npm - @gmod/cram - Versions diffs - 3.0.0 → 3.0.2 - Mend

@gmod/cram 3.0.0 → 3.0.2

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.

Files changed (72) hide show

package/dist/cram-bundle.js +1 -1
package/dist/cramFile/codecs/byteArrayStop.js +1 -1
package/dist/cramFile/codecs/huffman.js +1 -1
package/dist/cramFile/codecs/huffman.js.map +1 -1
package/dist/cramFile/codecs/subexp.js.map +1 -1
package/dist/cramFile/container/index.d.ts +1 -0
package/dist/cramFile/container/index.js +8 -5
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/file.d.ts +1 -0
package/dist/cramFile/file.js +14 -13
package/dist/cramFile/file.js.map +1 -1
package/dist/cramFile/record.js +2 -2
package/dist/cramFile/record.js.map +1 -1
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.js +5 -4
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/dist/cramFile/slice/index.js +2 -2
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/cramFile/util.js.map +1 -1
package/dist/rans/d04.js.map +1 -1
package/dist/rans/decoding.d.ts +4 -4
package/dist/rans/decoding.js +5 -6
package/dist/rans/decoding.js.map +1 -1
package/dist/rans/index.js +4 -3
package/dist/rans/index.js.map +1 -1
package/dist/unzip-pako.d.ts +1 -0
package/dist/unzip-pako.js +2 -1
package/dist/unzip-pako.js.map +1 -1
package/esm/cramFile/codecs/byteArrayStop.js +1 -1
package/esm/cramFile/codecs/huffman.js +1 -1
package/esm/cramFile/codecs/huffman.js.map +1 -1
package/esm/cramFile/codecs/subexp.js.map +1 -1
package/esm/cramFile/container/index.d.ts +1 -0
package/esm/cramFile/container/index.js +6 -3
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/file.d.ts +1 -0
package/esm/cramFile/file.js +6 -5
package/esm/cramFile/file.js.map +1 -1
package/esm/cramFile/record.js +2 -2
package/esm/cramFile/record.js.map +1 -1
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.js +5 -4
package/esm/cramFile/slice/decodeRecord.js.map +1 -1
package/esm/cramFile/slice/index.js +2 -2
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/util.js +3 -3
package/esm/cramFile/util.js.map +1 -1
package/esm/rans/d04.js.map +1 -1
package/esm/rans/decoding.d.ts +4 -4
package/esm/rans/decoding.js +5 -6
package/esm/rans/decoding.js.map +1 -1
package/esm/rans/index.js +3 -2
package/esm/rans/index.js.map +1 -1
package/esm/unzip-pako.d.ts +1 -0
package/esm/unzip-pako.js +1 -0
package/esm/unzip-pako.js.map +1 -1
package/package.json +1 -1
package/src/cramFile/codecs/byteArrayStop.ts +1 -1
package/src/cramFile/codecs/huffman.ts +1 -1
package/src/cramFile/codecs/subexp.ts +2 -2
package/src/cramFile/container/index.ts +6 -6
package/src/cramFile/declare.d.ts +1 -0
package/src/cramFile/file.ts +10 -11
package/src/cramFile/record.ts +3 -6
package/src/cramFile/sectionParsers.ts +4 -4
package/src/cramFile/slice/decodeRecord.ts +20 -12
package/src/cramFile/slice/index.ts +2 -2
package/src/cramFile/util.ts +5 -5
package/src/rans/d04.ts +1 -1
package/src/rans/decoding.ts +5 -7
package/src/rans/index.ts +3 -2
package/src/unzip-pako.ts +1 -0

package/dist/cramFile/codecs/byteArrayStop.js CHANGED Viewed

@@ -31,7 +31,7 @@ class ByteArrayStopCodec extends _base_1.default {
         while (dataBuffer[stopPosition] !== stopByte &&
             stopPosition < dataBuffer.length) {
             if (stopPosition === dataBuffer.length) {
-                throw new getBits_1.CramBufferOverrunError(`byteArrayStop reading beyond length of data buffer?`);
+                throw new getBits_1.CramBufferOverrunError('byteArrayStop reading beyond length of data buffer?');
             }
             stopPosition = stopPosition + 1;
         }

