Set default visibility window for bigbed tracks usin informatin in the header and chrom tree

Author: jrobinso

js/bigwig/bwReader.js

@@ -338,7 +338,7 @@ class BWReader {
             const startOffset = BBFILE_HEADER_SIZE
             let range = {
                 start: startOffset,
-                size: (header.fullDataOffset - startOffset + 5)
+                size: (header.fullDataOffset - startOffset + 4)
             }
             data = await this.loader.loadArrayBuffer(this.path, buildOptions(this.config, {range: range}))
 
@@ -381,8 +381,10 @@ class BWReader {
             }
 
             //Finally total data count
-           // binaryParser.position = header.fullDataOffset - startOffset
-           // header.dataCount = binaryParser.getInt()
+            binaryParser.position = header.fullDataOffset - startOffset
+            header.dataCount = binaryParser.getInt()
+
+            this.featureDensity = header.dataCount / this.chromTree.sumLengths
 
             this.header = header
 

js/bigwig/bwSource.js

@@ -65,7 +65,7 @@ class BWSource {
     }
 
     async defaultVisibilityWindow() {
-        return this.reader.defaultVisibilityWindow
+        return Math.floor(10000 / this.reader.featureDensity)
     }
 
     async getWGValues(windowFunction) {

js/bigwig/chromTree.js

@@ -11,10 +11,11 @@
  */
 export default class ChromTree {
 
-    constructor(header, nameToID, valueToKey) {
+    constructor(header, nameToID, valueToKey, sumLengths) {
         this.header = header
         this.nameToId = nameToID
         this.idToName = valueToKey
+        this.sumLengths = sumLengths
     }
 
     static parseTree(binaryParser, startOffset, genome = false) {
@@ -29,6 +30,7 @@ export default class ChromTree {
             const header = {magic, blockSize, keySize, valSize, itemCount, reserved}
             const nameToId = new Map()
             const idToName = []
+            let sumLengths = 0
             const readTreeNode = (offset) => {
 
                 if (offset >= 0) binaryParser.position = offset
@@ -44,6 +46,7 @@ export default class ChromTree {
                         if (valSize === 8) {
                             value = binaryParser.getInt()
                             const chromSize = binaryParser.getInt()
+                            sumLengths += chromSize
                             if (genome) key = genome.getChromosomeName(key)  // Translate to canonical chr name
                             nameToId.set(key, value)
                             idToName[value] = key
@@ -69,7 +72,7 @@ export default class ChromTree {
             // Recursively walk tree to populate dictionary
             readTreeNode(binaryParser, -1)
 
-            return new ChromTree(header, nameToId, idToName)
+            return new ChromTree(header, nameToId, idToName, sumLengths)
         }
     }
 

js/bigwig/rpTree.js

@@ -21,13 +21,12 @@ export default class RPTree {
     async init() {
         const binaryParser = await this.#getParserFor(this.startOffset, RPTREE_HEADER_SIZE)
         let magic = binaryParser.getInt()
-        console.log(magic)
-        if(magic !== RPTree.magic) {
+        if (magic !== RPTree.magic) {
             binaryParser.setPosition(0)
             this.littleEndian = !this.littleEndian
             binaryParser.littleEndian = this.littleEndian
             magic = binaryParser.getInt()
-            if(magic !== RPTree.magic) {
+            if (magic !== RPTree.magic) {
                 throw Error(`Bad magic number ${magic}`)
             }
         }
@@ -74,7 +73,7 @@ export default class RPTree {
                     if (node.type === 1) {   // Leaf node
                         leafItems.push(item)
                     } else { // Non leaf node
-                         await walkTreeNode(item.childOffset)
+                        await walkTreeNode(item.childOffset)
                     }
                 }
             }
@@ -89,7 +88,7 @@ export default class RPTree {
 
         const nodeKey = offset
         if (this.nodeCache.has(nodeKey)) {
-            return this.nodeCache
+            return this.nodeCache.get(nodeKey)
         }
 
         let binaryParser = await this.#getParserFor(offset, 4)
@@ -101,34 +100,22 @@ export default class RPTree {
         binaryParser = await this.#getParserFor(offset + 4, bytesRequired)
 
         const items = []
-
-        if (isLeaf) {
-            for (let i = 0; i < count; i++) {
-                let item = {
-                    isLeaf: true,
-                    startChrom: binaryParser.getInt(),
-                    startBase: binaryParser.getInt(),
-                    endChrom: binaryParser.getInt(),
-                    endBase: binaryParser.getInt(),
-                    dataOffset: binaryParser.getLong(),
-                    dataSize: binaryParser.getLong()
-                }
-                items.push(item)
+        for (let i = 0; i < count; i++) {
+            let item = {
+                isLeaf: isLeaf,
+                startChrom: binaryParser.getInt(),
+                startBase: binaryParser.getInt(),
+                endChrom: binaryParser.getInt(),
+                endBase: binaryParser.getInt(),
+                childOffset: binaryParser.getLong()
             }
-        } else { // non-leaf
-            for (let i = 0; i < count; i++) {
-
-                let item = {
-                    isLeaf: false,
-                    startChrom: binaryParser.getInt(),
-                    startBase: binaryParser.getInt(),
-                    endChrom: binaryParser.getInt(),
-                    endBase: binaryParser.getInt(),
-                    childOffset: binaryParser.getLong()
-                }
-                items[i] = item
+            if (isLeaf) {
+                item.dataSize =  binaryParser.getLong()
+                item.dataOffset = item.childOffset
             }
+            items.push(item)
         }
+
         const node = {type, items}
         this.nodeCache.set(nodeKey, node)
         return node