npm - @gmod/cram - Versions diffs - 3.0.7 → 4.0.0 - Mend

@gmod/cram 3.0.7 → 4.0.0

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 (268) hide show

package/dist/craiIndex.js +70 -87
package/dist/craiIndex.js.map +1 -1
package/dist/cram-bundle.js +1 -1
package/dist/cramFile/codecs/_base.d.ts +1 -1
package/dist/cramFile/codecs/beta.d.ts +2 -2
package/dist/cramFile/codecs/beta.js +1 -1
package/dist/cramFile/codecs/beta.js.map +1 -1
package/dist/cramFile/codecs/byteArrayLength.d.ts +2 -2
package/dist/cramFile/codecs/byteArrayStop.d.ts +4 -4
package/dist/cramFile/codecs/byteArrayStop.js +1 -1
package/dist/cramFile/codecs/byteArrayStop.js.map +1 -1
package/dist/cramFile/codecs/external.d.ts +1 -1
package/dist/cramFile/codecs/external.js +1 -1
package/dist/cramFile/codecs/external.js.map +1 -1
package/dist/cramFile/codecs/gamma.d.ts +1 -1
package/dist/cramFile/codecs/gamma.js +1 -1
package/dist/cramFile/codecs/gamma.js.map +1 -1
package/dist/cramFile/codecs/getBits.d.ts +1 -1
package/dist/cramFile/codecs/getBits.js.map +1 -1
package/dist/cramFile/codecs/huffman.d.ts +1 -1
package/dist/cramFile/codecs/huffman.js +1 -1
package/dist/cramFile/codecs/huffman.js.map +1 -1
package/dist/cramFile/codecs/index.d.ts +1 -1
package/dist/cramFile/codecs/index.js +5 -5
package/dist/cramFile/codecs/index.js.map +1 -1
package/dist/cramFile/codecs/subexp.d.ts +2 -2
package/dist/cramFile/codecs/subexp.js +1 -1
package/dist/cramFile/codecs/subexp.js.map +1 -1
package/dist/cramFile/container/compressionScheme.d.ts +2 -2
package/dist/cramFile/container/compressionScheme.js +1 -1
package/dist/cramFile/container/compressionScheme.js.map +1 -1
package/dist/cramFile/container/index.d.ts +1 -2
package/dist/cramFile/container/index.js +62 -79
package/dist/cramFile/container/index.js.map +1 -1
package/dist/cramFile/file.d.ts +9 -13
package/dist/cramFile/file.js +218 -247
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.d.ts +16 -16
package/dist/cramFile/sectionParsers.js +12 -9
package/dist/cramFile/sectionParsers.js.map +1 -1
package/dist/cramFile/slice/decodeRecord.d.ts +3 -3
package/dist/cramFile/slice/decodeRecord.js +11 -11
package/dist/cramFile/slice/decodeRecord.js.map +1 -1
package/dist/cramFile/slice/index.d.ts +2 -2
package/dist/cramFile/slice/index.js +241 -262
package/dist/cramFile/slice/index.js.map +1 -1
package/dist/cramFile/util.d.ts +4 -2
package/dist/cramFile/util.js +29 -6
package/dist/cramFile/util.js.map +1 -1
package/dist/htscodecs/arith_gen.d.ts +9 -17
package/dist/htscodecs/arith_gen.js +32 -272
package/dist/htscodecs/arith_gen.js.map +1 -1
package/dist/htscodecs/fqzcomp.d.ts +1 -2
package/dist/htscodecs/fqzcomp.js +2 -421
package/dist/htscodecs/fqzcomp.js.map +1 -1
package/dist/htscodecs/index.d.ts +5 -5
package/dist/htscodecs/index.js +10 -10
package/dist/htscodecs/index.js.map +1 -1
package/dist/htscodecs/iostream.d.ts +2 -1
package/dist/htscodecs/iostream.js +3 -2
package/dist/htscodecs/iostream.js.map +1 -1
package/dist/htscodecs/rans.d.ts +1 -2
package/dist/htscodecs/rans.js +3 -270
package/dist/htscodecs/rans.js.map +1 -1
package/dist/htscodecs/rans4x16.d.ts +0 -1
package/dist/htscodecs/rans4x16.js +6 -497
package/dist/htscodecs/rans4x16.js.map +1 -1
package/dist/htscodecs/tok3.js +17 -1
package/dist/htscodecs/tok3.js.map +1 -1
package/dist/index.d.ts +1 -1
package/dist/index.js +2 -2
package/dist/index.js.map +1 -1
package/dist/indexedCramFile.d.ts +4 -4
package/dist/indexedCramFile.js +97 -108
package/dist/indexedCramFile.js.map +1 -1
package/dist/io/index.d.ts +2 -2
package/dist/io/index.js +6 -6
package/dist/io/index.js.map +1 -1
package/dist/rans/constants.d.ts +1 -1
package/dist/rans/constants.js +1 -1
package/dist/rans/constants.js.map +1 -1
