@gmod/bbi - npm Package Compare versions

Comparing version 1.0.11 to 1.0.12

CHANGELOG.md

@@ -0,1 +1,5 @@
+## [1.0.12](https://github.com/GMOD/bbi-js/compare/v1.0.11...v1.0.12) (2019-04-12)
+
+
+
 ## [1.0.11](https://github.com/GMOD/bbi-js/compare/v1.0.10...v1.0.11) (2019-04-10)
@@ -2,0 +6,0 @@

dist/bbi.js

 "use strict";
 
-var _interopRequireWildcard = require("@babel/runtime/helpers/interopRequireWildcard");
-
 var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
@@ -26,10 +24,6 @@
 
-var Long = _interopRequireWildcard(require("long"));
+var _genericFilehandle = require("generic-filehandle");
 
 var _blockView = _interopRequireDefault(require("./blockView"));
 
-var _localFile = _interopRequireDefault(require("./localFile"));
-
-var _remoteFile = _interopRequireDefault(require("./remoteFile"));
-
 var _util = require("./util");
@@ -108,5 +102,5 @@
     } else if (url) {
-      this.bbi = new _remoteFile.default(url);
+      this.bbi = new _genericFilehandle.RemoteFile(url);
     } else if (path) {
-      this.bbi = new _localFile.default(path);
+      this.bbi = new _genericFilehandle.LocalFile(path);
     } else {
@@ -274,60 +268,9 @@ throw new Error('no file given');
       var le = isBE ? 'big' : 'little';
-      /* istanbul ignore next */
-
-      var headerParser = new _binaryParser.Parser().endianess(le).int32('magic').uint16('version').uint16('numZoomLevels').buffer('chromTreeOffset', {
-        length: 8,
-        formatter: function formatter(buf) {
-          return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-        }
-      }).buffer('unzoomedDataOffset', {
-        length: 8,
-        formatter: function formatter(buf) {
-          return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-        }
-      }).buffer('unzoomedIndexOffset', {
-        length: 8,
-        formatter: function formatter(buf) {
-          return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-        }
-      }).uint16('fieldCount').uint16('definedFieldCount').buffer('asOffset', {
-        length: 8,
-        formatter: function formatter(buf) {
-          return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-        }
-      }).buffer('totalSummaryOffset', {
-        length: 8,
-        formatter: function formatter(buf) {
-          return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-        }
-      }).uint32('uncompressBufSize').skip(8) // reserved
+      var headerParser = new _binaryParser.Parser().endianess(le).int32('magic').uint16('version').uint16('numZoomLevels').uint64('chromTreeOffset').uint64('unzoomedDataOffset').uint64('unzoomedIndexOffset').uint16('fieldCount').uint16('definedFieldCount').uint64('asOffset').uint64('totalSummaryOffset').uint32('uncompressBufSize').skip(8) // reserved
       .array('zoomLevels', {
         length: 'numZoomLevels',
-        type: new _binaryParser.Parser().uint32('reductionLevel').uint32('reserved').buffer('dataOffset', {
-          length: 8,
-          formatter: function formatter(buf) {
-            return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-          }
-        }).buffer('indexOffset', {
-          length: 8,
-          formatter: function formatter(buf) {
-            return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-          }
-        })
+        type: new _binaryParser.Parser().uint32('reductionLevel').uint32('reserved').uint64('dataOffset').uint64('indexOffset')
       });
-      /* istanbul ignore next */
-
-      var totalSummaryParser = new _binaryParser.Parser().endianess(le).buffer('basesCovered', {
-        length: 8,
-        formatter: function formatter(buf) {
-          return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-        }
-      }).double('scoreMin').double('scoreMax').double('scoreSum').double('scoreSumSquares');
-      /* istanbul ignore next */
-
-      var chromTreeParser = new _binaryParser.Parser().endianess(le).uint32('magic').uint32('blockSize').uint32('keySize').uint32('valSize').buffer('itemCount', {
-        length: 8,
-        formatter: function formatter(buf) {
-          return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-        }
-      });
+      var totalSummaryParser = new _binaryParser.Parser().endianess(le).uint64('basesCovered').double('scoreMin').double('scoreMax').double('scoreSum').double('scoreSumSquares');
+      var chromTreeParser = new _binaryParser.Parser().endianess(le).uint32('magic').uint32('blockSize').uint32('keySize').uint32('valSize').uint64('itemCount');
       var isLeafNode = new _binaryParser.Parser().endianess(le).uint8('isLeafNode').skip(1).uint16('cnt');
@@ -390,8 +333,3 @@ return {
                 }).uint32('refId').uint32('refSize');
-                nonleafNodeParser = new _binaryParser.Parser().endianess(le).skip(ret.keySize).buffer('childOffset', {
-                  length: 8,
-                  formatter: function formatter(buf) {
-                    return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-                  }
-                });
+                nonleafNodeParser = new _binaryParser.Parser().endianess(le).skip(ret.keySize).uint64('childOffset');
                 rootNodeOffset = 32;
@@ -398,0 +336,0 @@

dist/bigbed.js

@@ -28,2 +28,4 @@ "use strict";
 
