npm - @gmod/cram - Versions diffs - 2.0.4 → 3.0.0 - Mend

@gmod/cram 2.0.4 → 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.

Files changed (64) hide show

package/CHANGELOG.md +10 -0
package/dist/cram-bundle.js +1 -1
package/dist/cramFile/codecs/byteArrayLength.js +1 -1
package/dist/cramFile/codecs/byteArrayLength.js.map +1 -1
package/dist/cramFile/codecs/external.js +1 -1
package/dist/cramFile/codecs/external.js.map +1 -1
package/dist/cramFile/codecs/huffman.js +2 -1
package/dist/cramFile/codecs/huffman.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 +56 -3
package/dist/cramFile/container/index.js +15 -9
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/file.d.ts +24 -59
package/dist/cramFile/file.js +21 -26
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/record.d.ts +1 -1
package/dist/cramFile/sectionParsers.d.ts +195 -48
package/dist/cramFile/sectionParsers.js +621 -303
package/dist/cramFile/sectionParsers.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 -4
package/dist/cramFile/util.js +88 -6
package/dist/cramFile/util.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/external.js +1 -1
package/esm/cramFile/codecs/external.js.map +1 -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 +56 -3
package/esm/cramFile/container/index.js +15 -9
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/file.d.ts +24 -59
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 -48
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 -4
package/esm/cramFile/util.js +87 -6
package/esm/cramFile/util.js.map +1 -1
package/package.json +7 -8
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/typings/binary-parser.d.ts +0 -44

package/dist/cramFile/sectionParsers.js.map CHANGED Viewed

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package/dist/cramFile/slice/index.d.ts CHANGED Viewed

@@ -10,7 +10,29 @@ export default class CramSlice {
     containerPosition: number;
     private file;
     constructor(container: CramContainer, containerPosition: number, _unused: number);
-    getHeader(): Promise<SliceHeader>;
+    getHeader(): Promise<{
+        parsedContent: {
+            recordCounter: number;
+            md5: [number, number, number, number, number, number, number, number, number, number, number, number, number, number, number, number] | undefined;
+            contentIds: number[];
+            numContentIds: number;
+            numBlocks: number;
+            numRecords: number;
+        } & {
+            _endPosition: number;
+            _size: number;
+        };
+        compressionMethod: import("../sectionParsers").CompressionMethod;
+        contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
+        contentId: number;
+        compressedSize: number;
+        uncompressedSize: number;
+        _endPosition: number;
+        contentPosition: number;
+        _size: number;
+        content: Buffer;
+        crc32?: number;
+    }>;
     getBlocks(): Promise<CramFileBlock[]>;
     getCoreDataBlock(): Promise<CramFileBlock>;
     _getBlocksContentIdIndex(): Promise<Record<number, CramFileBlock>>;

