@gmod/cram 2.0.0 → 2.0.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CHANGELOG.md +4 -0
- package/dist/craiIndex.d.ts +2 -2
- package/dist/craiIndex.js +5 -9
- package/dist/craiIndex.js.map +1 -1
- package/dist/cram-bundle.js +1 -1
- package/dist/cramFile/codecs/_base.d.ts +6 -6
- package/dist/cramFile/codecs/beta.js.map +1 -1
- package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
- package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
- package/dist/cramFile/codecs/external.js +1 -0
- package/dist/cramFile/codecs/external.js.map +1 -1
- package/dist/cramFile/codecs/gamma.js.map +1 -1
- package/dist/cramFile/codecs/getBits.js.map +1 -1
- package/dist/cramFile/codecs/huffman.d.ts +0 -1
- package/dist/cramFile/codecs/huffman.js +1 -3
- package/dist/cramFile/codecs/huffman.js.map +1 -1
- package/dist/cramFile/codecs/index.js.map +1 -1
- package/dist/cramFile/codecs/subexp.js.map +1 -1
- package/dist/cramFile/container/compressionScheme.js +1 -1
- package/dist/cramFile/container/compressionScheme.js.map +1 -1
- package/dist/cramFile/container/index.js.map +1 -1
- package/dist/cramFile/encoding.d.ts +20 -20
- package/dist/cramFile/file.d.ts +14 -7
- package/dist/cramFile/file.js.map +1 -1
- package/dist/cramFile/filehandle.d.ts +1 -2
- package/dist/cramFile/index.d.ts +1 -2
- package/dist/cramFile/index.js +3 -3
- package/dist/cramFile/index.js.map +1 -1
- package/dist/cramFile/record.d.ts +6 -6
- package/dist/cramFile/record.js +7 -4
- package/dist/cramFile/record.js.map +1 -1
- package/dist/cramFile/sectionParsers.d.ts +9 -8
- package/dist/cramFile/sectionParsers.js +10 -11
- package/dist/cramFile/sectionParsers.js.map +1 -1
- package/dist/cramFile/slice/decodeRecord.js +7 -11
- package/dist/cramFile/slice/decodeRecord.js.map +1 -1
- package/dist/cramFile/slice/index.js +24 -22
- package/dist/cramFile/slice/index.js.map +1 -1
- package/dist/cramFile/util.d.ts +1 -0
- package/dist/cramFile/util.js +1 -1
- package/dist/cramFile/util.js.map +1 -1
- package/dist/index.d.ts +3 -4
- package/dist/index.js +7 -30
- package/dist/index.js.map +1 -1
- package/dist/indexedCramFile.d.ts +6 -6
- package/dist/indexedCramFile.js +13 -18
- package/dist/indexedCramFile.js.map +1 -1
- package/dist/io/index.d.ts +2 -1
- package/dist/io/index.js +4 -3
- package/dist/io/index.js.map +1 -1
- package/dist/rans/d04.js.map +1 -1
- package/dist/rans/d14.js.map +1 -1
- package/dist/rans/decoding.js.map +1 -1
- package/dist/rans/frequencies.js.map +1 -1
- package/dist/rans/index.js.map +1 -1
- package/dist/sam.d.ts +5 -6
- package/dist/sam.js +20 -7
- package/dist/sam.js.map +1 -1
- package/dist/typescript.js.map +1 -1
- package/dist/unzip.d.ts +2 -2
- package/dist/unzip.js +1 -1
- package/dist/unzip.js.map +1 -1
- package/esm/craiIndex.d.ts +2 -2
- package/esm/craiIndex.js +5 -9
- package/esm/craiIndex.js.map +1 -1
- package/esm/cramFile/codecs/_base.d.ts +6 -6
- package/esm/cramFile/codecs/beta.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayLength.js.map +1 -1
- package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
- package/esm/cramFile/codecs/external.js +1 -0
- package/esm/cramFile/codecs/external.js.map +1 -1
- package/esm/cramFile/codecs/gamma.js.map +1 -1
- package/esm/cramFile/codecs/getBits.js.map +1 -1
- package/esm/cramFile/codecs/huffman.d.ts +0 -1
- package/esm/cramFile/codecs/huffman.js +1 -3
- package/esm/cramFile/codecs/huffman.js.map +1 -1
- package/esm/cramFile/codecs/index.js.map +1 -1
- package/esm/cramFile/codecs/subexp.js.map +1 -1
- package/esm/cramFile/container/compressionScheme.js +1 -1
- package/esm/cramFile/container/compressionScheme.js.map +1 -1
- package/esm/cramFile/container/index.js.map +1 -1
- package/esm/cramFile/encoding.d.ts +20 -20
- package/esm/cramFile/file.d.ts +14 -7
- package/esm/cramFile/file.js.map +1 -1
- package/esm/cramFile/filehandle.d.ts +1 -2
- package/esm/cramFile/index.d.ts +1 -2
- package/esm/cramFile/index.js +1 -2
- package/esm/cramFile/index.js.map +1 -1
- package/esm/cramFile/record.d.ts +6 -6
- package/esm/cramFile/record.js +7 -4
- package/esm/cramFile/record.js.map +1 -1
- package/esm/cramFile/sectionParsers.d.ts +9 -8
- package/esm/cramFile/sectionParsers.js +10 -11
- package/esm/cramFile/sectionParsers.js.map +1 -1
- package/esm/cramFile/slice/decodeRecord.js +7 -11
- package/esm/cramFile/slice/decodeRecord.js.map +1 -1
- package/esm/cramFile/slice/index.js +24 -22
- package/esm/cramFile/slice/index.js.map +1 -1
- package/esm/cramFile/util.d.ts +1 -0
- package/esm/cramFile/util.js +1 -1
- package/esm/cramFile/util.js.map +1 -1
- package/esm/index.d.ts +3 -4
- package/esm/index.js +3 -4
- package/esm/index.js.map +1 -1
- package/esm/indexedCramFile.d.ts +6 -6
- package/esm/indexedCramFile.js +13 -18
- package/esm/indexedCramFile.js.map +1 -1
- package/esm/io/index.d.ts +2 -1
- package/esm/io/index.js +2 -1
- package/esm/io/index.js.map +1 -1
- package/esm/rans/d04.js.map +1 -1
- package/esm/rans/d14.js.map +1 -1
- package/esm/rans/decoding.js.map +1 -1
- package/esm/rans/frequencies.js.map +1 -1
- package/esm/rans/index.js.map +1 -1
- package/esm/sam.d.ts +5 -6
- package/esm/sam.js +20 -7
- package/esm/sam.js.map +1 -1
- package/esm/typescript.js.map +1 -1
- package/esm/unzip.d.ts +2 -2
- package/esm/unzip.js +1 -2
- package/esm/unzip.js.map +1 -1
- package/package.json +11 -11
- package/src/craiIndex.ts +8 -13
- package/src/cramFile/codecs/_base.ts +3 -3