package/dist/rans/d04.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 +5 -5
package/dist/rans/index.js.map +1 -1
package/dist/unzip.d.ts +1 -1
package/dist/unzip.js +5 -3
package/dist/unzip.js.map +1 -1
package/esm/craiIndex.js +10 -12
package/esm/craiIndex.js.map +1 -1
package/esm/cramFile/codecs/_base.d.ts +1 -1
package/esm/cramFile/codecs/beta.d.ts +2 -2
package/esm/cramFile/codecs/beta.js +1 -1
package/esm/cramFile/codecs/beta.js.map +1 -1
package/esm/cramFile/codecs/byteArrayLength.d.ts +2 -2
package/esm/cramFile/codecs/byteArrayStop.d.ts +4 -4
package/esm/cramFile/codecs/byteArrayStop.js +1 -1
package/esm/cramFile/codecs/byteArrayStop.js.map +1 -1
package/esm/cramFile/codecs/external.d.ts +1 -1
package/esm/cramFile/codecs/external.js +1 -1
package/esm/cramFile/codecs/external.js.map +1 -1
package/esm/cramFile/codecs/gamma.d.ts +1 -1
package/esm/cramFile/codecs/gamma.js +1 -1
package/esm/cramFile/codecs/gamma.js.map +1 -1
package/esm/cramFile/codecs/getBits.d.ts +1 -1
package/esm/cramFile/codecs/getBits.js.map +1 -1
package/esm/cramFile/codecs/huffman.d.ts +1 -1
package/esm/cramFile/codecs/huffman.js +1 -1
package/esm/cramFile/codecs/huffman.js.map +1 -1
package/esm/cramFile/codecs/index.d.ts +1 -1
package/esm/cramFile/codecs/index.js +5 -5
package/esm/cramFile/codecs/index.js.map +1 -1
package/esm/cramFile/codecs/subexp.d.ts +2 -2
package/esm/cramFile/codecs/subexp.js +1 -1
package/esm/cramFile/codecs/subexp.js.map +1 -1
package/esm/cramFile/container/compressionScheme.d.ts +2 -2
package/esm/cramFile/container/compressionScheme.js +1 -1
package/esm/cramFile/container/compressionScheme.js.map +1 -1
package/esm/cramFile/container/index.d.ts +1 -2
package/esm/cramFile/container/index.js +4 -7
package/esm/cramFile/container/index.js.map +1 -1
package/esm/cramFile/file.d.ts +9 -13
package/esm/cramFile/file.js +47 -52
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.d.ts +16 -16
package/esm/cramFile/sectionParsers.js +7 -7
package/esm/cramFile/sectionParsers.js.map +1 -1
package/esm/cramFile/slice/decodeRecord.d.ts +3 -3
package/esm/cramFile/slice/decodeRecord.js +11 -11
package/esm/cramFile/slice/decodeRecord.js.map +1 -1
package/esm/cramFile/slice/index.d.ts +2 -2
package/esm/cramFile/slice/index.js +7 -6
package/esm/cramFile/slice/index.js.map +1 -1
package/esm/cramFile/util.d.ts +4 -2
package/esm/cramFile/util.js +19 -2
package/esm/cramFile/util.js.map +1 -1
package/esm/htscodecs/arith_gen.d.ts +9 -17
package/esm/htscodecs/arith_gen.js +32 -272
package/esm/htscodecs/arith_gen.js.map +1 -1
package/esm/htscodecs/fqzcomp.d.ts +1 -2
package/esm/htscodecs/fqzcomp.js +2 -421
package/esm/htscodecs/fqzcomp.js.map +1 -1
package/esm/htscodecs/index.d.ts +5 -5
package/esm/htscodecs/index.js +10 -10
package/esm/htscodecs/index.js.map +1 -1
package/esm/htscodecs/iostream.d.ts +2 -1
package/esm/htscodecs/iostream.js +3 -2
package/esm/htscodecs/iostream.js.map +1 -1
package/esm/htscodecs/rans.d.ts +1 -2
package/esm/htscodecs/rans.js +3 -270
package/esm/htscodecs/rans.js.map +1 -1
package/esm/htscodecs/rans4x16.d.ts +0 -1
package/esm/htscodecs/rans4x16.js +6 -497
package/esm/htscodecs/rans4x16.js.map +1 -1
package/esm/htscodecs/tok3.js +17 -1
package/esm/htscodecs/tok3.js.map +1 -1
package/esm/index.d.ts +1 -1
package/esm/index.js +1 -1
package/esm/index.js.map +1 -1
package/esm/indexedCramFile.d.ts +4 -4
package/esm/indexedCramFile.js +10 -10
package/esm/indexedCramFile.js.map +1 -1
package/esm/io/index.d.ts +2 -2
package/esm/io/index.js +1 -1
package/esm/io/index.js.map +1 -1
package/esm/rans/constants.d.ts +1 -1
package/esm/rans/constants.js +1 -1
package/esm/rans/constants.js.map +1 -1
package/esm/rans/d04.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 +5 -5
package/esm/rans/index.js.map +1 -1
