@gmod/bbi 1.0.31 → 1.0.34

package/CHANGELOG.md

@@ -1,34 +1,49 @@
-## [1.0.31](https://github.com/GMOD/bbi-js/compare/v1.0.30...v1.0.31) (2021-12-14)
+## [1.0.34](https://github.com/GMOD/bbi-js/compare/v1.0.33...v1.0.34) (2022-03-11)
 
 
+### Reverts
 
-- Add esm module builds with less babelification for smaller bundle sizes
+* Revert "Use subarray instead of slice since slice is deprecated under node xref 'https://nodejs.org/api/buffer.html#bufslicestart-end'" ([44116cc](https://github.com/GMOD/bbi-js/commit/44116cce54601727d37f1c449bfcc60c1b4e602d))
 
-## [1.0.30](https://github.com/GMOD/bbi-js/compare/v1.0.29...v1.0.30) (2020-06-25)
 
 
+- Back to slice instead of subarray, as subarray returned a UInt8Array instead
+  of a true Buffer
 
-- Use abortable-promise-cache instead of abortable-memoize
-- Allow opts parameter to getHeader instead of just abortsignal
+## [1.0.33](https://github.com/GMOD/bbi-js/compare/v1.0.32...v1.0.33) (2022-02-25)
 
-## [1.0.29](https://github.com/GMOD/bbi-js/compare/v1.0.28...v1.0.29) (2020-01-28)
 
 
+- Use subarray instead of slice since slice is deprecated under node xref
+  'https://nodejs.org/api/buffer.html#bufslicestart-end'"
 
-- Accidentally made the package include itself as dependency in 1.0.28, republish
+## [1.0.32](https://github.com/GMOD/bbi-js/compare/v1.0.31...v1.0.32) (2022-02-16)
 
 
-## [1.0.28](https://github.com/GMOD/bbi-js/compare/v1.0.27...v1.0.28) (2020-01-28)
 
+- Use pako to decode on command line instead of using zlib to avoid need to
+  manually polyfill zlib
 
+## [1.0.31](https://github.com/GMOD/bbi-js/compare/v1.0.30...v1.0.31) (2021-12-14)
+
+- Add esm module builds with less babelification for smaller bundle sizes
+
+## [1.0.30](https://github.com/GMOD/bbi-js/compare/v1.0.29...v1.0.30) (2020-06-25)
+
+- Use abortable-promise-cache instead of abortable-memoize
+- Allow opts parameter to getHeader instead of just abortsignal
+
+## [1.0.29](https://github.com/GMOD/bbi-js/compare/v1.0.28...v1.0.29) (2020-01-28)
+
+- Accidentally made the package include itself as dependency in 1.0.28, republish
+
+## [1.0.28](https://github.com/GMOD/bbi-js/compare/v1.0.27...v1.0.28) (2020-01-28)
 
 - Change typescript interface to use object keys instead of Map type for refsByName, refsById
 - Typescript only release change
 
 ## [1.0.27](https://github.com/GMOD/bbi-js/compare/v1.0.26...v1.0.27) (2020-01-10)
 
-
-
 - Reduce number of requests needed on initial header
 - Add definedFieldCount to the returned Header
 
@@ -36,8 +51,6 @@ Thanks to @skinner for both of these contributions!
 
 ## [1.0.26](https://github.com/GMOD/bbi-js/compare/v1.0.25...v1.0.26) (2019-11-10)
 
-
-
 - Fix important bug with fixed step bigwig files not using the proper start coordinate
 
 ## [1.0.25](https://github.com/GMOD/bbi-js/compare/v1.0.24...v1.0.25) (2019-11-03)
@@ -46,138 +59,97 @@ Thanks to @skinner for both of these contributions!
 