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

@@ -58,7 +58,7 @@ class HuffmanIntCodec extends _base_1.default {
         let codeLength = 0;
         let codeValue = -1;
         Object.entries(this.codeBook).forEach(([bitLength, symbols]) => {
-            const bitLengthInt = parseInt(bitLength, 10);
+            const bitLengthInt = Number.parseInt(bitLength, 10);
             symbols.forEach(symbol => {
                 const code = {
                     bitLength: bitLengthInt,

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

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/cramFile/codecs/subexp.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,WAAY,SAAQ,eAGxC;IACC,YAAY,UAAwC,EAAE,QAAe;QACnE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,OAAO,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE,CAAC;YAC5D,cAAc,GAAG,cAAc,GAAG,CAAC,CAAA;QACrC,CAAC;QAED,IAAI,~~CAAC~~,CAAA;~~QACL~~,IAAI,~~CAAC~~,CAAA;~~QACL~~,IAAI,cAAc,KAAK,CAAC,EAAE,CAAC;YACzB,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QAC1D,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,IAAI,GAAG,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;YACjE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;QACrB,CAAC;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF;AArCD,8BAqCC"}
1	+ {"version":3,"file":"subexp.js","sourceRoot":"","sources":["../../../src/cramFile/codecs/subexp.ts"],"names":[],"mappings":";;;;;AAAA,yCAAqD;AACrD,oDAA4C;AAC5C,uCAAmC;AAKnC,MAAqB,WAAY,SAAQ,eAGxC;IACC,YAAY,UAAwC,EAAE,QAAe;QACnE,KAAK,CAAC,UAAU,EAAE,QAAQ,CAAC,CAAA;QAC3B,IAAI,IAAI,CAAC,QAAQ,KAAK,KAAK,EAAE,CAAC;YAC5B,MAAM,IAAI,+BAAsB,CAC9B,GAAG,IAAI,CAAC,QAAQ,+CAA+C,CAChE,CAAA;QACH,CAAC;IACH,CAAC;IAED,MAAM,CACJ,KAAgB,EAChB,aAA4B,EAC5B,iBAAgD,EAChD,OAAgB;QAEhB,IAAI,cAAc,GAAG,CAAC,CAAA;QACtB,OAAO,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,EAAE,CAAC;YAC5D,cAAc,GAAG,cAAc,GAAG,CAAC,CAAA;QACrC,CAAC;QAED,IAAI,CAAS,CAAA;QACb,IAAI,CAAS,CAAA;QACb,IAAI,cAAc,KAAK,CAAC,EAAE,CAAC;YACzB,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAA;YACrB,CAAC,GAAG,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;QAC1D,CAAC;aAAM,CAAC;YACN,CAAC,GAAG,cAAc,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,GAAG,CAAC,CAAA;YAC1C,MAAM,IAAI,GAAG,IAAA,iBAAO,EAAC,aAAa,CAAC,OAAO,EAAE,OAAO,CAAC,SAAS,EAAE,CAAC,CAAC,CAAA;YACjE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,IAAI,CAAA;QACrB,CAAC;QAED,OAAO,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,MAAM,CAAA;IACnC,CAAC;CACF;AArCD,8BAqCC"}

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

@@ -1,3 +1,4 @@
+import { Buffer } from 'buffer';
 import CramSlice from '../slice';
 import CramContainerCompressionScheme from './compressionScheme';
 import CramFile from '../file';