- package/src/cramFile/codecs/external.ts +1 -0
- package/src/cramFile/codecs/huffman.ts +7 -8
- package/src/cramFile/container/compressionScheme.ts +1 -1
- package/src/cramFile/encoding.ts +10 -10
- package/src/cramFile/file.ts +5 -5
- package/src/cramFile/filehandle.ts +1 -3
- package/src/cramFile/index.ts +1 -2
- package/src/cramFile/record.ts +13 -10
- package/src/cramFile/sectionParsers.ts +8 -9
- package/src/cramFile/slice/decodeRecord.ts +15 -17
- package/src/cramFile/slice/index.ts +26 -23
- package/src/cramFile/util.ts +1 -1
- package/src/index.ts +3 -5
- package/src/indexedCramFile.ts +19 -23
- package/src/io/index.ts +3 -1
- package/src/sam.ts +28 -14
- package/src/typings/binary-parser.d.ts +1 -1
- package/src/unzip.ts +1 -2
package/dist/indexedCramFile.js
CHANGED
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@@ -26,12 +26,10 @@ class IndexedCramFile {
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* 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.
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*/
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constructor(args) {
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+
var _a;
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// { cram, index, seqFetch /* fasta, fastaIndex */ }) {
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-
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-
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}
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else {
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this.cram = new cramFile_1.default({
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this.cram =
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(_a = args.cram) !== null && _a !== void 0 ? _a : new cramFile_1.default({
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url: args.cramUrl,
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path: args.cramPath,
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filehandle: args.cramFilehandle,
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@@ -39,7 +37,6 @@ class IndexedCramFile {
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checkSequenceMD5: args.checkSequenceMD5,
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cacheSize: args.cacheSize,
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});
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}
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if (!(this.cram instanceof cramFile_1.default)) {
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throw new Error('invalid arguments: no cramfile');
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}
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@@ -82,12 +79,12 @@ class IndexedCramFile {
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if (opts.viewAsPairs) {
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const readNames = {};
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const readIds = {};
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for (
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const name =
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for (const read of ret) {
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const name = read.readName;
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if (name === undefined) {
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throw new Error();
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throw new Error('readName undefined');
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}
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const id =
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const id = read.uniqueId;
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if (!readNames[name]) {
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readNames[name] = 0;
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}
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@@ -101,11 +98,10 @@ class IndexedCramFile {
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}
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});
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const matePromises = [];
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for (
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const cramRecord = ret[i];
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for (const cramRecord of ret) {
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const name = cramRecord.readName;
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if (name === undefined) {
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throw new Error();
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throw new Error('readName undefined');
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}
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if (unmatedPairs[name] &&
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cramRecord.mate &&
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@@ -118,8 +114,8 @@ class IndexedCramFile {
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}
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const mateBlocks = yield Promise.all(matePromises);
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let mateChunks = [];
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for (
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mateChunks.push(...
