rans/constants.js +3 -3
- package/dist/rans/constants.js.map +1 -1
- package/dist/rans/d04.js +15 -15
- package/dist/rans/d04.js.map +1 -1
- package/dist/rans/d14.js +21 -21
- package/dist/rans/d14.js.map +1 -1
- package/dist/rans/decoding.js +27 -30
- package/dist/rans/decoding.js.map +1 -1
- package/dist/rans/frequencies.js +11 -11
- package/dist/rans/frequencies.js.map +1 -1
- package/dist/rans/index.js +46 -49
- package/dist/rans/index.js.map +1 -1
- package/dist/sam.d.ts +8 -1
- package/dist/sam.js +7 -7
- package/dist/sam.js.map +1 -1
- package/dist/typescript.d.ts +3 -0
- package/dist/typescript.js +11 -0
- package/dist/typescript.js.map +1 -0
- package/dist/unzip-pako.js +1 -1
- package/dist/unzip-pako.js.map +1 -1
- package/dist/unzip.js +1 -1
- package/dist/unzip.js.map +1 -1
- package/errors.js +11 -62
- package/esm/craiIndex.d.ts +19 -12
- package/esm/craiIndex.js +7 -23
- package/esm/craiIndex.js.map +1 -1
- package/esm/cramFile/codecs/_base.d.ts +26 -5
- package/esm/cramFile/codecs/_base.js +1 -35
- package/esm/cramFile/codecs/_base.js.map +1 -1
- package/esm/cramFile/codecs/beta.d.ts +7 -3
- package/esm/cramFile/codecs/beta.js +4 -3
- package/esm/cramFile/codecs/beta.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayLength.d.ts +13 -7
- package/esm/cramFile/codecs/byteArrayLength.js +1 -1
- package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayStop.d.ts +9 -5
- package/esm/cramFile/codecs/byteArrayStop.js +7 -9
- package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
- package/esm/cramFile/codecs/dataSeriesTypes.d.ts +4 -0
- package/esm/cramFile/codecs/dataSeriesTypes.js +2 -0
- package/esm/cramFile/codecs/dataSeriesTypes.js.map +1 -0
- package/esm/cramFile/codecs/external.d.ts +10 -6
- package/esm/cramFile/codecs/external.js +4 -3
- package/esm/cramFile/codecs/external.js.map +1 -1
- package/esm/cramFile/codecs/gamma.d.ts +7 -3
- package/esm/cramFile/codecs/gamma.js +5 -4
- package/esm/cramFile/codecs/gamma.js.map +1 -1
- package/esm/cramFile/codecs/getBits.d.ts +7 -0
- package/esm/cramFile/codecs/getBits.js +21 -0
- package/esm/cramFile/codecs/getBits.js.map +1 -0
- package/esm/cramFile/codecs/huffman.d.ts +17 -13
- package/esm/cramFile/codecs/huffman.js +22 -9
- package/esm/cramFile/codecs/huffman.js.map +1 -1
- package/esm/cramFile/codecs/index.d.ts +4 -2
- package/esm/cramFile/codecs/index.js +1 -1
- package/esm/cramFile/codecs/index.js.map +1 -1
- package/esm/cramFile/codecs/subexp.d.ts +7 -3
- package/esm/cramFile/codecs/subexp.js +7 -5
- package/esm/cramFile/codecs/subexp.js.map +1 -1
- package/esm/cramFile/constants.d.ts +35 -35
- package/esm/cramFile/constants.js.map +1 -1
- package/esm/cramFile/container/compressionScheme.d.ts +57 -11
- package/esm/cramFile/container/compressionScheme.js +15 -8
- package/esm/cramFile/container/compressionScheme.js.map +1 -1
- package/esm/cramFile/container/index.d.ts +23 -9
- package/esm/cramFile/container/index.js +11 -9
- package/esm/cramFile/container/index.js.map +1 -1
- package/esm/cramFile/encoding.d.ts +78 -0
- package/esm/cramFile/encoding.js +2 -0
- package/esm/cramFile/encoding.js.map +1 -0
- package/esm/cramFile/file.d.ts +91 -41
- package/esm/cramFile/file.js +59 -47
- package/esm/cramFile/file.js.map +1 -1
- package/esm/cramFile/filehandle.d.ts +2 -0
- package/esm/cramFile/filehandle.js +2 -0
- package/esm/cramFile/filehandle.js.map +1 -0
- package/esm/cramFile/index.d.ts +2 -1
- package/esm/cramFile/index.js +1 -0
- package/esm/cramFile/index.js.map +1 -1
- package/esm/cramFile/record.d.ts +61 -17
- package/esm/cramFile/record.js +83 -5
- package/esm/cramFile/record.js.map +1 -1
- package/esm/cramFile/sectionParsers.d.ts +99 -8
- package/esm/cramFile/sectionParsers.js +7 -17
- package/esm/cramFile/sectionParsers.js.map +1 -1
- package/esm/cramFile/slice/decodeRecord.d.ts +30 -2
- package/esm/cramFile/slice/decodeRecord.js +102 -70
- package/esm/cramFile/slice/decodeRecord.js.map +1 -1
- package/esm/cramFile/slice/index.d.ts +21 -14
- package/esm/cramFile/slice/index.js +77 -38
- package/esm/cramFile/slice/index.js.map +1 -1
- package/esm/cramFile/util.d.ts +11 -5
- package/esm/cramFile/util.js +11 -82
- package/esm/cramFile/util.js.map +1 -1
- package/esm/errors.d.ts +5 -10
- package/esm/errors.js +0 -5
- package/esm/errors.js.map +1 -1
- package/esm/index.d.ts +4 -4
- package/esm/index.js +2 -2
- package/esm/index.js.map +1 -1