 ## [1.0.24](https://github.com/GMOD/bbi-js/compare/v1.0.23...v1.0.24) (2019-10-29)
 
-
-
 - Fix the uniqueIds generated via the bigbed features
 
 ## [1.0.23](https://github.com/GMOD/bbi-js/compare/v1.0.22...v1.0.23) (2019-10-06)
 
-
 - Small refactor of `filehandle.read()` to make it more robust
 
-
 ## [1.0.22](https://github.com/GMOD/bbi-js/compare/v1.0.21...v1.0.22) (2019-06-13)
 
-
-
 - Bump generic-filehandle
 - Add more checks for abort signal to allow early bailing
 
 ## [1.0.21](https://github.com/GMOD/bbi-js/compare/v1.0.20...v1.0.21) (2019-05-09)
 
-
-
 - Add fix for reading files with greater than 256 contigs
 
 ## [1.0.20](https://github.com/GMOD/bbi-js/compare/v1.0.19...v1.0.20) (2019-05-06)
 
-
-
 - Add fix that prevented accessing the lowest zoom/reduction level
 
 ## [1.0.19](https://github.com/GMOD/bbi-js/compare/v1.0.18...v1.0.19) (2019-05-02)
 
-
-
 - Add regression fix since 1.0.16 for uncompressed files. Thanks to @lidaof for reporting!
 
 ## [1.0.18](https://github.com/GMOD/bbi-js/compare/v1.0.17...v1.0.18) (2019-05-02)
 
-
-
 - Improve error handling of the observables (issue #20, pull #21)
 - Bump generic-filehandle to 1.0.9 to fix compatibility with native browser fetch
 
 ## [1.0.17](https://github.com/GMOD/bbi-js/compare/v1.0.16...v1.0.17) (2019-04-30)
 
-
-
 - Use some standard rxjs notions for combining operator results
 - Add parsing of the extraIndex data in BigBed, allowing you to call bigbed.searchExtraIndex(name[,opts])
 
 ## [1.0.16](https://github.com/GMOD/bbi-js/compare/v1.0.15...v1.0.16) (2019-04-23)
 
-
-
 - Pre-compile binary-parser instances for faster
 - Important: fixed bug that caused bigwig summary blocks to not be returned in output
 
 ## [1.0.15](https://github.com/GMOD/bbi-js/compare/v1.0.14...v1.0.15) (2019-04-18)
 
-
-
 - Make important performance improvement for BigWig data
 
 ## [1.0.14](https://github.com/GMOD/bbi-js/compare/v1.0.12...v1.0.14) (2019-04-17)
 
-
-
 - Improve documentation for integration with @gmod/bed@2
 - Fix some cases where abortSignal was passed incorrectly to filehandle
 
 ## [1.0.13](https://github.com/GMOD/bbi-js/compare/v1.0.12...v1.0.13) (2019-04-14)
 
-
-
 - Added uniqueId to objects returned from BigBed to avoid issue with duplicates
 
 ## [1.0.12](https://github.com/GMOD/bbi-js/compare/v1.0.11...v1.0.12) (2019-04-12)
 
 - Fix returning bigbed objects on empty regions
 
-
 ## [1.0.11](https://github.com/GMOD/bbi-js/compare/v1.0.10...v1.0.11) (2019-04-10)
 
-
-
 - Removed polyfill of Array.prototype.flat which modifies global scope
 
 ## [1.0.10](https://github.com/GMOD/bbi-js/compare/v1.0.9...v1.0.10) (2019-04-09)
 
-
-
 - Fix misinterpretation of variable step wig files in this module (the span is not variable in variable step files, only the step, use bedGraphToBigWig for variable span)
 - Improved docs
 
 ## [1.0.9](https://github.com/GMOD/bbi-js/compare/v1.0.8...v1.0.9) (2019-04-05)
 
-
-
 - Added caching of networking requests (thanks @rbuels for the abortable-promise-cache module!)
 - Fix some type errors on the range class
 - Correct using span on fixed size wiggle types
 
 ## [1.0.8](https://github.com/GMOD/bbi-js/compare/v1.0.7...v1.0.8) (2019-04-01)
 
-
-
 - Fix @babel/runtime in deployed package
 - Bugfix to the url argument to the BigWig/BigBed
 
 ## [1.0.7](https://github.com/GMOD/bbi-js/compare/v1.0.6...v1.0.7) (2019-04-01)
 
-
-
 - Added getFeatureStream which returns an Observable from rxjs
 - Added url option to BigWig and BigBed constructors to allow usage of RemoteFile filehandle
 - Added typescript backend for better processing
 