package/dist/cramFile/slice/index.js CHANGED Viewed

@@ -147,8 +147,12 @@ class CramSlice {
     getHeader() {
         return __awaiter(this, void 0, void 0, function* () {
             // fetch and parse the slice header
-            const sectionParsers = yield this.file.getSectionParsers();
+            const { majorVersion } = yield this.file.getDefinition();
+            const sectionParsers = (0, sectionParsers_1.getSectionParsers)(majorVersion);
             const containerHeader = yield this.container.getHeader();
+            if (!containerHeader) {
+                throw new Error('no container header detected');
+            }
             const header = yield this.file.readBlock(containerHeader._endPosition + this.containerPosition);
             if (header === undefined) {
                 throw new Error('block header undefined');
@@ -173,7 +177,7 @@ class CramSlice {
             // read all the blocks into memory and store them
             let blockPosition = header._endPosition;
             const blocks = new Array(header.parsedContent.numBlocks);
-            for (let i = 0; i < blocks.length; i += 1) {
+            for (let i = 0; i < blocks.length; i++) {
                 const block = yield this.file.readBlock(blockPosition);
                 if (block === undefined) {
                     throw new Error('block undefined');
@@ -266,6 +270,7 @@ class CramSlice {
     }
     _fetchRecords() {
         return __awaiter(this, void 0, void 0, function* () {
+            var _a, _b;
             const { majorVersion } = yield this.file.getDefinition();
             const compressionScheme = yield this.container.getCompressionScheme();
             if (compressionScheme === undefined) {
@@ -281,14 +286,12 @@ class CramSlice {
                 this.file.options.checkSequenceMD5 &&
                 (0, sectionParsers_1.isMappedSliceHeader)(sliceHeader.parsedContent) &&
                 sliceHeader.parsedContent.refSeqId >= 0 &&
-                sliceHeader.parsedContent.md5.join('') !== '0000000000000000') {
+                ((_a = sliceHeader.parsedContent.md5) === null || _a === void 0 ? void 0 : _a.join('')) !== '0000000000000000') {
                 const refRegion = yield this.getReferenceRegion();
                 if (refRegion) {
                     const { seq, start, end } = refRegion;
                     const seqMd5 = (0, util_1.sequenceMD5)(seq);
-                    const storedMd5 = sliceHeader.parsedContent.md5
-                        .map(byte => (byte < 16 ? '0' : '') + byte.toString(16))
-                        .join('');
+                    const storedMd5 = (_b = sliceHeader.parsedContent.md5) === null || _b === void 0 ? void 0 : _b.map(byte => (byte < 16 ? '0' : '') + byte.toString(16)).join('');
                     if (seqMd5 !== storedMd5) {
                         throw new errors_1.CramMalformedError(`MD5 checksum reference mismatch for ref ${sliceHeader.parsedContent.refSeqId} pos ${start}..${end}. recorded MD5: ${storedMd5}, calculated MD5: ${seqMd5}`);
                     }

package/dist/cramFile/slice/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/cramFile/util.d.ts CHANGED Viewed

@@ -1,10 +1,12 @@
-import { Parser } from '@gmod/binary-parser';
 export declare function itf8Size(v: number): 1 | 2 | 3 | 4 | 5;
-export declare function parseItf8(buffer: Uint8Array, initialOffset: number): [number, number];
-export type ParsedItem<T> = T & {
+export declare function parseItf8(buffer: Uint8Array, initialOffset: number): readonly [number, number];
+export declare function parseLtf8(buffer: Buffer, initialOffset: number): readonly [number, number];
+export declare function parseItem<T>(buffer: Buffer, parser: (buffer: Buffer, offset: number) => {
+    offset: number;
+    value: T;
+}, startBufferPosition?: number, startFilePosition?: number): T & {
     _endPosition: number;
     _size: number;
 };
-export declare function parseItem<T>(buffer: Buffer, parser: Parser<T>, startBufferPosition?: number, startFilePosition?: number): ParsedItem<T>;
 export declare function tinyMemoize(_class: any, methodName: any): void;
 export declare function sequenceMD5(seq: string): string;