- package/esm/indexedCramFile.d.ts +37 -12
- package/esm/indexedCramFile.js +19 -8
- package/esm/indexedCramFile.js.map +1 -1
- package/esm/io/index.d.ts +5 -5
- package/esm/io/index.js +3 -3
- package/esm/io/index.js.map +1 -1
- package/esm/sam.d.ts +8 -1
- package/esm/sam.js.map +1 -1
- package/esm/typescript.d.ts +3 -0
- package/esm/typescript.js +7 -0
- package/esm/typescript.js.map +1 -0
- package/package.json +18 -11
- package/src/{craiIndex.js → craiIndex.ts} +36 -30
- package/src/cramFile/codecs/_base.ts +45 -0
- package/src/cramFile/codecs/beta.ts +34 -0
- package/src/cramFile/codecs/{byteArrayLength.js → byteArrayLength.ts} +27 -5
- package/src/cramFile/codecs/{byteArrayStop.js → byteArrayStop.ts} +25 -12
- package/src/cramFile/codecs/dataSeriesTypes.ts +39 -0
- package/src/cramFile/codecs/{external.js → external.ts} +28 -12
- package/src/cramFile/codecs/gamma.ts +42 -0
- package/src/cramFile/codecs/getBits.ts +28 -0
- package/src/cramFile/codecs/{huffman.js → huffman.ts} +48 -15
- package/src/cramFile/codecs/{index.js → index.ts} +9 -3
- package/src/cramFile/codecs/subexp.ts +45 -0
- package/src/cramFile/{constants.js → constants.ts} +0 -0
- package/src/cramFile/container/{compressionScheme.js → compressionScheme.ts} +50 -18
- package/src/cramFile/container/{index.js → index.ts} +13 -13
- package/src/cramFile/encoding.ts +98 -0
- package/src/cramFile/{file.js → file.ts} +136 -62
- package/src/cramFile/filehandle.ts +3 -0
- package/src/cramFile/{index.js → index.ts} +1 -0
- package/src/cramFile/{record.js → record.ts} +185 -14
- package/src/cramFile/{sectionParsers.js → sectionParsers.ts} +148 -20
- package/src/cramFile/slice/{decodeRecord.js → decodeRecord.ts} +158 -105
- package/src/cramFile/slice/{index.js → index.ts} +138 -63
- package/src/cramFile/{util.js → util.ts} +28 -17
- package/src/{errors.js → errors.ts} +0 -5
- package/src/index.ts +5 -0
- package/src/{indexedCramFile.js → indexedCramFile.ts} +79 -19
- package/src/io/{index.js → index.ts} +10 -5
- package/src/{sam.js → sam.ts} +7 -2
- package/src/typescript.ts +17 -0
- package/src/typings/binary-parser.d.ts +44 -0
- package/src/typings/bzip2.d.ts +7 -0
- package/src/typings/htscodecs.d.ts +6 -0
- package/dist/io/bufferCache.d.ts +0 -12
- package/dist/io/bufferCache.js +0 -112
- package/dist/io/bufferCache.js.map +0 -1
- package/dist/io/localFile.d.ts +0 -10
- package/dist/io/localFile.js +0 -108
- package/dist/io/localFile.js.map +0 -1
- package/dist/io/remoteFile.d.ts +0 -16
- package/dist/io/remoteFile.js +0 -143
- package/dist/io/remoteFile.js.map +0 -1
- package/esm/io/bufferCache.d.ts +0 -12
- package/esm/io/bufferCache.js +0 -54
- package/esm/io/bufferCache.js.map +0 -1
- package/esm/io/localFile.d.ts +0 -10
- package/esm/io/localFile.js +0 -31
- package/esm/io/localFile.js.map +0 -1
- package/esm/io/remoteFile.d.ts +0 -16
- package/esm/io/remoteFile.js +0 -64
- package/esm/io/remoteFile.js.map +0 -1
- package/src/cramFile/codecs/_base.js +0 -49
- package/src/cramFile/codecs/beta.js +0 -23
- package/src/cramFile/codecs/gamma.js +0 -30
- package/src/cramFile/codecs/subexp.js +0 -32
- package/src/index.js +0 -5
- package/src/io/bufferCache.js +0 -66
- package/src/io/localFile.js +0 -35
- package/src/io/remoteFile.js +0 -71
package/src/io/remoteFile.js
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import fetch from 'cross-fetch'
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import BufferCache from './bufferCache'
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export default class RemoteFile {
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constructor(source) {
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this.cache = new BufferCache({
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})
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}
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async _fetch(position, length) {
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if (length < Infinity) {
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headers.range = `bytes=${position}-${position + length}`
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} else if (length === Infinity && position !== 0) {
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headers.range = `bytes=${position}-`
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}
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