+var _util = require("./util");
+
 var BigBed =
@@ -107,3 +109,4 @@ /*#__PURE__*/
         var opts,
-            observables,
+            features,
+            ob,
             _args2 = arguments;
@@ -114,11 +117,23 @@ return _regenerator.default.wrap(function _callee2$(_context2) {
               case 0:
-                opts = _args2.length > 3 && _args2[3] !== undefined ? _args2[3] : {};
-                _context2.next = 3;
+                opts = _args2.length > 3 && _args2[3] !== undefined ? _args2[3] : {
+                  scale: 1
+                };
+                features = [];
+                _context2.next = 4;
                 return this.getFeatureStream(refName, start, end, opts);
 
-              case 3:
-                observables = _context2.sent;
-                return _context2.abrupt("return", observables.toPromise());
+              case 4:
+                ob = _context2.sent;
+                return _context2.abrupt("return", new Promise(function (resolve, reject) {
+                  // prettier-ignore
+                  ob.subscribe(function (feats) {
+                    return features = features.concat(feats);
+                  }, function (error) {
+                    return reject(error);
+                  }, function () {
+                    resolve((0, _util.flatten)(features));
+                  });
+                }));
 
-              case 5:
+              case 6:
               case "end":
@@ -125,0 +140,0 @@ return _context2.stop();

dist/bigwig.js

@@ -28,7 +28,3 @@ "use strict";
 
-function flatten(items) {
-  return items.reduce(function (prev, next) {
-    return prev.concat(next);
-  }, []);
-}
+var _util = require("./util");
 
@@ -168,3 +164,3 @@ var BigWig =
                   }, function () {
-                    resolve(flatten(features));
+                    resolve((0, _util.flatten)(features));
                   });
@@ -171,0 +167,0 @@ }));

dist/requestWorker.js

@@ -26,4 +26,2 @@ "use strict";
 
-var Long = _interopRequireWildcard(require("long"));
-
 var zlib = _interopRequireWildcard(require("zlib"));
@@ -188,4 +186,2 @@
       var data = cirBlockData.slice(offset);
-      /* istanbul ignore next */
-
       var parser = new _binaryParser.Parser().endianess(this.opts.isBigEndian ? 'big' : 'little').uint8('isLeaf').skip(1).uint16('cnt').choice({
@@ -196,22 +192,7 @@ tag: 'isLeaf',
             length: 'cnt',
-            type: new _binaryParser.Parser().uint32('startChrom').uint32('startBase').uint32('endChrom').uint32('endBase').buffer('blockOffset', {
-              length: 8,
-              formatter: function formatter(buf) {
-                return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-              }
-            }).buffer('blockSize', {
-              length: 8,
-              formatter: function formatter(buf) {
-                return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-              }
-            })
+            type: new _binaryParser.Parser().uint32('startChrom').uint32('startBase').uint32('endChrom').uint32('endBase').uint64('blockOffset').uint64('blockSize')
           }),
           0: new _binaryParser.Parser().array('recurOffsets', {
             length: 'cnt',
-            type: new _binaryParser.Parser().uint32('startChrom').uint32('startBase').uint32('endChrom').uint32('endBase').buffer('blockOffset', {
-              length: 8,
-              formatter: function formatter(buf) {
-                return Long.fromBytes(buf, true, this.endian === 'le').toNumber();
-              }
-            })
+            type: new _binaryParser.Parser().uint32('startChrom').uint32('startBase').uint32('endChrom').uint32('endBase').uint64('blockOffset')
           })
@@ -218,0 +199,0 @@ }

dist/util.js

@@ -11,2 +11,3 @@ "use strict";
 exports.abortBreakPoint = abortBreakPoint;
+exports.flatten = flatten;
 exports.AbortError = void 0;
@@ -139,2 +140,8 @@
   return _abortBreakPoint.apply(this, arguments);
+}
+
+function flatten(items) {
+  return items.reduce(function (prev, next) {
+    return prev.concat(next);
+  }, []);
 }