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for (const block of mateBlocks) {
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mateChunks.push(...block);
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}
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// filter out duplicates
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mateChunks = mateChunks
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@@ -142,10 +138,9 @@ class IndexedCramFile {
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mateRecordPromises.push(recordPromise);
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const featPromise = recordPromise.then(feats => {
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const mateRecs = [];
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for (
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const feature = feats[i];
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for (const feature of feats) {
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if (feature.readName === undefined) {
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throw new Error();
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throw new Error('readName undefined');
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}
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if (unmatedPairs[feature.readName] && !readIds[feature.uniqueId]) {
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mateRecs.push(feature);
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"indexedCramFile.js","sourceRoot":"","sources":["../src/indexedCramFile.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,qCAAqE;AAErE,0DAAiC;AAqBjC,MAAqB,eAAe;IAKlC;;;;;;;;;OASG;IACH,YACE,IAWC
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1
|
+
{"version":3,"file":"indexedCramFile.js","sourceRoot":"","sources":["../src/indexedCramFile.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,qCAAqE;AAErE,0DAAiC;AAqBjC,MAAqB,eAAe;IAKlC;;;;;;;;;OASG;IACH,YACE,IAWC;;QAED,uDAAuD;QACvD,IAAI,CAAC,IAAI;YACP,MAAA,IAAI,CAAC,IAAI,mCACT,IAAI,kBAAQ,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,kBAAQ,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;QAED,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,cAAc,IAAI,OAAO,CAAA;IACtD,CAAC;IAED;;;;;;OAMG;IACG,kBAAkB,CACtB,GAAW,EACX,KAAa,EACb,GAAW,EACX,OAII,EAAE;;YAEN,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,IAAI,KAAK,CAAA;YAC5C,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,KAAK,CAAA;YAChD,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,IAAI,MAAM,CAAA;YAEjD,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;gBAC5B,wDAAwD;gBACxD,MAAM,IAAI,+BAAsB,CAC9B,yCAAyC,CAC1C,CAAA;YACH,CAAC;YACD,MAAM,KAAK,GAAG,GAAG,CAAA;YACjB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,kBAAkB,CAAC,KAAK,EAAE,KAAK,EAAE,GAAG,CAAC,CAAA;YACrE,MAAM,SAAS,GAAG,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;YAC1E,IAAI,SAAS,GAAG,IAAI,CAAC,cAAc,EAAE,CAAC;gBACpC,MAAM,IAAI,2BAAkB,CAC1B,gBAAgB,SAAS,CAAC,cAAc,EAAE,uCAAuC,IAAI,CAAC,cAAc,CAAC,cAAc,EAAE,QAAQ,CAC9H,CAAA;YACH,CAAC;YAED,wDAAwD;YAExD,kDAAkD;YAClD,MAAM,MAAM,GAAG,CAAC,OAAmB,EAAE,EAAE,CACrC,OAAO,CAAC,UAAU,KAAK,GAAG;gBAC1B,OAAO,CAAC,cAAc,IAAI,GAAG;gBAC7B,OAAO,CAAC,WAAW,KAAK,SAAS;gBACjC,OAAO,CAAC,cAAc,GAAG,OAAO,CAAC,WAAW,GAAG,CAAC,IAAI,KAAK,CAAA;YAC3D,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;YAED,IAAI,GAAG,GAAiB,KAAK,CAAC,SAAS,CAAC,MAAM,CAAC,GAAG,YAAY,CAAC,CAAA;YAC/D,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;gBACrB,MAAM,SAAS,GAA2B,EAAE,CAAA;gBAC5C,MAAM,OAAO,GAA2B,EAAE,CAAA;gBAC1C,KAAK,MAAM,IAAI,IAAI,GAAG,EAAE,CAAC;oBACvB,MAAM,IAAI,GAAG,IAAI,CAAC,QAAQ,CAAA;oBAC1B,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;wBACvB,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;oBACvC,CAAC;oBACD,MAAM,EAAE,GAAG,IAAI,CAAC,QAAQ,CAAA;oBACxB,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,CAAC;wBACrB,SAAS,CAAC,IAAI,CAAC,GAAG,CAAC,CAAA;oBACrB,CAAC;oBACD,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;oBACpB,OAAO,CAAC,EAAE,CAAC,GAAG,CAAC,CAAA;gBACjB,CAAC;gBACD,MAAM,YAAY,GAA4B,EAAE,CAAA;gBAChD,MAAM,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE;oBAC3C,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;wBACZ,YAAY,CAAC,CAAC,CAAC,GAAG,IAAI,CAAA;oBACxB,CAAC;gBACH,CAAC,CAAC,CAAA;gBACF,MAAM,YAAY,GAAG,EAAE,CAAA;gBACvB,KAAK,MAAM,UAAU,IAAI,GAAG,EAAE,CAAC;oBAC7B,MAAM,IAAI,GAAG,UAAU,CAAC,QAAQ,CAAA;oBAChC,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;wBACvB,MAAM,IAAI,KAAK,CAAC,oBAAoB,CAAC,CAAA;oBACvC,CAAC;oBACD,IACE,YAAY,CAAC,IAAI,CAAC;wBAClB,UAAU,CAAC,IAAI;wBACf,CAAC,UAAU,CAAC,IAAI,CAAC,UAAU,KAAK,KAAK,IAAI,IAAI,CAAC,aAAa,CAAC;wBAC5D,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,cAAc,GAAG,UAAU,CAAC,IAAI,CAAC,cAAc,CAAC;4BAClE,IAAI,CAAC,aAAa,EACpB,CAAC;wBACD,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;wBACD,YAAY,CAAC,IAAI,CAAC,UAAU,CAAC,CAAA;oBAC/B,CAAC;gBACH,CAAC;gBACD,MAAM,UAAU,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,CAAA;gBAClD,IAAI,UAAU,GAAG,EAAa,CAAA;gBAC9B,KAAK,MAAM,KAAK,IAAI,UAAU,EAAE,CAAC;oBAC/B,UAAU,CAAC,IAAI,CAAC,GAAG,KAAK,CAAC,CAAA;gBAC3B,CAAC;gBACD,wBAAwB;gBACxB,UAAU,GAAG,UAAU;qBACpB,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,aAAa,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAC;qBACxD,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;gBAEH,MAAM,kBAAkB,GAAG,EAAE,CAAA;gBAC7B,MAAM,gBAAgB,GAA4B,EAAE,CAAA;gBAEpD,MAAM,aAAa,GAAG,UAAU;qBAC7B,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,UAAU,CAAC;qBACtB,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,CAAA;gBAC7B,IAAI,aAAa,GAAG,IAAI,CAAC,cAAc,EAAE,CAAC;oBACxC,MAAM,IAAI,KAAK,CACb,qBAAqB,aAAa,CAAC,cAAc,EAAE,uCAAuC,IAAI,CAAC,cAAc,CAAC,cAAc,EAAE,QAAQ,CACvI,CAAA;gBACH,CAAC;gBAED,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC,EAAE;oBACrB,IAAI,aAAa,GAAG,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,CAAA;oBAC5D,IAAI,CAAC,aAAa,EAAE,CAAC;wBACnB,aAAa,GAAG,IAAI,CAAC,iBAAiB,CAAC,CAAC,EAAE,GAAG,EAAE,CAAC,IAAI,CAAC,CAAA;wBACrD,IAAI,CAAC,IAAI,CAAC,YAAY,CAAC,GAAG,CAAC,CAAC,CAAC,QAAQ,EAAE,EAAE,aAAa,CAAC,CAAA;oBACzD,CAAC;oBACD,kBAAkB,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;oBACtC,MAAM,WAAW,GAAG,aAAa,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE;wBAC7C,MAAM,QAAQ,GAAG,EAAE,CAAA;wBACnB,KAAK,MAAM,OAAO,IAAI,KAAK,EAAE,CAAC;4BAC5B,IAAI,OAAO,CAAC,QAAQ,KAAK,SAAS,EAAE,CAAC;gCACnC,MAAM,IAAI,K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|
package/dist/io/index.d.ts
CHANGED
|
@@ -2,4 +2,5 @@ import { Filehandle } from '../cramFile/filehandle';
|
|
|
2
2
|
import { LocalFile, RemoteFile } from 'generic-filehandle';
|
|
3
3
|
declare function fromUrl(source: string): LocalFile | RemoteFile;
|
|
4
4
|
declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: Filehandle): Filehandle;
|
|
5
|
-
export {
|
|
5
|
+
export { fromUrl, open };
|
|
6
|
+
export { LocalFile, RemoteFile } from 'generic-filehandle';
|
package/dist/io/index.js
CHANGED
|
@@ -3,12 +3,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
|
|
|
3
3
|
return (mod && mod.__esModule) ? mod : { "default": mod };
|
|
4
4
|
};
|
|
5
5
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
6
|
-
exports.