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

@@ -12,7 +12,9 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
+const buffer_1 = require("buffer");
 const errors_1 = require("../../errors");
+// locals
 const util_1 = require("../util");
 const slice_1 = __importDefault(require("../slice"));
 const compressionScheme_1 = __importDefault(require("./compressionScheme"));
@@ -40,7 +42,7 @@ class CramContainer {
                 return undefined;
             }
             if (block.contentType !== 'COMPRESSION_HEADER') {
-                throw new errors_1.CramMalformedError(`invalid content type ${block.contentType} in what is supposed to be the compression header block`);
+                throw new errors_1.CramMalformedError(`invalid content type ${block.contentType} in compression header block`);
             }
             const content = (0, util_1.parseItem)(block.content, sectionParsers.cramCompressionHeader.parser, 0, block.contentPosition);
             return Object.assign(Object.assign({}, block), { parsedContent: content });
@@ -78,20 +80,21 @@ class CramContainer {
             const { cramContainerHeader1, cramContainerHeader2 } = sectionParsers;
             const { size: fileSize } = yield this.file.stat();
             if (position >= fileSize) {
-                console.warn(`position:${position}>=fileSize:${fileSize} in cram container`);
+                console.warn(`pos:${position}>=fileSize:${fileSize} in cram container`);
                 return undefined;
             }
             // parse the container header. do it in 2 pieces because you cannot tell
             // how much to buffer until you read numLandmarks
-            const bytes1 = Buffer.allocUnsafe(cramContainerHeader1.maxLength);
+            const bytes1 = buffer_1.Buffer.allocUnsafe(cramContainerHeader1.maxLength);
             yield this.file.read(bytes1, 0, cramContainerHeader1.maxLength, position);
             const header1 = (0, util_1.parseItem)(bytes1, cramContainerHeader1.parser);
             const numLandmarksSize = (0, util_1.itf8Size)(header1.numLandmarks);
             if (position + header1.length >= fileSize) {
-                console.warn(`container header at ${position} indicates that the container has length ${header1.length}, which extends beyond the length of the file. Skipping this container.`);
+                // header indicates container goes beyond fileSize
+                console.warn(`container at ${position} is beyond fileSize:${fileSize}, skipping`);
                 return undefined;
             }
-            const bytes2 = Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
+            const bytes2 = buffer_1.Buffer.allocUnsafe(cramContainerHeader2.maxLength(header1.numLandmarks));
             yield this.file.read(bytes2, 0, cramContainerHeader2.maxLength(header1.numLandmarks), position + header1._size - numLandmarksSize);
             const header2 = (0, util_1.parseItem)(bytes2, cramContainerHeader2.parser);
             if (this.file.validateChecksums && header2.crc32 !== undefined) {

