@gmod/bbi - npm Package Compare versions

Comparing version 1.0.12 to 1.0.13

CHANGELOG.md

@@ -0,3 +1,10 @@
+## [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
 
@@ -4,0 +11,0 @@

dist/requestWorker.js

@@ -234,3 +234,3 @@ "use strict";
         length: data.byteLength / 64,
-        type: new _binaryParser.Parser().int32('chromId').int32('startBase').int32('endBase').int32('validCnt').float('minVal').float('maxVal').float('sumData').float('sumSqData')
+        type: new _binaryParser.Parser().int32('chromId').int32('start').int32('end').int32('validCnt').float('minScore').float('maxScore').float('sumData').float('sumSqData')
       });
@@ -241,7 +241,7 @@ return p.parse(data).result.summary.filter(function (elt) {
         return {
-          start: elt.startBase,
-          end: elt.endBase,
-          score: elt.sumData / elt.validCnt || 1,
-          maxScore: elt.maxVal,
-          minScore: elt.minVal,
+          start: elt.start,
+          end: elt.end,
+          maxScore: elt.maxScore,
+          minScore: elt.minScore,
+          score: elt.sumData / (elt.validCnt || 1),
           summary: true
@@ -255,13 +255,19 @@ };
     key: "parseBigBedBlock",
-    value: function parseBigBedBlock(bytes, startOffset) {
+    value: function parseBigBedBlock(data, startOffset) {
       var _this3 = this;
 
-      var data = bytes.slice(startOffset);
-      var p = new _binaryParser.Parser().endianess(this.opts.isBigEndian ? 'big' : 'little').array('items', {
-        type: new _binaryParser.Parser().uint32('chromId').int32('start').int32('end').string('rest', {
-          zeroTerminated: true
-        }),
-        readUntil: 'eof'
+      var features = [];
+      var p = new _binaryParser.Parser().endianess(this.opts.isBigEndian ? 'big' : 'little').uint32('chromId').int32('start').int32('end').string('rest', {
+        zeroTerminated: true
       });
-      return p.parse(data).result.items.filter(function (f) {
+      var currOffset = startOffset;
+
+      while (currOffset < data.byteLength) {
+        var res = p.parse(data.slice(currOffset));
+        res.result.uniqueId = "bb-".concat(startOffset + currOffset);
+        features.push(res.result);
+        currOffset += res.offset;
+      }
+
+      return features.filter(function (f) {
         return _this3.coordFilter(f);
@@ -268,0 +274,0 @@ });

package.json

 {
   "name": "@gmod/bbi",
-  "version": "1.0.12",
+  "version": "1.0.13",
   "description": "Parser for BigWig/BigBed files",
@@ -57,3 +57,3 @@ "license": "MIT",
     "@babel/preset-typescript": "^7.3.3",
-    "@gmod/bed": "^1.0.3",
+    "@gmod/bed": "^1.0.4",
     "@types/jest": "^24.0.11",
@@ -60,0 +60,0 @@ "@types/long": "^4.0.0",

README.md

@@ -92,3 +92,5 @@ # bbi-js
     const parser = new BED({autoSql})
-    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
+    const lines = feats.map(f => parser.parseBedText('chr7', f.start, f.end, f.rest, { offset: 3, uniqueId: f.uniqueId }))
+    // note: offset 3 indicates skipping first 3 columns of the autoSql since these are provided by BigBed
+    // uniqueId is supplied by bbi-js based on the bigbed file offsets to help  distinguish exact duplicate features
     
@@ -95,0 +97,0 @@ ```

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Found 1 instance in 1 package

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Improved metrics

Total package byte prevSize

69153

increased by0.76%

Lines of code

1478

increased by0.27%

Number of lines in readme file

125

increased by1.63%

No dependency changes