package/dist/cramFile/util.js CHANGED Viewed

@@ -5,10 +5,12 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.itf8Size = itf8Size;
 exports.parseItf8 = parseItf8;
+exports.parseLtf8 = parseLtf8;
 exports.parseItem = parseItem;
 exports.tinyMemoize = tinyMemoize;
 exports.sequenceMD5 = sequenceMD5;
 const md5_1 = __importDefault(require("md5"));
+const long_1 = __importDefault(require("long"));
 const getBits_1 = require("./codecs/getBits");
 function itf8Size(v) {
     if (!(v & ~0x7f)) {
@@ -68,14 +70,94 @@ function parseItf8(buffer, initialOffset) {
     }
     return [result, offset - initialOffset];
 }
+function parseLtf8(buffer, initialOffset) {
+    let offset = initialOffset;
+    const countFlags = buffer[offset];
+    let n;
+    if (countFlags < 0x80) {
+        n = countFlags;
+        offset += 1;
+    }
+    else if (countFlags < 0xc0) {
+        n = ((buffer[offset] << 8) | buffer[offset + 1]) & 0x3fff;
+        offset += 2;
+    }
+    else if (countFlags < 0xe0) {
+        n =
+            ((buffer[offset] << 16) |
+                (buffer[offset + 1] << 8) |
+                buffer[offset + 2]) &
+                0x1fffff;
+        n = ((countFlags & 63) << 16) | buffer.readUInt16LE(offset + 1);
+        offset += 3;
+    }
+    else if (countFlags < 0xf0) {
+        n =
+            ((buffer[offset] << 24) |
+                (buffer[offset + 1] << 16) |
+                (buffer[offset + 2] << 8) |
+                buffer[offset + 3]) &
+                0x0fffffff;
+        offset += 4;
+    }
+    else if (countFlags < 0xf8) {
+        n =
+            ((buffer[offset] & 15) * Math.pow(2, 32) + (buffer[offset + 1] << 24)) |
+                ((buffer[offset + 2] << 16) |
+                    (buffer[offset + 3] << 8) |
+                    buffer[offset + 4]);
+        // TODO *val_p = uv < 0x80000000UL ? uv : -((int32_t) (0xffffffffUL - uv)) - 1;
+        offset += 5;
+    }
+    else if (countFlags < 0xfc) {
+        n =
+            ((((buffer[offset] & 7) << 8) | buffer[offset + 1]) * Math.pow(2, 32) +
+                (buffer[offset + 2] << 24)) |
+                ((buffer[offset + 3] << 16) |
+                    (buffer[offset + 4] << 8) |
+                    buffer[offset + 5]);
+        offset += 6;
+    }
+    else if (countFlags < 0xfe) {
+        n =
+            ((((buffer[offset] & 3) << 16) |
+                (buffer[offset + 1] << 8) |
+                buffer[offset + 2]) *
+                Math.pow(2, 32) +
+                (buffer[offset + 3] << 24)) |
+                ((buffer[offset + 4] << 16) |
+                    (buffer[offset + 5] << 8) |
+                    buffer[offset + 6]);
+        offset += 7;
+    }
+    else if (countFlags < 0xff) {
+        n = long_1.default.fromBytesBE(buffer.slice(offset + 1, offset + 8));
+        if (n.greaterThan(Number.MAX_SAFE_INTEGER) ||
+            n.lessThan(Number.MIN_SAFE_INTEGER)) {
+            throw new Error('integer overflow');
+        }
+        n = n.toNumber();
+        offset += 8;
+    }
+    else {
+        n = long_1.default.fromBytesBE(buffer.slice(offset + 1, offset + 9));
+        if (n.greaterThan(Number.MAX_SAFE_INTEGER) ||
+            n.lessThan(Number.MIN_SAFE_INTEGER)) {
+            throw new Error('integer overflow');
+        }
+        n = n.toNumber();
+        offset += 9;
+    }
+    return [n, offset - initialOffset];
+}
 function parseItem(buffer, parser, startBufferPosition = 0, startFilePosition = 0) {
-    const { offset, result } = parser.parse(buffer);
-    return Object.assign(Object.assign({}, result), { _endPosition: offset + startFilePosition, _size: offset - startBufferPosition });
+    const { offset, value } = parser(buffer, startBufferPosition);
+    return Object.assign(Object.assign({}, value), { _endPosition: offset + startFilePosition, _size: offset - startBufferPosition });
 }
-// this would be nice as a decorator, but i'm a little worried about
-// babel support for it going away or changing.
-// memoizes a method in the stupidest possible way, with no regard for the
-// arguments.  actually, this only works on methods that take no arguments
+// this would be nice as a decorator, but i'm a little worried about babel
+// support for it going away or changing. memoizes a method in the stupidest
+// possible way, with no regard for the arguments.  actually, this only works
+// on methods that take no arguments
 function tinyMemoize(_class, methodName) {
     const method = _class.prototype[methodName];
     const memoAttrName = `_memo_${methodName}`;

package/dist/cramFile/util.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/cramFile/codecs/byteArrayLength.js CHANGED Viewed