 ## [1.0.6](https://github.com/GMOD/bbi-js/compare/v1.0.5...v1.0.6) (2019-03-15)
 
-
-
 - Fix issue with fixed step and variable step bigwig files not working at all
 
 ## [1.0.5](https://github.com/GMOD/bbi-js/compare/v1.0.4...v1.0.5) (2019-03-07)
 
-
-
 - Fix issue with jest being in deps instead of devDeps
 
 ## [1.0.4](https://github.com/GMOD/bbi-js/compare/v1.0.3...v1.0.4) (2019-01-28)
 
-
-
 - Add renameRefSeqs functionality where you can apply a callback to the refseq names
 - Consistently apply start/end coordinate filters at different zoom levels
 
@@ -187,19 +159,13 @@ Thanks to @skinner for both of these contributions!
 
 ## [1.0.2](https://github.com/GMOD/bbi-js/compare/v1.0.1...v1.0.2) (2019-01-24)
 
-
-
 - Added regenerator-runtime to babel dist compilation
 
 ## [1.0.1](https://github.com/GMOD/bbi-js/compare/v1.0.0...v1.0.1) (2019-01-24)
 
-
-
 - Added exports for BigWig and BigBed. const {BigWig, BigBed} = require('@gmod/bbi')
 
 # 1.0.0 (2019-01-23)
 
-
-
 - Initial version
 - Has support for bigwig and bigbed files

package/dist/blockView.js

@@ -53,7 +53,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.BlockView = void 0;
 var binary_parser_1 = require("@gmod/binary-parser");
 var abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
-var zlib_1 = __importDefault(require("zlib"));
+var unzip_1 = require("./unzip");
 var quick_lru_1 = __importDefault(require("quick-lru"));
 var range_1 = __importDefault(require("./range"));
 var util_1 = require("./util");
@@ -213,10 +213,33 @@ var BlockView = /** @class */ (function () {
                             : buffer.readUInt32LE(4);
                         blocksToFetch_1 = [];
                         outstanding_1 = 0;
+                        cirFobRecur2_1 = function (cirBlockData, offset, level) {
+                            try {
+                                var data = cirBlockData.slice(offset);
+                                var p = _this.leafParser.parse(data).result;
+                                if (p.blocksToFetch) {
+                                    blocksToFetch_1 = blocksToFetch_1.concat(p.blocksToFetch.filter(filterFeats_1).map(function (l) { return ({
+                                        offset: l.blockOffset,
+                                        length: l.blockSize,
+                                    }); }));
+                                }
+                                if (p.recurOffsets) {
+                                    var recurOffsets = p.recurOffsets
+                                        .filter(filterFeats_1)
+                                        .map(function (l) { return l.blockOffset; });
+                                    if (recurOffsets.length > 0) {
+                                        cirFobRecur_1(recurOffsets, level + 1);
+                                    }
+                                }
+                            }
+                            catch (e) {
+                                observer.error(e);
+                            }
+                        };
                         filterFeats_1 = function (b) {
-                            return (b.startChrom < chrId_1 ||
-                                (b.startChrom === chrId_1 && b.startBase <= end)) &&
-                                (b.endChrom > chrId_1 || (b.endChrom === chrId_1 && b.endBase >= start));
+                            var startChrom = b.startChrom, startBase = b.startBase, endChrom = b.endChrom, endBase = b.endBase;
+                            return ((startChrom < chrId_1 || (startChrom === chrId_1 && startBase <= end)) &&
+                                (endChrom > chrId_1 || (endChrom === chrId_1 && endBase >= start)));
                         };
                         cirFobStartFetch_1 = function (off, fr, level) { return __awaiter(_this, void 0, void 0, function () {
                             var length_1, offset, resultBuffer, i, e_2;
@@ -231,7 +254,7 @@ var BlockView = /** @class */ (function () {
                                         resultBuffer = _a.sent();
                                         for (i = 0; i < off.length; i += 1) {
                                             if (fr.contains(off[i])) {
-                                                cirFobRecur2_1(resultBuffer, off[i] - offset, level, observer, opts);
+                                                cirFobRecur2_1(resultBuffer, off[i] - offset, level);
                                                 outstanding_1 -= 1;
                                                 if (outstanding_1 === 0) {