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/cramFile/container/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;AAAA,mCAA+B;AAC/B,yCAAiD;AACjD,SAAS;AACT,kCAA0D;AAC1D,qDAAgC;AAChC,4EAAgE;AAEhE,sDAAqD;AAErD,MAAqB,aAAa;IAChC,YACS,IAAc,EACd,YAAoB;QADpB,SAAI,GAAJ,IAAI,CAAU;QACd,iBAAY,GAAZ,YAAY,CAAQ;IAC1B,CAAC;IAEJ,SAAS;QACP,OAAO,IAAI,CAAC,oBAAoB,CAAC,IAAI,CAAC,YAAY,CAAC,CAAA;IACrD,CAAC;IAEK,yBAAyB;;YAC7B,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAE9C,yEAAyE;YACzE,SAAS;YACT,IAAI,CAAC,CAAA,eAAe,aAAf,eAAe,uBAAf,eAAe,CAAE,UAAU,CAAA,EAAE,CAAC;gBACjC,OAAO,IAAI,CAAA;YACb,CAAC;YACD,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;YACxD,MAAM,cAAc,GAAG,IAAA,kCAAiB,EAAC,YAAY,CAAC,CAAA;YAEtD,MAAM,KAAK,GAAG,MAAM,IAAI,CAAC,aAAa,EAAE,CAAA;YACxC,IAAI,KAAK,KAAK,SAAS,EAAE,CAAC;gBACxB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,IAAI,KAAK,CAAC,WAAW,KAAK,oBAAoB,EAAE,CAAC;gBAC/C,MAAM,IAAI,2BAAkB,CAC1B,wBAAwB,KAAK,CAAC,WAAW,8BAA8B,CACxE,CAAA;YACH,CAAC;YAED,MAAM,OAAO,GAAG,IAAA,gBAAS,EACvB,KAAK,CAAC,OAAO,EACb,cAAc,CAAC,qBAAqB,CAAC,MAAM,EAC3C,CAAC,EACD,KAAK,CAAC,eAAe,CACtB,CAAA;YACD,uCACK,KAAK,KACR,aAAa,EAAE,OAAO,IACvB;QACH,CAAC;KAAA;IAEK,aAAa;;YACjB,MAAM,eAAe,GAAG,MAAM,IAAI,CAAC,SAAS,EAAE,CAAA;YAC9C,IAAI,CAAC,eAAe,EAAE,CAAC;gBACrB,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,OAAO,IAAI,CAAC,IAAI,CAAC,SAAS,CAAC,eAAe,CAAC,YAAY,CAAC,CAAA;QAC1D,CAAC;KAAA;IAED,2EAA2E;IAC3E,SAAS;IACH,oBAAoB;;YACxB,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,yBAAyB,EAAE,CAAA;YACrD,IAAI,CAAC,MAAM,EAAE,CAAC;gBACZ,OAAO,SAAS,CAAA;YAClB,CAAC;YAED,OAAO,IAAI,2BAA8B,CAAC,MAAM,CAAC,aAAa,CAAC,CAAA;QACjE,CAAC;KAAA;IAED,QAAQ,CAAC,aAAqB,EAAE,SAAiB;QAC/C,qEAAqE;QACrE,wCAAwC;QACxC,OAAO,IAAI,eAAS,CAAC,IAAI,EAAE,aAAa,EAAE,SAAS,CAAC,CAAA;IACtD,CAAC;IAEK,oBAAoB,CAAC,QAAgB;;YACzC,MAAM,EAAE,YAAY,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,aAAa,EAAE,CAAA;YACxD,MAAM,cAAc,GAAG,IAAA,kCAAiB,EAAC,YAAY,CAAC,CAAA;YACtD,MAAM,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,GAAG,cAAc,CAAA;YACrE,MAAM,EAAE,IAAI,EAAE,QAAQ,EAAE,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,EAAE,CAAA;YAEjD,IAAI,QAAQ,IAAI,QAAQ,EAAE,CAAC;gBACzB,OAAO,CAAC,IAAI,CAAC,OAAO,QAAQ,cAAc,QAAQ,oBAAoB,CAAC,CAAA;gBACvE,OAAO,SAAS,CAAA;YAClB,CAAC;YAED,wEAAwE;YACxE,iDAAiD;YACjD,MAAM,MAAM,GAAG,eAAM,CAAC,WAAW,CAAC,oBAAoB,CAAC,SAAS,CAAC,CAAA;YACjE,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC,EAAE,oBAAoB,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAA;YACzE,MAAM,OAAO,GAAG,IAAA,gBAAS,EAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;YAC9D,MAAM,gBAAgB,GAAG,IAAA,eAAQ,EAAC,OAAO,CAAC,YAAY,CAAC,CAAA;YACvD,IAAI,QAAQ,GAAG,OAAO,CAAC,MAAM,IAAI,QAAQ,EAAE,CAAC;gBAC1C,kDAAkD;gBAClD,OAAO,CAAC,IAAI,CACV,gBAAgB,QAAQ,uBAAuB,QAAQ,YAAY,CACpE,CAAA;gBACD,OAAO,SAAS,CAAA;YAClB,CAAC;YACD,MAAM,MAAM,GAAG,eAAM,CAAC,WAAW,CAC/B,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,CACrD,CAAA;YACD,MAAM,IAAI,CAAC,IAAI,CAAC,IAAI,CAClB,MAAM,EACN,CAAC,EACD,oBAAoB,CAAC,SAAS,CAAC,OAAO,CAAC,YAAY,CAAC,EACpD,QAAQ,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,CAC5C,CAAA;YACD,MAAM,OAAO,GAAG,IAAA,gBAAS,EAAC,MAAM,EAAE,oBAAoB,CAAC,MAAM,CAAC,CAAA;YAE9D,IAAI,IAAI,CAAC,IAAI,CAAC,iBAAiB,IAAI,OAAO,CAAC,KAAK,KAAK,SAAS,EAAE,CAAC;gBAC/D,MAAM,IAAI,CAAC,IAAI,CAAC,UAAU,CACxB,QAAQ,EACR,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,CAAC,EACpD,OAAO,CAAC,KAAK,EACb,0CAA0C,QAAQ,EAAE,CACrD,CAAA;YACH,CAAC;YAED,MAAM,cAAc,GAAG,MAAM,CAAC,MAAM,CAAC,OAAO,EAAE,OAAO,EAAE;gBACrD,KAAK,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB;gBACvD,YAAY,EAAE,OAAO,CAAC,KAAK,GAAG,OAAO,CAAC,KAAK,GAAG,gBAAgB,GAAG,QAAQ;aAC1E,CAAC,CAAA;YAEF,OAAO,cAAc,CAAA;QACvB,CAAC;KAAA;CACF;AAvHD,gCAuHC;AAED,0DAA0D;KACvD,KAAK,CAAC,GAAG,CAAC;KACV,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC,IAAA,kBAAW,EAAC,aAAa,EAAE,MAAM,CAAC,CAAC,CAAA"}