@@ -1,5 +1,5 @@
-import { tinyMemoize } from '../util';
 import CramCodec from './_base';
+import { tinyMemoize } from '../util';
 export default class ByteArrayStopCodec extends CramCodec {
     constructor(parameters, dataType, instantiateCodec) {
         super(parameters, dataType);

package/esm/cramFile/codecs/byteArrayLength.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"byteArrayLength.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/byteArrayLength.ts"],"names":[],"mappings":"AAAA,OAAO,SAAsB,MAAM,SAAS,CAAA;AAK5C,OAAO,EAAE,WAAW,EAAE,MAAM,SAAS,CAAA;AAOrC,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"}

package/esm/cramFile/codecs/external.js CHANGED Viewed

@@ -20,7 +20,7 @@ export default class ExternalCodec extends CramCodec {
         const { blockContentId } = this.parameters;
         const contentBlock = blocksByContentId[blockContentId];
         if (!contentBlock) {
-            throw new CramMalformedError(`no block found with content ID ${blockContentId}`);
+            throw new CramMalformedError(`no block found with content ID ${blockContentId}}`);
         }
         const cursor = cursors.externalBlocks.getCursor(blockContentId);
         return this._decodeData(contentBlock, cursor);

package/esm/cramFile/codecs/external.js.map CHANGED Viewed

	@@ -1 +1 @@
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	+ {"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,GAAG,CACpD,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"}

package/esm/cramFile/codecs/huffman.js CHANGED Viewed

@@ -23,7 +23,8 @@ export default class HuffmanIntCodec extends CramCodec {
         this.buildCodeBook();
         this.buildCodes();
         this.buildCaches();
-        // if this is a degenerate zero-length huffman code, special-case the decoding
+        // if this is a degenerate zero-length huffman code, special-case the
+        // decoding
         if (this.sortedCodes[0].bitLength === 0) {
             this._decode = this._decodeZeroLengthCode;
         }

