igv 2.13.9 → 2.13.10

package/dist/igv.js

@@ -21936,7 +21936,7 @@
       }
     };
 
-    const _version = "2.13.9";
+    const _version = "2.13.10";
     function version$1() {
       return _version;
     }
@@ -27260,12 +27260,15 @@
       /**
        * Return inflated data from startBlock through endBlock as an UInt8Array
        *
-       * @param startBlock
-       * @param endBlock
+       * @param minv minimum virtual pointer  {block, offset}
+       * @param maxv maximum virtual pointer  {block, offset}
        * @returns {Promise<Uint8Array>}
        */
-      async getData(startBlock, endBlock) {
-        const blocks = await this.getInflatedBlocks(startBlock, endBlock);
+      async getData(minv, maxv) {
+        const startBlock = minv.block;
+        const endBlock = maxv.block;
+        const skipEnd = maxv.offset === 0;
+        const blocks = await this.getInflatedBlocks(startBlock, endBlock, skipEnd);
         if (blocks.length === 1) {
           return blocks[0];
         }
@@ -27289,14 +27292,16 @@
        * @param endBlock
        * @returns {Promise<*[Uint8Array]>}
        */
-      async getInflatedBlocks(startBlock, endBlock) {
+      async getInflatedBlocks(startBlock, endBlock, skipEnd) {
         if (!this.cacheBlocks) {
-          const buffer = await this.loadBLockData(startBlock, endBlock);
+          const buffer = await this.loadBLockData(startBlock, endBlock, {
+            skipEnd
+          });
           return inflateBlocks(buffer);
         } else {
           const c = this.cache;
-          if (c && c.startBlock <= startBlock && c.endBlock >= endBlock) {
-            //console.log("Complete overlap")
+          if (c && c.startBlock <= startBlock && (c.endBlock >= endBlock || skipEnd && c.nextEndBlock === endBlock)) {
+            console.log("Complete overlap");
             const startOffset = startBlock - c.startBlock;
             const endOffset = endBlock - c.startBlock;
             return inflateBlocks(c.buffer, startOffset, endOffset);
@@ -27305,7 +27310,9 @@
             let buffer;
             if (!c || c.startBlock > endBlock || c.endBlock < startBlock) {
               // no overlap with cache
-              buffer = await this.loadBLockData(startBlock, endBlock);
+              buffer = await this.loadBLockData(startBlock, endBlock, {
+                skipEnd
+              });
             } else {
               //console.log("Some overlap")
               const arrayBuffers = [];
@@ -27347,15 +27354,24 @@
               // Load end blocks, if any
               if (endBlock > c.endBlock) {
                 const endBuffer = await this.loadBLockData(c.endBlock, endBlock, {
-                  skipStart: true
+                  skipStart: true,
+                  skipEnd
                 });
                 arrayBuffers.push(endBuffer);
               }
               buffer = concatenateArrayBuffers(arrayBuffers);
             }
+
+            // If skipEnd === true we need to find boundary of last block in cache
+            let nextEndBlock = endBlock;
+            if (skipEnd) {
+              const boundaries = findBlockBoundaries(buffer);
+              endBlock = boundaries[boundaries.length - 1];
+            }
             this.cache = {
               startBlock,
               endBlock,
+              nextEndBlock,
               buffer
             };
             return inflateBlocks(buffer);
@@ -27647,7 +27663,7 @@
           for (let chunk of chunks) {
             let inflated;
             if (tabix) {
-              inflated = await this._blockLoader.getData(chunk.minv.block, chunk.maxv.block);
+              inflated = await this._blockLoader.getData(chunk.minv, chunk.maxv);
             } else {
               const options = buildOptions(config, {
                 range: {
@@ -33595,7 +33611,7 @@
             return alignmentContainer;
           }
           for (let c of chunks) {
-            const ba = await this._blockLoader.getData(c.minv.block, c.maxv.block);
+            const ba = await this._blockLoader.getData(c.minv, c.maxv);
             const done = BamUtils.decodeBamRecords(ba, c.minv.offset, alignmentContainer, this.indexToChr, chrId, bpStart, bpEnd, this.filter);
             if (done) {
               break;