                                                     this.readFeatures(observer, blocksToFetch_1, __assign(__assign({}, opts), { request: request_1 }));
@@ -256,32 +279,7 @@ var BlockView = /** @class */ (function () {
                                     var blockSpan = new range_1.default(offset[i], offset[i] + maxCirBlockSpan);
                                     spans = spans.union(blockSpan);
                                 }
-                                spans
-                                    .getRanges()
-                                    .map(function (fr) { return cirFobStartFetch_1(offset, fr, level); });
-                            }
-                            catch (e) {
-                                observer.error(e);
-                            }
-                        };
-                        cirFobRecur2_1 = function (cirBlockData, offset, level) {
-                            try {
-                                var data = cirBlockData.slice(offset);
-                                var p = _this.leafParser.parse(data).result;
-                                if (p.blocksToFetch) {
-                                    blocksToFetch_1 = blocksToFetch_1.concat(p.blocksToFetch.filter(filterFeats_1).map(function (l) { return ({
-                                        offset: l.blockOffset,
-                                        length: l.blockSize,
-                                    }); }));
-                                }
-                                if (p.recurOffsets) {
-                                    var recurOffsets = p.recurOffsets
-                                        .filter(filterFeats_1)
-                                        .map(function (l) { return l.blockOffset; });
-                                    if (recurOffsets.length > 0) {
-                                        cirFobRecur_1(recurOffsets, level + 1);
-                                    }
-                                }
+                                spans.getRanges().map(function (fr) { return cirFobStartFetch_1(offset, fr, level); });
                             }
                             catch (e) {
                                 observer.error(e);
@@ -309,7 +307,7 @@ var BlockView = /** @class */ (function () {
         if (request) {
             items = items.filter(function (elt) { return elt.chromId === request.chrId; });
         }
-        items = items.map(function (elt) { return ({
+        var feats = items.map(function (elt) { return ({
             start: elt.start,
             end: elt.end,
             maxScore: elt.maxScore,
@@ -318,8 +316,8 @@ var BlockView = /** @class */ (function () {
             summary: true,
         }); });
         return request
-            ? items.filter(function (f) { return BlockView.coordFilter(f, request); })
-            : items;
+            ? feats.filter(function (f) { return BlockView.coordFilter(f, request); })
+            : feats;
     };
     BlockView.prototype.parseBigBedBlock = function (data, startOffset, offset, request) {
         var items = [];
@@ -385,7 +383,7 @@ var BlockView = /** @class */ (function () {
                                                 var blockOffset = block.offset - blockGroup.offset;
                                                 var resultData = data;
                                                 if (isCompressed_1) {
-                                                    resultData = zlib_1.default.inflateSync(data.slice(blockOffset));
+                                                    resultData = (0, unzip_1.unzip)(data.slice(blockOffset));
                                                     blockOffset = 0;
                                                 }
                                                 (0, util_1.checkAbortSignal)(signal_2);

package/dist/unzip-pako.d.ts

@@ -0,0 +1,2 @@
+/// <reference types="node" />
+export declare function unzip(input: Buffer): Buffer;

package/dist/unzip-pako.js

@@ -0,0 +1,8 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.unzip = void 0;
+var pako_1 = require("pako");
+function unzip(input) {
+    return Buffer.from((0, pako_1.inflate)(input));
+}
+exports.unzip = unzip;

package/dist/unzip.d.ts

@@ -0,0 +1,2 @@
+import { inflateSync } from 'zlib';
+export { inflateSync as unzip };

package/dist/unzip.js

@@ -0,0 +1,5 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.unzip = void 0;
+var zlib_1 = require("zlib");
+Object.defineProperty(exports, "unzip", { enumerable: true, get: function () { return zlib_1.inflateSync; } });