package.json

 {
   "name": "@gmod/bbi",
-  "version": "1.0.11",
+  "version": "1.0.12",
   "description": "Parser for BigWig/BigBed files",
@@ -41,3 +41,3 @@ "license": "MIT",
     "@babel/runtime": "^7.4.2",
-    "@gmod/binary-parser": "^1.3.4",
+    "@gmod/binary-parser": "^1.3.5",
     "abortable-promise-cache": "^1.0.1",
@@ -47,3 +47,3 @@ "buffer-crc32": "^0.2.13",
     "es6-promisify": "^6.0.1",
-    "long": "^4.0.0",
+    "generic-filehandle": "^1.0.2",
     "quick-lru": "^3.0.0",
@@ -65,3 +65,2 @@ "rxjs": "^6.4.0"
     "babel-eslint": "^10.0.1",
-    "babel-loader": "^8.0.5",
     "babel-preset-typescript": "^7.0.0-alpha.19",
@@ -68,0 +67,0 @@ "documentation": "^9.3.1",

README.md

@@ -27,5 +27,5 @@ # bbi-js
 
-* path - uses the LocalFile class in this repo
-* url - uses the RemoteFile class in this repo
-* filehandle - accepts some custom file handle class that you provide
+* path - path to a local file
+* url - path to a url
+* filehandle - a filehandle instance that you can implement as a custom class yourself. path and url are based on https://www.npmjs.com/package/generic-filehandle but by implementing a class containing the Filehandle interface specified therein, you can pass it to this module
 
@@ -40,6 +40,7 @@
 * end - a 0-based half open end coordinate
-* opts.scale - 1 is the maximum zoom level, fractional values indicate a accessing multiple zoom levels based on pixelsPerBp
-* opts.signal - an AbortSignal to halt processing
-* opts.basesPerScale - inverse of opts.scale
+* opts.scale - indicates zoom level to use, specified as pixels per basepair, e.g. being zoomed out, you might have 100bp per pixel so opts.scale would be 1/100. the zoom level that is returned is the one which has reductionLevel<=2/opts.scale (reductionLevel is a property of the zoom level structure in the bigwig file data)
+* opts.basesPerScale - optional, just the inverse of opts.scale. one of opts.scale or opts.basesPerScale can be specified, otherwise the most granular zoom level is used
+* opts.signal - optional, an AbortSignal to halt processing
 
+
 Returns a promise to an array of features.
@@ -70,12 +71,17 @@
 * end - a 0-based half open end coordinate
-* opts.signal - an AbortSignal to halt processing
+* opts.signal - optional, an AbortSignal to halt processing
 
-returns a promise to an array of features
+returns a promise to an array of features. no concept of zoom levels is used with bigwig data
 
-#### note about BigBed file processing
+#### getFeatureStream(refName, start, end, opts)
 
-The BigBed line contents can be parsed by @gmod/bed, it is not integrated with this module by default but for example
+Similar to BigWig, returns an RxJS observable for a observable stream
 
+#### how to parse BigBed results
+
+The BigBed line contents are returned as a raw text line e.g. {start: 0, end:100, rest: "ENST00000456328.2\t1000\t..."} where "rest" contains tab delimited text for the fields from 4 and on in the BED format.  The rest line can be parsed by the @gmod/bed module, which is not by integrated with this module, but can be combined with it as follows
+
+
 ```js
-    import {BigBed} from '@gmod/bed'
+    import {BigBed} from '@gmod/bbi'
     import BED from '@gmod/bed'
@@ -89,3 +95,4 @@
     const parser = new BED({autoSql})
-    const lines = feats.map(f => parser.parseBedText('chr7', f.start, f.end, f.rest, 3))
+    const lines = feats.map(f => parser.parseBedText('chr7', f.start, f.end, f.rest, 3)) // 3 indicates skipping first 3 columns of the autoSql since these are provided by BigBed
+    
 ```
@@ -92,0 +99,0 @@

New alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Fixed alerts

License Policy Violation

License

This package is not allowed per your license policy. Review the package's license to ensure compliance.

Found 1 instance in 1 package

Filesystem access

Supply chain risk

Accesses the file system, and could potentially read sensitive data.

Found 1 instance in 1 package

Improved metrics

Dev dependency count

27

decreased by-3.57%

Number of lines in readme file

123

increased by6.03%

Number of low supply chain risk alerts

1

decreased by-50%

Worsened metrics

Total package byte prevSize

68629

decreased by-20.57%

Number of package files

14

decreased by-17.65%

Lines of code

1474

decreased by-24.72%

Dependency changes

• + Addedgeneric-filehandle@^1.0.2

• + Addedfile-uri-to-path@1.0.0(transitive)

• + Addedgeneric-filehandle@1.0.9(transitive)

• - Removedlong@^4.0.0

• Updated@gmod/binary-parser@^1.3.5