package/esm/unzip.d.ts +1 -1
package/esm/unzip.js +4 -1
package/esm/unzip.js.map +1 -1
package/package.json +7 -9
package/src/craiIndex.ts +17 -16
package/src/cramFile/codecs/_base.ts +1 -1
package/src/cramFile/codecs/beta.ts +3 -3
package/src/cramFile/codecs/byteArrayLength.ts +1 -1
package/src/cramFile/codecs/byteArrayStop.ts +3 -4
package/src/cramFile/codecs/external.ts +3 -3
package/src/cramFile/codecs/gamma.ts +2 -2
package/src/cramFile/codecs/getBits.ts +1 -1
package/src/cramFile/codecs/huffman.ts +2 -3
package/src/cramFile/codecs/index.ts +7 -8
package/src/cramFile/codecs/subexp.ts +3 -3
package/src/cramFile/container/compressionScheme.ts +3 -3
package/src/cramFile/container/index.ts +7 -10
package/src/cramFile/file.ts +71 -77
package/src/cramFile/record.ts +3 -3
package/src/cramFile/sectionParsers.ts +27 -22
package/src/cramFile/slice/decodeRecord.ts +17 -17
package/src/cramFile/slice/index.ts +8 -9
package/src/cramFile/util.ts +24 -5
package/src/htscodecs/arith_gen.js +33 -296
package/src/htscodecs/fqzcomp.js +2 -476
package/src/htscodecs/index.js +9 -11
package/src/htscodecs/iostream.js +3 -2
package/src/htscodecs/rans.js +3 -315
package/src/htscodecs/rans4x16.js +6 -557
package/src/htscodecs/tok3.js +18 -1
package/src/index.ts +1 -1
package/src/indexedCramFile.ts +6 -5
package/src/io/index.ts +5 -4
package/src/rans/constants.ts +1 -1
package/src/rans/d04.ts +0 -1
package/src/rans/decoding.ts +0 -1
package/src/rans/frequencies.ts +0 -1
package/src/rans/index.ts +5 -7
package/src/unzip.ts +5 -1
package/dist/cramFile/filehandle.d.ts +0 -1
package/dist/cramFile/filehandle.js +0 -3
package/dist/cramFile/filehandle.js.map +0 -1
package/dist/htscodecs/main_arith_gen.d.ts +0 -1
package/dist/htscodecs/main_arith_gen.js +0 -86
package/dist/htscodecs/main_arith_gen.js.map +0 -1
package/dist/htscodecs/main_fqzcomp.d.ts +0 -1
package/dist/htscodecs/main_fqzcomp.js +0 -112
package/dist/htscodecs/main_fqzcomp.js.map +0 -1
package/dist/htscodecs/main_rans.d.ts +0 -1
package/dist/htscodecs/main_rans.js +0 -83
package/dist/htscodecs/main_rans.js.map +0 -1
package/dist/htscodecs/main_rans4x16.d.ts +0 -1
package/dist/htscodecs/main_rans4x16.js +0 -82
package/dist/htscodecs/main_rans4x16.js.map +0 -1
package/dist/htscodecs/main_tok3.d.ts +0 -1
package/dist/htscodecs/main_tok3.js +0 -84
package/dist/htscodecs/main_tok3.js.map +0 -1
package/dist/unzip-pako.d.ts +0 -2
package/dist/unzip-pako.js +0 -9
package/dist/unzip-pako.js.map +0 -1
package/esm/cramFile/filehandle.d.ts +0 -1
package/esm/cramFile/filehandle.js +0 -2
package/esm/cramFile/filehandle.js.map +0 -1
package/esm/htscodecs/main_arith_gen.d.ts +0 -1
package/esm/htscodecs/main_arith_gen.js +0 -86
package/esm/htscodecs/main_arith_gen.js.map +0 -1
package/esm/htscodecs/main_fqzcomp.d.ts +0 -1
package/esm/htscodecs/main_fqzcomp.js +0 -112
package/esm/htscodecs/main_fqzcomp.js.map +0 -1
package/esm/htscodecs/main_rans.d.ts +0 -1
package/esm/htscodecs/main_rans.js +0 -83
package/esm/htscodecs/main_rans.js.map +0 -1
package/esm/htscodecs/main_rans4x16.d.ts +0 -1
package/esm/htscodecs/main_rans4x16.js +0 -82
package/esm/htscodecs/main_rans4x16.js.map +0 -1
package/esm/htscodecs/main_tok3.d.ts +0 -1
package/esm/htscodecs/main_tok3.js +0 -84
package/esm/htscodecs/main_tok3.js.map +0 -1
package/esm/unzip-pako.d.ts +0 -2
package/esm/unzip-pako.js +0 -6
package/esm/unzip-pako.js.map +0 -1
package/src/cramFile/filehandle.ts +0 -1
package/src/htscodecs/Makefile +0 -142
package/src/htscodecs/README.md +0 -64
package/src/htscodecs/main_arith_gen.js +0 -96
package/src/htscodecs/main_fqzcomp.js +0 -113
package/src/htscodecs/main_rans.js +0 -88
package/src/htscodecs/main_rans4x16.js +0 -87
package/src/htscodecs/main_tok3.js +0 -86
package/src/unzip-pako.ts +0 -6