package/esm/cramFile/codecs/huffman.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"huffman.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/huffman.ts"],"names":[],"mappings":"AAAA,sDAAsD;AACtD,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;AAQD,MAAM,CAAC,OAAO,OAAO,eAAgB,SAAQ,SAG5C;IASC,YACE,UAAyC,EACzC,QAAwB;QAExB,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAZrB,UAAK,GAAyB,EAAE,CAAA;QAChC,aAAQ,GAA6B,EAAE,CAAA;QACvC,gBAAW,GAAW,EAAE,CAAA;QACxB,0BAAqB,GAAa,EAAE,CAAA;QACpC,mBAAc,GAAa,EAAE,CAAA;QAC7B,8BAAyB,GAAa,EAAE,CAAA;QACxC,mBAAc,GAAa,EAAE,CAAA;QAOnC,IAAI,CAAC,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC;YAC7C,MAAM,IAAI,SAAS,CACjB,GAAG,IAAI,CAAC,QAAQ,oDAAoD,CACrE,CAAA;QACH,CAAC;QAED,IAAI,CAAC,aAAa,EAAE,CAAA;QACpB,IAAI,CAAC,UAAU,EAAE,CAAA;QACjB,IAAI,CAAC,WAAW,EAAE,CAAA;QAElB,~~8EAA8E~~;~~QAC9E~~,IAAI,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,KAAK,CAAC,EAAE,CAAC;YACxC,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,qBAAqB,CAAA;QAC3C,CAAC;IACH,CAAC;IAED,aAAa;QACX,8DAA8D;QAC9D,IAAI,KAAK,GAAG,IAAI,KAAK,CACnB,IAAI,CAAC,UAAU,CAAC,QAAQ,CACzB,CAAA;QACD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACrD,KAAK,CAAC,CAAC,CAAC,GAAG;gBACT,MAAM,EAAE,IAAI,CAAC,UAAU,CAAC,OAAO,CAAC,CAAC,CAAC;gBAClC,SAAS,EAAE,IAAI,CAAC,UAAU,CAAC,UAAU,CAAC,CAAC,CAAC;aACzC,CAAA;QACH,CAAC;QACD,gDAAgD;QAChD,KAAK,GAAG,KAAK,CAAC,IAAI,CAChB,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,MAAM,CAC3D,CAAA;QAED,IAAI,CAAC,QAAQ,GAAG,EAAE,CAAA;QAClB,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE;YACnB,IAAI,CAAC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;gBACnC,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,CAAA;YACpC,CAAC;YACD,IAAI,CAAC,QAAQ,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACjD,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,UAAU;QACR,IAAI,CAAC,KAAK,GAAG,EAAE,CAAA,CAAC,8CAA8C;QAC9D,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,IAAI,SAAS,GAAG,CAAC,CAAC,CAAA;QAClB,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,EAAE,OAAO,CAAC,EAAE,EAAE;YAC7D,MAAM,YAAY,GAAG,QAAQ,CAAC,SAAS,EAAE,EAAE,CAAC,CAAA;YAC5C,OAAO,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE;gBACvB,MAAM,IAAI,GAAG;oBACX,SAAS,EAAE,YAAY;oBACvB,KAAK,EAAE,MAAM;oBACb,OAAO,EAAE,CAAC;iBACX,CAAA;gBACD,SAAS,GAAG,SAAS,GAAG,CAAC,CAAA;gBACzB,MAAM,KAAK,GAAG,YAAY,GAAG,UAAU,CAAA,CAAC,cAAc;gBACtD,SAAS,GAAG,SAAS,IAAI,KAAK,CAAA,CAAC,eAAe;gBAC9C,IAAI,CAAC,OAAO,GAAG,SAAS,CAAA,CAAC,2BAA2B;gBACpD,UAAU,GAAG,UAAU,GAAG,KAAK,CAAA,CAAC,6BAA6B;gBAE7D,IAAI,eAAe,CAAC,SAAS,CAAC,GAAG,YAAY,EAAE,CAAC;oBAC9C,MAAM,IAAI,kBAAkB,CAAC,qBAAqB,CAAC,CAAA;gBACrD,CAAC;gBAED,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,GAAG,IAAI,CAAA;YAC3B,CAAC,CAAC,CAAA;QACJ,CAAC,CAAC,CAAA;IACJ,CAAC;IAED,WAAW;QACT,IAAI,CAAC,WAAW,GAAG,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,CAC/C,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,SAAS,GAAG,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,OAAO,GAAG,CAAC,CAAC,OAAO,CAC7D,CAAA;QAED,IAAI,CAAC,qBAAqB,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,KAAK,CAAC,CAAA;QAC/D,IAAI,CAAC,cAAc,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAA;QAC1D,IAAI,CAAC,yBAAyB,GAAG,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAA;QACvE,MAAM,UAAU,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,IAAI,CAAC,cAAc,CAAC,CAAA;QAEnD,IAAI,CAAC,cAAc,GAAG,IAAI,KAAK,CAAC,UAAU,GAAG,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAA;QACxD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,cAAc,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACvD,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,GAAG,CAAC,CAAA;QACtD,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,OAAO,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE,aAAa,EAAE,OAAO,CAAC,SAAS,CAAC,CAAA;IAC9D,CAAC;IAED,kBAAkB;IAClB,cAAc;IACd,IAAI;IAEJ,yCAAyC;IACzC,qBAAqB;QACnB,OAAO,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,KAAK,CAAA;IAClC,CAAC;IAED,OAAO,CAAC,KAAgB,EAAE,aAA4B,EAAE,UAAkB;QACxE,MAAM,KAAK,GAAG,aAAa,CAAC,OAAO,CAAA;QAEnC,IAAI,OAAO,GAAG,CAAC,CAAA;QACf,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACpD,MAAM,MAAM,GAAG,IAAI,CAAC,WAAW,CAAC,CAAC,CAAC,CAAC,SAAS,CAAA;YAC5C,IAAI,KAAK,MAAM,GAAG,OAAO,CAAA;YACzB,IAAI,IAAI,OAAO,CAAC,KAAK,EAAE,UAAU,EAAE,MAAM,GAAG,OAAO,CAAC,CAAA;YACpD,OAAO,GAAG,MAAM,CAAA;YAChB,CAAC;gBACC,MAAM,KAAK,GAAG,IAAI,CAAC,cAAc,CAAC,IAAI,CAAC,CAAA;gBACvC,IAAI,KAAK,GAAG,CAAC,CAAC,IAAI,IAAI,CAAC,yBAAyB,CAAC,KAAK,CAAC,KAAK,MAAM,EAAE,CAAC;oBACnE,OAAO,IAAI,CAAC,qBAAqB,CAAC,KAAK,CAAC,CAAA;gBAC1C,CAAC;gBAED,KACE,IAAI,CAAC,GAAG,CAAC,EACT,IAAI,CAAC,WAAW,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS,KAAK,MAAM;oBAC5C,CAAC,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,EAC3B,CAAC,IAAI,CA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1	+ 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package/esm/cramFile/container/compressionScheme.d.ts CHANGED Viewed