|
|
6
|
+
exports.RemoteFile = exports.LocalFile = exports.open = exports.fromUrl = void 0;
|
|
7
7
|
const url_1 = __importDefault(require("url"));
|
|
8
8
|
const typescript_1 = require("../typescript");
|
|
9
9
|
const generic_filehandle_1 = require("generic-filehandle");
|
|
10
|
-
Object.defineProperty(exports, "LocalFile", { enumerable: true, get: function () { return generic_filehandle_1.LocalFile; } });
|
|
11
|
-
Object.defineProperty(exports, "RemoteFile", { enumerable: true, get: function () { return generic_filehandle_1.RemoteFile; } });
|
|
12
10
|
function fromUrl(source) {
|
|
13
11
|
const { protocol, pathname } = url_1.default.parse(source);
|
|
14
12
|
if (protocol === 'file:') {
|
|
@@ -30,4 +28,7 @@ function open(maybeUrl, maybePath, maybeFilehandle) {
|
|
|
30
28
|
throw new Error('no url, path, or filehandle provided, cannot open');
|
|
31
29
|
}
|
|
32
30
|
exports.open = open;
|
|
31
|
+
var generic_filehandle_2 = require("generic-filehandle");
|
|
32
|
+
Object.defineProperty(exports, "LocalFile", { enumerable: true, get: function () { return generic_filehandle_2.LocalFile; } });
|
|
33
|
+
Object.defineProperty(exports, "RemoteFile", { enumerable: true, get: function () { return generic_filehandle_2.RemoteFile; } });
|
|
33
34
|
//# sourceMappingURL=index.js.map
|
package/dist/io/index.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.ts"],"names":[],"mappings":";;;;;;AAAA,8CAAqB;AACrB,8CAAgD;AAEhD,2DAA0D;
|
|
1
|
+
{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/io/index.ts"],"names":[],"mappings":";;;;;;AAAA,8CAAqB;AACrB,8CAAgD;AAEhD,2DAA0D;AAE1D,SAAS,OAAO,CAAC,MAAc;IAC7B,MAAM,EAAE,QAAQ,EAAE,QAAQ,EAAE,GAAG,aAAG,CAAC,KAAK,CAAC,MAAM,CAAC,CAAA;IAChD,IAAI,QAAQ,KAAK,OAAO,EAAE,CAAC;QACzB,OAAO,IAAI,8BAAS,CAAC,QAAQ,CAAC,IAAA,6BAAgB,EAAC,QAAQ,CAAC,CAAC,CAAC,CAAA;IAC5D,CAAC;IACD,OAAO,IAAI,+BAAU,CAAC,MAAM,CAAC,CAAA;AAC/B,CAAC;AAmBQ,0BAAO;AAjBhB,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,OAAO,CAAC,QAAQ,CAAC,CAAA;IAC1B,CAAC;IACD,IAAI,SAAS,EAAE,CAAC;QACd,OAAO,IAAI,8BAAS,CAAC,SAAS,CAAC,CAAA;IACjC,CAAC;IACD,MAAM,IAAI,KAAK,CAAC,mDAAmD,CAAC,CAAA;AACtE,CAAC;AAEiB,oBAAI;AAEtB,yDAA0D;AAAjD,+GAAA,SAAS,OAAA;AAAE,gHAAA,UAAU,OAAA"}
|
package/dist/rans/d04.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"d04.js","sourceRoot":"","sources":["../../src/rans/d04.ts"],"names":[],"mappings":";;;;;AAAA,aAAa;AACb,sCAA8C;AAE9C,2CAAsC;AACtC,0DAAiC;AAEjC,SAAwB,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;
|
|
1
|
+
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package/dist/rans/d14.js.map
CHANGED
|
@@ -1 +1 @@
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|
|
1
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-
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|
|
@@ -1 +1 @@
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1
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|
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1
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|
|
@@ -1 +1 @@
|
|
|
1
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-
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|
|
1
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package/dist/rans/index.js.map
CHANGED
|
@@ -1 +1 @@
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1
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|
package/dist/sam.d.ts
CHANGED
|
@@ -1,8 +1,7 @@
|
|
|
1
|
-
export
|
|
1
|
+
export declare function parseHeaderText(text: string): {
|
|
2
2
|
tag: string;
|
|
3
|
-
data:
|
|
3
|
+
data: {
|
|
4
4
|
tag: string;
|
|
5
|
-
value: string;
|
|
6
|
-
}
|
|
7
|
-
};
|
|
8
|
-
export declare function parseHeaderText(text: string): HeaderDataItem[];
|
|
5
|
+
value: string | undefined;
|
|
6
|
+
}[];
|
|
7
|
+
}[];
|
package/dist/sam.js
CHANGED
|
@@ -4,16 +4,29 @@ exports.parseHeaderText = void 0;
|
|
|
4
4
|
function parseHeaderText(text) {
|
|
5
5
|
const lines = text.split(/\r?\n/);
|
|
6
6
|
const data = [];
|
|
7
|
-
|
|
7
|
+
for (const line of lines) {
|
|
8
8
|
const [tag, ...fields] = line.split(/\t/);
|
|
9
|
-
const parsedFields = fields.map(f => {
|
|
10
|
-
const [fieldTag, value] = f.split(':', 2);
|
|
11
|
-
return { tag: fieldTag, value };
|
|
12
|
-
});
|
|
13
9
|
if (tag) {
|
|
14
|
-
data.push({
|
|
10
|
+
data.push({
|
|
11
|
+
tag: tag.slice(1),
|
|
12
|
+
data: fields.map(f => {
|
|
13
|
+
const r = f.indexOf(':');
|
|
14
|
+
return r !== -1
|
|
15
|
+
? {
|
|
16
|
+
tag: f.slice(0, r),
|
|
17
|
+
value: f.slice(r + 1),
|
|
18
|
+
}
|
|
19
|
+
: // @CO lines are not comma separated.