package/dist/htscodecs/rans4x16.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/htscodecs/tok3.js CHANGED Viewed

@@ -39,6 +39,22 @@
 const IOStream = require('./iostream');
 const rans = require('./rans4x16');
 const arith_gen = require('./arith_gen');
+function sum(array) {
+    let sum = 0;
+    for (const entry of array) {
+        sum += entry.length;
+    }
+    return sum;
+}
+function concatUint8Array(args) {
+    const mergedArray = new Uint8Array(sum(args));
+    let offset = 0;
+    for (const entry of args) {
+        mergedArray.set(entry, offset);
+        offset += entry.length;
+    }
+    return mergedArray;
+}
 var arith = new arith_gen();
 const TOK_TYPE = 0;
 const TOK_STRING = 1;
@@ -69,7 +85,7 @@ function DecodeTokenByteStreams(src, in_size, use_arith, nnames) {
         }
         if (type != TOK_TYPE && tok_new) {
             var M = new Array(nnames - 1).fill(TOK_MATCH);
-            B[t][TOK_TYPE] = new IOStream(Buffer.from([type].concat(M)));
+            B[t][TOK_TYPE] = new IOStream(concatUint8Array([new Uint8Array(type), M]));
         }
         if (tok_dup) {
             var dup_pos = src.ReadByte();