package/dist/cramFile/file.d.ts CHANGED Viewed

@@ -1,3 +1,4 @@
+import { Buffer } from 'buffer';
 import QuickLRU from 'quick-lru';
 import { BlockHeader, CompressionMethod } from './sectionParsers';
 import CramContainer from './container';

package/dist/cramFile/file.js CHANGED Viewed

@@ -12,14 +12,15 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const unzip_1 = require("../unzip");
+const buffer_1 = require("buffer");
 const buffer_crc32_1 = __importDefault(require("buffer-crc32"));
 const quick_lru_1 = __importDefault(require("quick-lru"));
 const htscodecs_1 = __importDefault(require("@jkbonfield/htscodecs"));
-// @ts-expect-error
 const bzip2_1 = __importDefault(require("bzip2"));
 const xz_decompress_1 = require("xz-decompress");
 const errors_1 = require("../errors");
+// locals
+const unzip_1 = require("../unzip");
 const rans_1 = __importDefault(require("../rans"));
 const sectionParsers_1 = require("./sectionParsers");
 const container_1 = __importDefault(require("./container"));
@@ -34,7 +35,7 @@ function bufferToStream(buf) {
         },
     });
 }
-// source:https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
+// source: https://abdulapopoola.com/2019/01/20/check-endianness-with-javascript/
 function getEndianness() {
     const uInt32 = new Uint32Array([0x11223344]);
     const uInt8 = new Uint8Array(uInt32.buffer);
@@ -81,7 +82,7 @@ class CramFile {
     getDefinition() {
         return __awaiter(this, void 0, void 0, function* () {
             const { maxLength, parser } = (0, sectionParsers_1.cramFileDefinition)();
-            const headbytes = Buffer.allocUnsafe(maxLength);
+            const headbytes = buffer_1.Buffer.allocUnsafe(maxLength);
             yield this.file.read(headbytes, 0, maxLength, 0);
             const definition = parser(headbytes).value;
             if (definition.majorVersion !== 2 && definition.majorVersion !== 3) {
@@ -162,7 +163,7 @@ class CramFile {
     }
     checkCrc32(position, length, recordedCrc32, description) {
         return __awaiter(this, void 0, void 0, function* () {
-            const b = Buffer.allocUnsafe(length);
+            const b = buffer_1.Buffer.allocUnsafe(length);
             yield this.file.read(b, 0, length, position);
             const calculatedCrc32 = buffer_crc32_1.default.unsigned(b);
             if (calculatedCrc32 !== recordedCrc32) {
@@ -220,7 +221,7 @@ class CramFile {
             if (position + cramBlockHeader.maxLength >= fileSize) {
                 return undefined;
             }
-            const buffer = Buffer.allocUnsafe(cramBlockHeader.maxLength);
+            const buffer = buffer_1.Buffer.allocUnsafe(cramBlockHeader.maxLength);
             yield this.file.read(buffer, 0, cramBlockHeader.maxLength, position);
             return (0, util_1.parseItem)(buffer, cramBlockHeader.parser, 0, position);
         });
@@ -236,7 +237,7 @@ class CramFile {
                 if (position + size >= fileSize) {
                     return undefined;
                 }
-                buffer = Buffer.allocUnsafe(size);
+                buffer = buffer_1.Buffer.allocUnsafe(size);
                 yield this.file.read(buffer, 0, size, position);
             }
             const data = (0, util_1.parseItem)(buffer, section.parser, 0, position);
@@ -259,16 +260,16 @@ class CramFile {
                 let chunk;
                 do {
                     chunk = bzip2_1.default.decompress(bits, size);
-                    if (chunk != -1) {
-                        Buffer.from(chunk).copy(outputBuffer, j);
+                    if (chunk !== -1) {
+                        buffer_1.Buffer.from(chunk).copy(outputBuffer, j);
                         j += chunk.length;
                         size -= chunk.length;
                     }
-                } while (chunk != -1);
+                } while (chunk !== -1);
             }
             else if (compressionMethod === 'lzma') {
                 const decompressedResponse = new Response(new xz_decompress_1.XzReadableStream(bufferToStream(inputBuffer)));
-                const ret = Buffer.from(yield decompressedResponse.arrayBuffer());
+                const ret = buffer_1.Buffer.from(yield decompressedResponse.arrayBuffer());
                 ret.copy(outputBuffer);
             }
             else if (compressionMethod === 'rans') {
@@ -302,10 +303,10 @@ class CramFile {
                 return undefined;
             }
             const blockContentPosition = blockHeader._endPosition;
-            const uncompressedData = Buffer.allocUnsafe(blockHeader.uncompressedSize);
+            const uncompressedData = buffer_1.Buffer.allocUnsafe(blockHeader.uncompressedSize);
             const block = Object.assign(Object.assign({}, blockHeader), { _endPosition: blockContentPosition, contentPosition: blockContentPosition, content: uncompressedData });
             if (blockHeader.compressionMethod !== 'raw') {
-                const compressedData = Buffer.allocUnsafe(blockHeader.compressedSize);
+                const compressedData = buffer_1.Buffer.allocUnsafe(blockHeader.compressedSize);
                 yield this.read(compressedData, 0, blockHeader.compressedSize, blockContentPosition);
                 yield this._uncompress(blockHeader.compressionMethod, compressedData, uncompressedData);
             }