|
|
20
|
+
// See "samtools view -H c2\#pad.3.0.cram"
|
|
21
|
+
// so, just store value tag itself
|
|
22
|
+
{
|
|
23
|
+
tag: f,
|
|
24
|
+
value: undefined,
|
|
25
|
+
};
|
|
26
|
+
}),
|
|
27
|
+
});
|
|
15
28
|
}
|
|
16
|
-
}
|
|
29
|
+
}
|
|
17
30
|
return data;
|
|
18
31
|
}
|
|
19
32
|
exports.parseHeaderText = parseHeaderText;
|
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,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,kCAAkC;4BAClC;gCACE,GAAG,EAAE,CAAC;gCACN,KAAK,EAAE,SAAS;6BACjB,CAAA;gBACP,CAAC,CAAC;aACH,CAAC,CAAA;QACJ,CAAC;IACH,CAAC;IACD,OAAO,IAAI,CAAA;AACb,CAAC;AAjCD,0CAiCC"}
|
package/dist/typescript.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":";;;AAAA,SAAgB,gBAAgB,CAAI,CAAuB;IACzD,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,SAAS,EAAE;
|
|
1
|
+
{"version":3,"file":"typescript.js","sourceRoot":"","sources":["../src/typescript.ts"],"names":[],"mappings":";;;AAAA,SAAgB,gBAAgB,CAAI,CAAuB;IACzD,IAAI,CAAC,KAAK,IAAI,IAAI,CAAC,KAAK,SAAS,EAAE,CAAC;QAClC,MAAM,IAAI,KAAK,CAAC,4BAA4B,CAAC,CAAA;IAC/C,CAAC;IACD,OAAO,CAAC,CAAA;AACV,CAAC;AALD,4CAKC"}
|
package/dist/unzip.d.ts
CHANGED
|
@@ -1,2 +1,2 @@
|
|
|
1
|
-
|
|
2
|
-
export { gunzipSync as unzip };
|
|
1
|
+
/// <reference types="node" />
|
|
2
|
+
export { gunzipSync as unzip } from 'zlib';
|
package/dist/unzip.js
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
3
|
exports.unzip = void 0;
|
|
4
|
-
|
|
4
|
+
var zlib_1 = require("zlib");
|
|
5
5
|
Object.defineProperty(exports, "unzip", { enumerable: true, get: function () { return zlib_1.gunzipSync; } });
|
|
6
6
|
//# sourceMappingURL=unzip.js.map
|
package/dist/unzip.js.map
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA
|
|
1
|
+
{"version":3,"file":"unzip.js","sourceRoot":"","sources":["../src/unzip.ts"],"names":[],"mappings":";;;AAAA,6BAA0C;AAAjC,6FAAA,UAAU,OAAS"}
|
package/esm/craiIndex.d.ts
CHANGED
|
@@ -1,11 +1,11 @@
|
|
|
1
1
|
import { CramFileSource } from './cramFile/file';
|
|
2
|
-
export
|
|
2
|
+
export interface Slice {
|
|
3
3
|
start: number;
|
|
4
4
|
span: number;
|
|
5
5
|
containerStart: number;
|
|
6
6
|
sliceStart: number;
|
|
7
7
|
sliceBytes: number;
|
|
8
|
-
}
|
|
8
|
+
}
|
|
9
9
|
type ParsedIndex = Record<string, Slice[]>;
|
|
10
10
|
export default class CraiIndex {
|
|
11
11
|
private _parseCache;
|
package/esm/craiIndex.js
CHANGED
|
@@ -5,9 +5,6 @@ import { open } from './io';
|
|
|
5
5
|
import { CramMalformedError } from './errors';
|
|
6
6
|
const BAI_MAGIC = 21578050; // BAI\1
|
|
7
7
|
function addRecordToIndex(index, record) {
|
|
8
|
-
if (record.some(el => el === undefined)) {
|
|
9
|
-
throw new CramMalformedError('invalid .crai index file');
|
|
10
|
-
}
|
|
11
8
|
const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record;
|
|
12
9
|
if (!index[seqId]) {
|
|
13
10
|
index[seqId] = [];
|
|
@@ -32,7 +29,7 @@ export default class CraiIndex {
|
|
|
32
29
|
this.filehandle = open(args.url, args.path, args.filehandle);
|
|
33
30
|
this._parseCache = new AbortablePromiseCache({
|
|
34
31
|
cache: new QuickLRU({ maxSize: 1 }),
|
|
35
|
-
fill: (
|
|
32
|
+
fill: (_data, _signal) => this.parseIndex(),
|
|
36
33
|
});
|
|
37
34
|
}
|
|
38
35
|
parseIndex() {
|
|
@@ -56,8 +53,7 @@ export default class CraiIndex {
|
|
|
56
53
|
// because some .crai files can be pretty large.