package/dist/htscodecs/tok3.js.map CHANGED Viewed

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

@@ -1,3 +1,3 @@
-export { default as CramFile, CramRecord } from './cramFile';
+export { CramRecord, default as CramFile } from './cramFile';
 export { default as CraiIndex } from './craiIndex';
 export { default as IndexedCramFile } from './indexedCramFile';

package/dist/index.js CHANGED Viewed

@@ -3,10 +3,10 @@ var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.IndexedCramFile = exports.CraiIndex = exports.CramRecord = exports.CramFile = void 0;
+exports.IndexedCramFile = exports.CraiIndex = exports.CramFile = exports.CramRecord = void 0;
 var cramFile_1 = require("./cramFile");
-Object.defineProperty(exports, "CramFile", { enumerable: true, get: function () { return __importDefault(cramFile_1).default; } });
 Object.defineProperty(exports, "CramRecord", { enumerable: true, get: function () { return cramFile_1.CramRecord; } });
+Object.defineProperty(exports, "CramFile", { enumerable: true, get: function () { return __importDefault(cramFile_1).default; } });
 var craiIndex_1 = require("./craiIndex");
 Object.defineProperty(exports, "CraiIndex", { enumerable: true, get: function () { return __importDefault(craiIndex_1).default; } });
 var indexedCramFile_1 = require("./indexedCramFile");

package/dist/index.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,uCAA4D;AAAnD,~~qHAAA~~,~~OAAO~~,~~OAAY~~;AAAE,~~sGAAA~~,~~UAAU~~,~~OAAA~~;AACxC,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,qDAA8D;AAArD,mIAAA,OAAO,OAAmB"}
1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";;;;;;AAAA,uCAA4D;AAAnD,sGAAA,UAAU,OAAA;AAAE,qHAAA,OAAO,OAAY;AACxC,yCAAkD;AAAzC,uHAAA,OAAO,OAAa;AAC7B,qDAA8D;AAArD,mIAAA,OAAO,OAAmB"}

package/dist/indexedCramFile.d.ts CHANGED Viewed

@@ -1,10 +1,10 @@
+import { Slice } from './craiIndex';
 import CramFile from './cramFile';
-import CramRecord from './cramFile/record';
 import { SeqFetch } from './cramFile/file';
-import { Filehandle } from './cramFile/filehandle';
-import { Slice } from './craiIndex';
+import CramRecord from './cramFile/record';
+import type { GenericFilehandle } from 'generic-filehandle2';
 export interface CramFileSource {
-    cramFilehandle?: Filehandle;
+    cramFilehandle?: GenericFilehandle;
     cramUrl?: string;
     cramPath?: string;
 }