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

	@@ -1 +1 @@
1	- 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package/dist/cramFile/record.js CHANGED Viewed

@@ -164,8 +164,8 @@ exports.MateFlags = [
 function makeFlagsHelper(x) {
     const r = {};
     for (const [code, name] of x) {
-        r['is' + name] = (flags) => !!(flags & code);
-        r['set' + name] = (flags) => flags | code;
+        r[`is${name}`] = (flags) => !!(flags & code);
+        r[`set${name}`] = (flags) => flags | code;
     }
     return r;
 }

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

	@@ -1 +1 @@
1	- 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package/dist/cramFile/slice/decodeRecord.js CHANGED Viewed

@@ -71,7 +71,7 @@ function parseTagValueArray(buffer) {
         }
     }
     else {
-        throw new Error('unknown type: ' + arrayType);
+        throw new Error(`unknown type: ${arrayType}`);
     }
     return array;
 }
@@ -209,8 +209,8 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
     let mateRecordNumber;
     // mate record
     if (record_1.CramFlagsDecoder.isDetached(cramFlags)) {
-        // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't matter for javascript
-        // const mate: any = {}
+        // note: the MF is a byte in 1.0, int32 in 2+, but once again this doesn't
+        // matter for javascript
         const mateFlags = decodeDataSeries('MF');
         let mateReadName;
         if (!compressionScheme.readNamesIncluded) {
@@ -274,7 +274,8 @@ function decodeRecord(slice, decodeDataSeries, compressionScheme, sliceHeader, c
         if (readFeatureCount) {
             readFeatures = decodeReadFeatures(alignmentStart, readFeatureCount, decodeDataSeries, compressionScheme, majorVersion);
         }
-        // compute the read's true span on the reference sequence, and the end coordinate of the alignment on the reference
+        // compute the read's true span on the reference sequence, and the end
+        // coordinate of the alignment on the reference
         lengthOnRef = readLength;
         if (readFeatures) {
             for (const { code, data } of readFeatures) {

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

	@@ -1 +1 @@
1	- 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package/dist/cramFile/slice/index.js CHANGED Viewed

@@ -135,7 +135,7 @@ function associateIntraSliceMate(allRecords, currentRecordNumber, thisRecord, ma
     }
     // delete this last because it's used by the
     // complicated template length estimation
-    delete thisRecord.mateRecordNumber;
+    thisRecord.mateRecordNumber = undefined;
 }
 class CramSlice {
     constructor(container, containerPosition, _unused) {
@@ -394,7 +394,7 @@ class CramSlice {
                             refRegion = {
                                 id: seqId,
                                 start: record.alignmentStart,
-                                end: -Infinity,
+                                end: Number.NEGATIVE_INFINITY,
                                 seq: null,
                             };
                             refRegions[seqId] = refRegion;