|
|
57
54
|
let currentRecord = [];
|
|
58
55
|
let currentString = '';
|
|
59
|
-
for (
|
|
60
|
-
const charCode = uncompressedBuffer[i];
|
|
56
|
+
for (const charCode of uncompressedBuffer) {
|
|
61
57
|
if ((charCode >= 48 && charCode <= 57) /* 0-9 */ ||
|
|
62
58
|
(!currentString && charCode === 45) /* leading - */) {
|
|
63
59
|
currentString += String.fromCharCode(charCode);
|
|
@@ -131,9 +127,9 @@ export default class CraiIndex {
|
|
|
131
127
|
return 0; // entry overlaps query
|
|
132
128
|
};
|
|
133
129
|
const bins = [];
|
|
134
|
-
for (
|
|
135
|
-
if (compare(
|
|
136
|
-
bins.push(
|
|
130
|
+
for (const entry of seqEntries) {
|
|
131
|
+
if (compare(entry) === 0) {
|
|
132
|
+
bins.push(entry);
|
|
137
133
|
}
|
|
138
134
|
}
|
|
139
135
|
return bins;
|
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,yBAAyB,CAAA;AAC3D,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,
|
|
1
|
+
{"version":3,"file":"craiIndex.js","sourceRoot":"","sources":["../src/craiIndex.ts"],"names":[],"mappings":"AAAA,OAAO,qBAAqB,MAAM,yBAAyB,CAAA;AAC3D,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"}
|
|
@@ -1,24 +1,24 @@
|
|
|
1
1
|
import CramSlice from '../slice';
|
|
2
2
|
import { CramFileBlock } from '../file';
|
|
3
3
|
import { DataType } from './dataSeriesTypes';
|
|
4
|
-
export
|
|
4
|
+
export interface DataTypeMapping {
|
|
5
5
|
byte: number;
|
|
6
6
|
int: number;
|
|
7
7
|
long: number;
|
|
8
8
|
byteArray: Uint8Array;
|
|
9
|
-
}
|
|
10
|
-
export
|
|
9
|
+
}
|
|
10
|
+
export interface Cursor {
|
|
11
11
|
bitPosition: 0 | 1 | 2 | 3 | 4 | 5 | 6 | 7;
|
|
12
12
|
bytePosition: number;
|
|
13
|
-
}
|
|
14
|
-
export
|
|
13
|
+
}
|
|
14
|
+
export interface Cursors {
|
|
15
15
|
lastAlignmentStart: number;
|
|
16
16
|
coreBlock: Cursor;
|
|
17
17
|
externalBlocks: {
|
|
18
18
|
map: Map<any, any>;
|
|
19
19
|
getCursor: (contentId: number) => Cursor;
|
|
20
20
|
};
|
|
21
|
-
}
|
|
21
|
+
}
|
|
22
22
|
export default abstract class CramCodec<TResult extends DataType = DataType, TParameters = unknown> {
|
|
23
23
|
parameters: TParameters;
|
|
24
24
|
dataType: DataType;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AAKnC,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,SAGtC;IACC,YAAY,UAAsC,EAAE,QAAe;QACjE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;
|
|
1
|
+
{"version":3,"file":"beta.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/beta.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AAKnC,MAAM,CAAC,OAAO,OAAO,SAAU,SAAQ,SAGtC;IACC,YAAY,UAAsC,EAAE,QAAe;QACjE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,6CAA6C,CAC9D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,QAAQ,GAAG,OAAO,CACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,IAAI,CAAC,UAAU,CAAC,MAAM,CACvB,CAAA;QACD,OAAO,QAAQ,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IAC1C,CAAC;CACF"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAErC,OAAO,SAAsB,MAAM,SAAS,CAAA;AAW5C,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/C;IAGC,YACE,UAAiD,EACjD,QAAqB,EACrB,gBAAkC;QAElC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;QACxC,IAAI,QAAQ,KAAK,WAAW,EAAE;
|
|
1
|
+
{"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAErC,OAAO,SAAsB,MAAM,SAAS,CAAA;AAW5C,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/C;IAGC,YACE,UAAiD,EACjD,QAAqB,EACrB,gBAAkC;QAElC,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,CAAC,gBAAgB,GAAG,gBAAgB,CAAA;QACxC,IAAI,QAAQ,KAAK,WAAW,EAAE,CAAC;YAC7B,MAAM,IAAI,SAAS,CACjB,8CAA8C,QAAQ,EAAE,CACzD,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,WAAW,GAAG,IAAI,CAAC,eAAe,EAAE,CAAA;QAC1C,MAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CACpC,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QAED,MAAM,SAAS,GAAG,IAAI,CAAC,aAAa,EAAE,CAAA;QACtC,MAAM,IAAI,GAAG,IAAI,UAAU,CAAC,WAAW,CAAC,CAAA;QACxC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,WAAW,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,CAAC,CAAC,GAAG,SAAS,CAAC,MAAM,CACxB,KAAK,EACL,aAAa,EACb,iBAAiB,EACjB,OAAO,CACR,CAAA;QACH,CAAC;QAED,OAAO,IAAI,CAAA;IACb,CAAC;IAED,UAAU;IACV,eAAe;QACb,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,eAAe,CAAA;QACtD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,KAAK,CAAC,CAAA;IACrD,CAAC;IAED,UAAU;IACV,aAAa;QACX,MAAM,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,cAAc,CAAA;QACrD,OAAO,IAAI,CAAC,gBAAgB,CAAC,cAAc,EAAE,MAAM,CAAC,CAAA;IACtD,CAAC;CACF;AAED,+BAA+B;KAC5B,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,WAAW,CAAC,kBAAkB,EAAE,MAAM,CAAC,CAAC,CAAA"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AAEjD,OAAO,SAA8B,MAAM,SAAS,CAAA;AAIpD,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/C;IACC,YACE,UAAmD,EACnD,QAAqB;QAErB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,QAAQ,KAAK,WAAW,EAAE;