package/esm/blockView.js

@@ -6,7 +6,7 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.BlockView = void 0;
 const binary_parser_1 = require("@gmod/binary-parser");
 const abortable_promise_cache_1 = __importDefault(require("abortable-promise-cache"));
-const zlib_1 = __importDefault(require("zlib"));
+const unzip_1 = require("./unzip");
 const quick_lru_1 = __importDefault(require("quick-lru"));
 const range_1 = __importDefault(require("./range"));
 const util_1 = require("./util");
@@ -148,11 +148,34 @@ class BlockView {
                 : buffer.readUInt32LE(4);
             let blocksToFetch = [];
             let outstanding = 0;
-            //eslint-disable-next-line prefer-const
-            let cirFobRecur2;
-            const filterFeats = (b) => (b.startChrom < chrId ||
-                (b.startChrom === chrId && b.startBase <= end)) &&
-                (b.endChrom > chrId || (b.endChrom === chrId && b.endBase >= start));
+            const cirFobRecur2 = (cirBlockData, offset, level) => {
+                try {
+                    const data = cirBlockData.slice(offset);
+                    const p = this.leafParser.parse(data).result;
+                    if (p.blocksToFetch) {
+                        blocksToFetch = blocksToFetch.concat(p.blocksToFetch.filter(filterFeats).map((l) => ({
+                            offset: l.blockOffset,
+                            length: l.blockSize,
+                        })));
+                    }
+                    if (p.recurOffsets) {
+                        const recurOffsets = p.recurOffsets
+                            .filter(filterFeats)
+                            .map((l) => l.blockOffset);
+                        if (recurOffsets.length > 0) {
+                            cirFobRecur(recurOffsets, level + 1);
+                        }
+                    }
+                }
+                catch (e) {
+                    observer.error(e);
+                }
+            };
+            const filterFeats = (b) => {
+                const { startChrom, startBase, endChrom, endBase } = b;
+                return ((startChrom < chrId || (startChrom === chrId && startBase <= end)) &&
+                    (endChrom > chrId || (endChrom === chrId && endBase >= start)));
+            };
             const cirFobStartFetch = async (off, fr, level) => {
                 try {
                     const length = fr.max() - fr.min();
@@ -160,7 +183,7 @@ class BlockView {
                     const resultBuffer = await this.featureCache.get(`${length}_${offset}`, { length, offset }, signal);
                     for (let i = 0; i < off.length; i += 1) {
                         if (fr.contains(off[i])) {
-                            cirFobRecur2(resultBuffer, off[i] - offset, level, observer, opts);
+                            cirFobRecur2(resultBuffer, off[i] - offset, level);
                             outstanding -= 1;
                             if (outstanding === 0) {
                                 this.readFeatures(observer, blocksToFetch, { ...opts, request });
@@ -181,32 +204,7 @@ class BlockView {
                         const blockSpan = new range_1.default(offset[i], offset[i] + maxCirBlockSpan);
                         spans = spans.union(blockSpan);
                     }
-                    spans
-                        .getRanges()
-                        .map((fr) => cirFobStartFetch(offset, fr, level));
-                }
-                catch (e) {
-                    observer.error(e);
-                }
-            };
-            cirFobRecur2 = (cirBlockData, offset, level) => {
-                try {
-                    const data = cirBlockData.slice(offset);
-                    const p = this.leafParser.parse(data).result;
-                    if (p.blocksToFetch) {
-                        blocksToFetch = blocksToFetch.concat(p.blocksToFetch.filter(filterFeats).map((l) => ({
-                            offset: l.blockOffset,
-                            length: l.blockSize,
-                        })));
-                    }
-                    if (p.recurOffsets) {
-                        const recurOffsets = p.recurOffsets
-                            .filter(filterFeats)
-                            .map((l) => l.blockOffset);
-                        if (recurOffsets.length > 0) {
-                            cirFobRecur(recurOffsets, level + 1);
-                        }
-                    }
+                    spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level));
                 }
                 catch (e) {
                     observer.error(e);
@@ -228,9 +226,9 @@ class BlockView {
         }
         let items = features;
         if (request) {
-            items = items.filter((elt) => elt.chromId === request.chrId);
+            items = items.filter(elt => elt.chromId === request.chrId);
         }
-        items = items.map((elt) => ({
+        const feats = items.map((elt) => ({
             start: elt.start,
             end: elt.end,
             maxScore: elt.maxScore,
@@ -239,8 +237,8 @@ class BlockView {
             summary: true,
         }));
         return request
-            ? items.filter(f => BlockView.coordFilter(f, request))
-            : items;
+            ? feats.filter(f => BlockView.coordFilter(f, request))
+            : feats;
     }
     parseBigBedBlock(data, startOffset, offset, request) {
         const items = [];
@@ -292,7 +290,7 @@ class BlockView {
                     let blockOffset = block.offset - blockGroup.offset;
                     let resultData = data;
                     if (isCompressed) {
-                        resultData = zlib_1.default.inflateSync(data.slice(blockOffset));
+                        resultData = (0, unzip_1.unzip)(data.slice(blockOffset));
                         blockOffset = 0;
                     }
                     (0, util_1.checkAbortSignal)(signal);