package/dist/indexedCramFile.js CHANGED Viewed

@@ -1,19 +1,10 @@
 "use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
 var __importDefault = (this && this.__importDefault) || function (mod) {
     return (mod && mod.__esModule) ? mod : { "default": mod };
 };
 Object.defineProperty(exports, "__esModule", { value: true });
-const errors_1 = require("./errors");
 const cramFile_1 = __importDefault(require("./cramFile"));
+const errors_1 = require("./errors");
 class IndexedCramFile {
     /**
      *
@@ -25,17 +16,17 @@ class IndexedCramFile {
      * 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.
      */
     constructor(args) {
-        var _a;
         // { cram, index, seqFetch /* fasta, fastaIndex */ }) {
         this.cram =
-            (_a = args.cram) !== null && _a !== void 0 ? _a : new cramFile_1.default({
-                url: args.cramUrl,
-                path: args.cramPath,
-                filehandle: args.cramFilehandle,
-                seqFetch: args.seqFetch,
-                checkSequenceMD5: args.checkSequenceMD5,
-                cacheSize: args.cacheSize,
-            });
+            args.cram ??
+                new cramFile_1.default({
+                    url: args.cramUrl,
+                    path: args.cramPath,
+                    filehandle: args.cramFilehandle,
+                    seqFetch: args.seqFetch,
+                    checkSequenceMD5: args.checkSequenceMD5,
+                    cacheSize: args.cacheSize,
+                });
         if (!(this.cram instanceof cramFile_1.default)) {
             throw new Error('invalid arguments: no cramfile');
         }
@@ -48,101 +39,99 @@ class IndexedCramFile {
      * @param {number} end end of the range of interest. 1-based closed coordinates.
      * @returns {Promise[Array[CramRecord]]}
      */
-    getRecordsForRange(seq_1, start_1, end_1) {
-        return __awaiter(this, arguments, void 0, function* (seq, start, end, opts = {}) {
-            opts.viewAsPairs = opts.viewAsPairs || false;
-            opts.pairAcrossChr = opts.pairAcrossChr || false;
-            opts.maxInsertSize = opts.maxInsertSize || 200000;
-            if (typeof seq === 'string') {
-                // TODO: support string reference sequence names somehow
-                throw new errors_1.CramUnimplementedError('string sequence names not yet supported');
-            }
-            const seqId = seq;
-            const slices = yield this.index.getEntriesForRange(seqId, start, end);
-            // TODO: do we need to merge or de-duplicate the blocks?
-            // fetch all the slices and parse the feature data
-            const filter = (feature) => feature.sequenceId === seq &&
-                feature.alignmentStart <= end &&
-                feature.lengthOnRef !== undefined &&
-                feature.alignmentStart + feature.lengthOnRef - 1 >= start;
-            const sliceResults = yield Promise.all(slices.map(slice => this.getRecordsInSlice(slice, filter)));
-            let ret = Array.prototype.concat(...sliceResults);
-            if (opts.viewAsPairs) {
-                const readNames = {};
-                const readIds = {};
-                for (const read of ret) {
-                    const name = read.readName;
-                    if (name === undefined) {
-                        throw new Error('readName undefined');
-                    }
-                    const id = read.uniqueId;
-                    if (!readNames[name]) {
-                        readNames[name] = 0;
-                    }
-                    readNames[name] += 1;
-                    readIds[id] = 1;
+    async getRecordsForRange(seq, start, end, opts = {}) {
+        opts.viewAsPairs = opts.viewAsPairs || false;
+        opts.pairAcrossChr = opts.pairAcrossChr || false;
+        opts.maxInsertSize = opts.maxInsertSize || 200000;
+        if (typeof seq === 'string') {
+            // TODO: support string reference sequence names somehow
+            throw new errors_1.CramUnimplementedError('string sequence names not yet supported');
+        }
+        const seqId = seq;
+        const slices = await this.index.getEntriesForRange(seqId, start, end);
+        // TODO: do we need to merge or de-duplicate the blocks?
+        // fetch all the slices and parse the feature data
+        const filter = (feature) => feature.sequenceId === seq &&
+            feature.alignmentStart <= end &&
+            feature.lengthOnRef !== undefined &&
+            feature.alignmentStart + feature.lengthOnRef - 1 >= start;
+        const sliceResults = await Promise.all(slices.map(slice => this.getRecordsInSlice(slice, filter)));
+        let ret = Array.prototype.concat(...sliceResults);
+        if (opts.viewAsPairs) {
+            const readNames = {};
+            const readIds = {};
+            for (const read of ret) {
+                const name = read.readName;
+                if (name === undefined) {
+                    throw new Error('readName undefined');
                 }
-                const unmatedPairs = {};
-                Object.entries(readNames).forEach(([k, v]) => {
-                    if (v === 1) {
-                        unmatedPairs[k] = true;
-                    }
-                });
-                const matePromises = [];
-                for (const cramRecord of ret) {
-                    const name = cramRecord.readName;
-                    if (name === undefined) {
-                        throw new Error('readName undefined');
-                    }
-                    if (unmatedPairs[name] &&
-                        cramRecord.mate &&
-                        (cramRecord.mate.sequenceId === seqId || opts.pairAcrossChr) &&