|
|
1
|
+
{"version":3,"file":"byteArrayStop.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayStop.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AAEjD,OAAO,SAA8B,MAAM,SAAS,CAAA;AAIpD,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAElD,MAAM,CAAC,OAAO,OAAO,kBAAmB,SAAQ,SAG/C;IACC,YACE,UAAmD,EACnD,QAAqB;QAErB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,QAAQ,KAAK,WAAW,EAAE,CAAC;YAC7B,MAAM,IAAI,SAAS,CACjB,kDAAkD,QAAQ,EAAE,CAC7D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,kBAAkB,CAC1B,kCAAkC,cAAc,EAAE,CACnD,CAAA;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,gBAAgB,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IACpD,CAAC;IAED,gBAAgB,CAAC,YAA2B,EAAE,MAAc;QAC1D,MAAM,UAAU,GAAG,YAAY,CAAC,OAAO,CAAA;QACvC,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,6BAA6B;QAC7B,MAAM,aAAa,GAAG,MAAM,CAAC,YAAY,CAAA;QACzC,IAAI,YAAY,GAAG,MAAM,CAAC,YAAY,CAAA;QACtC,OACE,UAAU,CAAC,YAAY,CAAC,KAAK,QAAQ;YACrC,YAAY,GAAG,UAAU,CAAC,MAAM,EAChC,CAAC;YACD,IAAI,YAAY,KAAK,UAAU,CAAC,MAAM,EAAE,CAAC;gBACvC,MAAM,IAAI,sBAAsB,CAC9B,qDAAqD,CACtD,CAAA;YACH,CAAC;YACD,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACjC,CAAC;QACD,MAAM,CAAC,YAAY,GAAG,YAAY,GAAG,CAAC,CAAA;QACtC,OAAO,UAAU,CAAC,QAAQ,CAAC,aAAa,EAAE,YAAY,CAAC,CAAA;IACzD,CAAC;CACF"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACzE,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAGnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;
|
|
1
|
+
{"version":3,"file":"external.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/external.ts"],"names":[],"mappings":"AAAA,sDAAsD;AACtD,OAAO,EAAE,kBAAkB,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACzE,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,SAAS,EAAE,MAAM,SAAS,CAAA;AAGnC,OAAO,EAAE,sBAAsB,EAAE,MAAM,WAAW,CAAA;AAGlD,MAAM,CAAC,OAAO,OAAO,aAAc,SAAQ,SAG1C;IAMC,YACE,UAA8C,EAC9C,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,UAAU,CAAA;QACpC,CAAC;aAAM,IAAI,IAAI,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpC,IAAI,CAAC,WAAW,GAAG,IAAI,CAAC,WAAW,CAAA;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,iDAAiD,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,MAAM,EAAE,cAAc,EAAE,GAAG,IAAI,CAAC,UAAU,CAAA;QAC1C,MAAM,YAAY,GAAG,iBAAiB,CAAC,cAAc,CAAC,CAAA;QACtD,IAAI,CAAC,YAAY,EAAE,CAAC;YAClB,MAAM,IAAI,kBAAkB,CAC1B,kCAAkC,cAAc,EAAE,CACnD,CAAA;QACH,CAAC;QACD,MAAM,MAAM,GAAG,OAAO,CAAC,cAAc,CAAC,SAAS,CAAC,cAAc,CAAC,CAAA;QAC/D,OAAO,IAAI,CAAC,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,CAAA;IAC/C,CAAC;IAED,UAAU,CAAC,YAA2B,EAAE,MAAc;QACpD,MAAM,CAAC,MAAM,EAAE,SAAS,CAAC,GAAG,SAAS,CACnC,YAAY,CAAC,OAAO,EACpB,MAAM,CAAC,YAAY,CACpB,CAAA;QACD,MAAM,CAAC,YAAY,GAAG,MAAM,CAAC,YAAY,GAAG,SAAS,CAAA;QACrD,OAAO,MAAM,CAAA;IACf,CAAC;IAED,WAAW,CAAC,YAA2B,EAAE,MAAc;QACrD,IAAI,MAAM,CAAC,YAAY,IAAI,YAAY,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;YACvD,MAAM,IAAI,sBAAsB,CAC9B,mEAAmE,CACpE,CAAA;QACH,CAAC;QACD,OAAO,YAAY,CAAC,OAAO,CAAC,MAAM,CAAC,YAAY,EAAE,CAAC,CAAA;IACpD,CAAC;CACF"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AAKnC,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAGvC;IACC,YAAY,UAAuC,EAAE,QAAe;QAClE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE;
|
|
1
|
+