package/esm/unzip-pako.d.ts

@@ -0,0 +1,2 @@
+/// <reference types="node" />
+export declare function unzip(input: Buffer): Buffer;

package/esm/unzip-pako.js

@@ -0,0 +1,8 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.unzip = void 0;
+const pako_1 = require("pako");
+function unzip(input) {
+    return Buffer.from((0, pako_1.inflate)(input));
+}
+exports.unzip = unzip;

package/esm/unzip.d.ts

@@ -0,0 +1,2 @@
+import { inflateSync } from 'zlib';
+export { inflateSync as unzip };

package/esm/unzip.js

@@ -0,0 +1,5 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.unzip = void 0;
+const zlib_1 = require("zlib");
+Object.defineProperty(exports, "unzip", { enumerable: true, get: function () { return zlib_1.inflateSync; } });

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "1.0.31",
+  "version": "1.0.34",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -24,10 +24,12 @@
     "lint": "eslint --report-unused-disable-directives --max-warnings 0 --ext .js,.ts src",
     "clean": "rimraf dist esm",
     "prebuild": "npm run clean",
-    "build": "tsc --target es2018 --outDir esm && tsc --target es5 --outDir dist",
+    "build:esm": "tsc --target es2018 --outDir esm",
+    "build:es5": "tsc --target es5 --outDir dist",
+    "build": "npm run build:esm && npm run build:es5",
     "preversion": "npm run lint && npm test && npm run build",
     "version": "standard-changelog && git add CHANGELOG.md",
-    "postpublish": "git push origin master --follow-tags"
+    "postversion": "git push origin master --follow-tags"
   },
   "keywords": [
     "bionode",
@@ -43,6 +45,7 @@
     "buffer-crc32": "^0.2.13",
     "es6-promisify": "^6.0.1",
     "generic-filehandle": "^2.0.0",
+    "pako": "^1.0.0",
     "quick-lru": "^4.0.0",
     "rxjs": "^6.5.2"
   },
@@ -51,21 +54,26 @@
     "@types/jest": "^27.0.3",
     "@types/long": "^4.0.0",
     "@types/node": "^12.0.2",
-    "@typescript-eslint/eslint-plugin": "^2.0.0",
-    "@typescript-eslint/parser": "^2.0.0",
+    "@types/pako": "^1.0.3",
+    "@typescript-eslint/eslint-plugin": "^5.10.0",
+    "@typescript-eslint/parser": "^5.10.0",
     "cross-fetch": "^3.0.2",
-    "eslint": "^7.0.0",
+    "eslint": "^8.7.0",
     "eslint-config-prettier": "^8.3.0",
     "eslint-plugin-import": "^2.25.3",
     "eslint-plugin-prettier": "^4.0.0",
     "jest": "^27.4.3",
     "prettier": "^2.5.1",
-    "rimraf": "^2.6.3",
+    "rimraf": "^3.0.2",
     "standard-changelog": "^2.0.11",
     "ts-jest": "^27.0.7",
     "typescript": "^4.5.2"
   },
   "publishConfig": {
     "access": "public"
+  },
+  "browser": {
+    "./esm/unzip.js": "./esm/unzip-pako.js",
+    "./dist/unzip.js": "./dist/unzip-pako.js"
   }
 }