@@ -48,9 +48,6 @@ export default class CramContainerCompressionScheme {
     tagCodecCache: Record<string, CramCodec>;
     tagEncoding: Record<string, CramEncoding>;
     dataSeriesEncoding: DataSeriesEncodingMap;
-    private preservation;
-    private _endPosition;
-    private _size;
     constructor(content: CramCompressionHeader);
     /**
      * @param {string} tagName three-character tag name

package/esm/cramFile/container/compressionScheme.js CHANGED Viewed

@@ -68,7 +68,6 @@ export default class CramContainerCompressionScheme {
         this.dataSeriesCodecCache = {};
         this.tagCodecCache = {};
         this.tagEncoding = {};
-        // Object.assign(this, content)
         // interpret some of the preservation map tags for convenient use
         this.readNamesIncluded = content.preservation.RN;
         this.APdelta = content.preservation.AP;
@@ -77,9 +76,6 @@ export default class CramContainerCompressionScheme {
         this.substitutionMatrix = parseSubstitutionMatrix(content.preservation.SM);
         this.dataSeriesEncoding = content.dataSeriesEncoding;
         this.tagEncoding = content.tagEncoding;
-        this.preservation = content.preservation;
-        this._size = content._size;
-        this._endPosition = content._endPosition;
     }
     /**
      * @param {string} tagName three-character tag name

package/esm/cramFile/container/compressionScheme.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ 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
package/esm/cramFile/container/index.d.ts CHANGED Viewed

@@ -5,9 +5,39 @@ export default class CramContainer {
     file: CramFile;
     filePosition: number;
     constructor(file: CramFile, filePosition: number);
-    getHeader(): Promise<any>;
+    getHeader(): Promise<({
+        length: number;
+        refSeqId: number;
+        refSeqStart: number;
+        alignmentSpan: number;
+        numBlocks: number;
+        numLandmarks: number;
+        numBases: number | undefined;
+        recordCounter: number;
+        numRecords: number;
+    } & {
+        _endPosition: number;
+        _size: number;
+    } & {
+        numLandmarks: number;
+        landmarks: number[];
+        crc32?: number | undefined;
+    } & {
+        _endPosition: number;
+        _size: number;
+    } & {
+        _size: number;
+        _endPosition: number;
+    }) | undefined>;
     getCompressionHeaderBlock(): Promise<{
-        parsedContent: import("../util").ParsedItem<import("../sectionParsers").CramCompressionHeader>;
+        parsedContent: {
+            dataSeriesEncoding: import("../codecs/dataSeriesTypes").DataSeriesEncodingMap;
+            preservation: import("../sectionParsers").CramPreservationMap;
+            tagEncoding: Record<string, import("../encoding").CramEncoding>;
+        } & {
+            _endPosition: number;
+            _size: number;
+        };
         compressionMethod: import("../sectionParsers").CompressionMethod;
         contentType: "FILE_HEADER" | "COMPRESSION_HEADER" | "MAPPED_SLICE_HEADER" | "UNMAPPED_SLICE_HEADER" | "EXTERNAL_DATA" | "CORE_DATA";
         contentId: number;
@@ -22,5 +52,28 @@ export default class CramContainer {
     getFirstBlock(): Promise<import("../file").CramFileBlock | undefined>;
     getCompressionScheme(): Promise<CramContainerCompressionScheme | undefined>;
     getSlice(slicePosition: number, sliceSize: number): CramSlice;
-    _readContainerHeader(position: number): Promise<any>;
+    _readContainerHeader(position: number): Promise<({
+        length: number;
+        refSeqId: number;
+        refSeqStart: number;
+        alignmentSpan: number;
+        numBlocks: number;
+        numLandmarks: number;
+        numBases: number | undefined;
+        recordCounter: number;
+        numRecords: number;
+    } & {
+        _endPosition: number;
+        _size: number;
+    } & {
+        numLandmarks: number;
+        landmarks: number[];
+        crc32?: number | undefined;
+    } & {
+        _endPosition: number;
+        _size: number;
+    } & {
+        _size: number;
+        _endPosition: number;
+    }) | undefined>;
 }