{"version":3,"file":"gamma.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/gamma.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,sBAAsB,EAAE,MAAM,cAAc,CAAA;AACrD,OAAO,SAAsB,MAAM,SAAS,CAAA;AAC5C,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AAKnC,MAAM,CAAC,OAAO,OAAO,UAAW,SAAQ,SAGvC;IACC,YAAY,UAAuC,EAAE,QAAe;QAClE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,sBAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,8CAA8C,CAC/D,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,MAAM,GAAG,CAAC,CAAA;QAEd,OAAO,OAAO,CAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YAClE,MAAM,GAAG,MAAM,GAAG,CAAC,CAAA;QACrB,CAAC;QAED,MAAM,QAAQ,GAAG,OAAO,CACtB,aAAa,CAAC,OAAO,EACrB,OAAO,CAAC,SAAS,EACjB,MAAM,GAAG,CAAC,CACX,CAAA;QAED,MAAM,KAAK,GAAG,QAAQ,GAAG,CAAC,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAA;QAC5C,OAAO,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACvC,CAAC;CACF"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":"AAAA,MAAM,OAAO,sBAAuB,SAAQ,KAAK;CAAG;AAEpD,MAAM,UAAU,OAAO,CACrB,IAAY,EACZ,MAAqD,EACrD,OAAe;IAEf,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IACE,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC;QAC5D,IAAI,CAAC,MAAM,EACX;
|
|
1
|
+
{"version":3,"file":"getBits.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/getBits.ts"],"names":[],"mappings":"AAAA,MAAM,OAAO,sBAAuB,SAAQ,KAAK;CAAG;AAEpD,MAAM,UAAU,OAAO,CACrB,IAAY,EACZ,MAAqD,EACrD,OAAe;IAEf,IAAI,GAAG,GAAG,CAAC,CAAA;IACX,IACE,MAAM,CAAC,YAAY,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,WAAW,GAAG,OAAO,CAAC,GAAG,CAAC;QAC5D,IAAI,CAAC,MAAM,EACX,CAAC;QACD,MAAM,IAAI,sBAAsB,CAC9B,6DAA6D,CAC9D,CAAA;IACH,CAAC;IACD,KAAK,IAAI,IAAI,GAAG,OAAO,EAAE,IAAI,EAAE,IAAI,EAAE,EAAE,CAAC;QACtC,yDAAyD;QACzD,GAAG,KAAK,CAAC,CAAA;QACT,GAAG,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,YAAY,CAAC,IAAI,MAAM,CAAC,WAAW,CAAC,GAAG,CAAC,CAAA;QAC5D,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;QACvB,IAAI,MAAM,CAAC,WAAW,GAAG,CAAC,EAAE,CAAC;YAC3B,MAAM,CAAC,YAAY,IAAI,CAAC,CAAA;QAC1B,CAAC;QACD,MAAM,CAAC,WAAW,IAAI,CAAC,CAAA;IACzB,CAAC;IACD,OAAO,GAAG,CAAA;AACZ,CAAC"}
|
|
@@ -5,7 +5,6 @@ import { CramFileBlock } from '../file';
|
|
|
5
5
|
export default class HuffmanIntCodec extends CramCodec<'byte' | 'int', HuffmanEncoding['parameters']> {
|
|
6
6
|
private codes;
|
|
7
7
|
private codeBook;
|
|
8
|
-
private sortedByValue;
|
|
9
8
|
private sortedCodes;
|
|
10
9
|
private sortedValuesByBitCode;
|
|
11
10
|
private sortedBitCodes;
|
|
@@ -1,3 +1,4 @@
|
|
|
1
|
+
/* eslint-disable @typescript-eslint/unbound-method */
|
|
1
2
|
import { CramMalformedError } from '../../errors';
|
|
2
3
|
import CramCodec from './_base';
|
|
3
4
|
import { getBits } from './getBits';
|
|
@@ -11,7 +12,6 @@ export default class HuffmanIntCodec extends CramCodec {
|
|
|
11
12
|
super(parameters, dataType);
|
|
12
13
|
this.codes = {};
|
|
13
14
|
this.codeBook = {};
|
|
14
|
-
this.sortedByValue = [];
|
|
15
15
|
this.sortedCodes = [];
|
|
16
16
|
this.sortedValuesByBitCode = [];
|
|
17
17
|
this.sortedBitCodes = [];
|
|
@@ -73,8 +73,6 @@ export default class HuffmanIntCodec extends CramCodec {
|
|
|
73
73
|
}
|
|
74
74
|
buildCaches() {
|
|
75
75
|
this.sortedCodes = Object.values(this.codes).sort((a, b) => a.bitLength - b.bitLength || a.bitCode - b.bitCode);
|
|
76
|
-
// this.sortedValues = this.parameters.values.sort((a,b) => a-b)
|
|
77
|
-
this.sortedByValue = Object.values(this.codes).sort((a, b) => a.value - b.value);
|
|
78
76
|
this.sortedValuesByBitCode = this.sortedCodes.map(c => c.value);
|
|
79
77
|
this.sortedBitCodes = this.sortedCodes.map(c => c.bitCode);
|
|
80
78
|
this.sortedBitLengthsByBitCode = this.sortedCodes.map(c => c.bitLength);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"huffman.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/huffman.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,kBAAkB,EAAE,MAAM,cAAc,CAAA;AACjD,OAAO,SAA8B,MAAM,SAAS,CAAA;AACpD,OAAO,EAAE,OAAO,EAAE,MAAM,WAAW,CAAA;AAMnC,SAAS,eAAe,CAAC,EAAU;IACjC,IAAI,CAAC,GAAG,CAAC,EAAE,GAAG,CAAC,EAAE,IAAI,CAAC,CAAC,CAAC,GAAG,UAAU,CAAA;IACrC,CAAC,GAAG,CAAC,CAAC,GAAG,UAAU,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,UAAU,CAAC,CAAA;IAC9C,OAAO,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,GAAG,UAAU,CAAC,GAAG,UAAU,CAAC,IAAI,EAAE,CAAA;AAC3D,CAAC;
|
|
1
|
+
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@@ -1 +1 @@
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1
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-
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