-                        Math.abs(cramRecord.alignmentStart - cramRecord.mate.alignmentStart) <
-                            opts.maxInsertSize) {
-                        const mateSlices = this.index.getEntriesForRange(cramRecord.mate.sequenceId, cramRecord.mate.alignmentStart, cramRecord.mate.alignmentStart + 1);
-                        matePromises.push(mateSlices);
-                    }
+                const id = read.uniqueId;
+                if (!readNames[name]) {
+                    readNames[name] = 0;
                 }
-                const mateBlocks = yield Promise.all(matePromises);
-                let mateChunks = [];
-                for (const block of mateBlocks) {
-                    mateChunks.push(...block);
+                readNames[name] += 1;
+                readIds[id] = 1;
+            }
+            const unmatedPairs = {};
+            Object.entries(readNames).forEach(([k, v]) => {
+                if (v === 1) {
+                    unmatedPairs[k] = true;
                 }
-                // filter out duplicates
-                mateChunks = mateChunks
-                    .sort((a, b) => a.toString().localeCompare(b.toString()))
-                    .filter((item, pos, ary) => !pos || item.toString() !== ary[pos - 1].toString());
-                const mateRecordPromises = [];
-                const mateFeatPromises = [];
-                for (const c of mateChunks) {
-                    let recordPromise = this.cram.featureCache.get(c.toString());
-                    if (!recordPromise) {
-                        recordPromise = this.getRecordsInSlice(c, () => true);
-                        this.cram.featureCache.set(c.toString(), recordPromise);
-                    }
-                    mateRecordPromises.push(recordPromise);
-                    const featPromise = recordPromise.then(feats => {
-                        const mateRecs = [];
-                        for (const feature of feats) {
-                            if (feature.readName === undefined) {
-                                throw new Error('readName undefined');
-                            }
-                            if (unmatedPairs[feature.readName] && !readIds[feature.uniqueId]) {
-                                mateRecs.push(feature);
-                            }
-                        }
-                        return mateRecs;
-                    });
-                    mateFeatPromises.push(featPromise);
+            });
+            const matePromises = [];
+            for (const cramRecord of ret) {
+                const name = cramRecord.readName;
+                if (name === undefined) {
+                    throw new Error('readName undefined');
                 }
-                const newMateFeats = yield Promise.all(mateFeatPromises);
-                if (newMateFeats.length) {
-                    const newMates = newMateFeats.reduce((result, current) => result.concat(current));
-                    ret = ret.concat(newMates);
+                if (unmatedPairs[name] &&
+                    cramRecord.mate &&
+                    (cramRecord.mate.sequenceId === seqId || opts.pairAcrossChr) &&
+                    Math.abs(cramRecord.alignmentStart - cramRecord.mate.alignmentStart) <
+                        opts.maxInsertSize) {
+                    const mateSlices = this.index.getEntriesForRange(cramRecord.mate.sequenceId, cramRecord.mate.alignmentStart, cramRecord.mate.alignmentStart + 1);
+                    matePromises.push(mateSlices);
                 }
             }
-            return ret;
-        });
+            const mateBlocks = await Promise.all(matePromises);
+            let mateChunks = [];
+            for (const block of mateBlocks) {
+                mateChunks.push(...block);
+            }
+            // filter out duplicates
+            mateChunks = mateChunks
+                .sort((a, b) => a.toString().localeCompare(b.toString()))
+                .filter((item, pos, ary) => !pos || item.toString() !== ary[pos - 1].toString());
+            const mateRecordPromises = [];
+            const mateFeatPromises = [];
+            for (const c of mateChunks) {
+                let recordPromise = this.cram.featureCache.get(c.toString());
+                if (!recordPromise) {
+                    recordPromise = this.getRecordsInSlice(c, () => true);
+                    this.cram.featureCache.set(c.toString(), recordPromise);
+                }
+                mateRecordPromises.push(recordPromise);
+                const featPromise = recordPromise.then(feats => {
+                    const mateRecs = [];
+                    for (const feature of feats) {
+                        if (feature.readName === undefined) {
+                            throw new Error('readName undefined');
+                        }
+                        if (unmatedPairs[feature.readName] && !readIds[feature.uniqueId]) {
+                            mateRecs.push(feature);
+                        }
+                    }
+                    return mateRecs;
+                });
+                mateFeatPromises.push(featPromise);
+            }
+            const newMateFeats = await Promise.all(mateFeatPromises);
+            if (newMateFeats.length) {
+                const newMates = newMateFeats.reduce((result, current) => result.concat(current));
+                ret = ret.concat(newMates);
+            }
+        }
+        return ret;
     }
     getRecordsInSlice({ containerStart, sliceStart, sliceBytes, }, filterFunction) {
         const container = this.cram.getContainerAtPosition(containerStart);

package/dist/indexedCramFile.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/io/index.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
-import { Filehandle } from '../cramFile/filehandle';
-declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: Filehandle): Filehandle;
+import type { GenericFilehandle } from 'generic-filehandle2';
+declare function open(maybeUrl?: string, maybePath?: string, maybeFilehandle?: GenericFilehandle): GenericFilehandle;
 export { open };
 export { LocalFile, RemoteFile } from 'generic-filehandle';

package/dist/io/index.js CHANGED Viewed

@@ -2,20 +2,20 @@
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.RemoteFile = exports.LocalFile = void 0;
 exports.open = open;
-const generic_filehandle_1 = require("generic-filehandle");
+const generic_filehandle2_1 = require("generic-filehandle2");
 function open(maybeUrl, maybePath, maybeFilehandle) {
     if (maybeFilehandle) {
         return maybeFilehandle;
     }
     if (maybeUrl) {
-        return new generic_filehandle_1.RemoteFile(maybeUrl);
+        return new generic_filehandle2_1.RemoteFile(maybeUrl);
     }
     if (maybePath) {
-        return new generic_filehandle_1.LocalFile(maybePath);
+        return new generic_filehandle2_1.LocalFile(maybePath);
     }
     throw new Error('no url, path, or filehandle provided, cannot open');
 }
-var generic_filehandle_2 = require("generic-filehandle");
-Object.defineProperty(exports, "LocalFile", { enumerable: true, get: function () { return generic_filehandle_2.LocalFile; } });
-Object.defineProperty(exports, "RemoteFile", { enumerable: true, get: function () { return generic_filehandle_2.RemoteFile; } });
+var generic_filehandle_1 = require("generic-filehandle");
+Object.defineProperty(exports, "LocalFile", { enumerable: true, get: function () { return generic_filehandle_1.LocalFile; } });
+Object.defineProperty(exports, "RemoteFile", { enumerable: true, get: function () { return generic_filehandle_1.RemoteFile; } });
 //# sourceMappingURL=index.js.map

package/dist/io/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/rans/constants.d.ts CHANGED Viewed

@@ -1,4 +1,4 @@
 declare const TF_SHIFT = 12;
 declare const TOTFREQ: number;
 declare const RANS_BYTE_L: number;
-export { TF_SHIFT, TOTFREQ, RANS_BYTE_L };
+export { RANS_BYTE_L, TF_SHIFT, TOTFREQ };

package/dist/rans/constants.js CHANGED Viewed

@@ -1,6 +1,6 @@
 "use strict";
 Object.defineProperty(exports, "__esModule", { value: true });
-exports.RANS_BYTE_L = exports.TOTFREQ = exports.TF_SHIFT = void 0;
+exports.TOTFREQ = exports.TF_SHIFT = exports.RANS_BYTE_L = void 0;
 const TF_SHIFT = 12;
 exports.TF_SHIFT = TF_SHIFT;
 const TOTFREQ = 1 << TF_SHIFT;

package/dist/rans/constants.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"constants.js","sourceRoot":"","sources":["../../src/rans/constants.ts"],"names":[],"mappings":";;;AAAA,MAAM,QAAQ,GAAG,EAAE,CAAA;AAIG,4BAAQ;AAH9B,MAAM,OAAO,GAAG,CAAC,IAAI,QAAQ,CAAA;AAGG,0BAAO;AAFvC,MAAM,WAAW,GAAG,CAAC,IAAI,EAAE,CAAA;AAElB,kCAAW"}

package/dist/rans/d04.js.map CHANGED Viewed

	@@ -1 +1 @@
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