npm - @gmod/bbi - Versions diffs - 8.0.0 → 8.0.2 - Mend

@gmod/bbi 8.0.0 → 8.0.2

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (29) hide show

package/CHANGELOG.md +8 -0
package/dist/bbi.js +4 -1
package/dist/bbi.js.map +1 -1
package/dist/bigbed.js +2 -1
package/dist/bigbed.js.map +1 -1
package/dist/block-view.d.ts +1 -0
package/dist/block-view.js +112 -15
package/dist/block-view.js.map +1 -1
package/dist/unzip.js.map +1 -1
package/dist/wasm/inflate-wasm-inlined.d.ts +6 -7
package/dist/wasm/inflate-wasm-inlined.js +452 -114
package/dist/wasm/inflate-wasm-inlined.js.map +1 -1
package/esm/bbi.js +4 -1
package/esm/bbi.js.map +1 -1
package/esm/bigbed.js +2 -1
package/esm/bigbed.js.map +1 -1
package/esm/block-view.d.ts +1 -0
package/esm/block-view.js +112 -15
package/esm/block-view.js.map +1 -1
package/esm/unzip.js.map +1 -1
package/esm/wasm/inflate-wasm-inlined.d.ts +6 -7
package/esm/wasm/inflate-wasm-inlined.js +448 -110
package/esm/wasm/inflate-wasm-inlined.js.map +1 -1
package/package.json +7 -7
package/src/bbi.ts +5 -3
package/src/bigbed.ts +3 -3
package/src/block-view.ts +135 -21
package/src/unzip.ts +1 -3
package/src/wasm/inflate-wasm-inlined.js +547 -1

package/dist/wasm/inflate-wasm-inlined.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/bbi.js CHANGED Viewed

@@ -195,7 +195,10 @@ export class BBI {
                 offset = 0;
                 for (let n = 0; n < count; n++) {
                     const keyEnd = b.indexOf(0, offset);
-                    const key = decoder.decode(b.subarray(offset, keyEnd !== -1 ? keyEnd : offset + keySize));
+                    const effectiveKeyEnd = keyEnd !== -1 && keyEnd < offset + keySize
+                        ? keyEnd
+                        : offset + keySize;
+                    const key = decoder.decode(b.subarray(offset, effectiveKeyEnd));
                     offset += keySize;
                     const refId = dataView.getUint32(offset, true);
                     offset += 4;

package/esm/bbi.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/bigbed.js CHANGED Viewed

@@ -25,7 +25,8 @@ function getTabField(str, fieldIndex) {
 // Parses a null-terminated string key from a B+ tree node
 function parseKey(buffer, offset, keySize) {
     const keyEnd = buffer.indexOf(0, offset);
-    return decoder.decode(buffer.subarray(offset, keyEnd !== -1 ? keyEnd : offset + keySize));
+    const effectiveKeyEnd = keyEnd !== -1 && keyEnd < offset + keySize ? keyEnd : offset + keySize;
+    return decoder.decode(buffer.subarray(offset, effectiveKeyEnd));
 }
 // Recursively traverses a B+ tree to search for a specific name in the BigBed extraIndex
 // B+ trees are balanced tree structures optimized for disk-based searches

package/esm/bigbed.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/block-view.d.ts CHANGED Viewed

@@ -30,6 +30,7 @@ export declare class BlockView {
     private parseSummaryBlock;
     private parseBigBedBlock;
     private parseBigWigBlock;
+    private parseBigWigBlockAsArrays;
     readFeatures(observer: Observer<Feature[]>, blocks: {
         offset: number;
         length: number;

package/esm/block-view.js CHANGED Viewed

@@ -329,6 +329,112 @@ export class BlockView {
         }
         return items;
     }
+    parseBigWigBlockAsArrays(buffer, startOffset, req) {
+        const dataView = new DataView(buffer.buffer, buffer.byteOffset + startOffset, buffer.length - startOffset);
+        const blockStart = dataView.getInt32(4, true);
+        const itemStep = dataView.getUint32(12, true);
+        const itemSpan = dataView.getUint32(16, true);
+        const blockType = dataView.getUint8(20);
+        const itemCount = dataView.getUint16(22, true);
+        const starts = new Int32Array(itemCount);
+        const ends = new Int32Array(itemCount);
+        const scores = new Float32Array(itemCount);
+        if (!req) {
+            switch (blockType) {
+                case 1: {
+                    let offset = 24;
+                    for (let i = 0; i < itemCount; i++) {
+                        starts[i] = dataView.getInt32(offset, true);
+                        ends[i] = dataView.getInt32(offset + 4, true);
+                        scores[i] = dataView.getFloat32(offset + 8, true);
+                        offset += 12;
+                    }
+                    return { starts, ends, scores };
+                }
+                case 2: {
+                    let offset = 24;
+                    for (let i = 0; i < itemCount; i++) {
+                        const start = dataView.getInt32(offset, true);
+                        starts[i] = start;
+                        ends[i] = start + itemSpan;
+                        scores[i] = dataView.getFloat32(offset + 4, true);
+                        offset += 8;
+                    }
+                    return { starts, ends, scores };
+                }
+                case 3: {
+                    let offset = 24;
+                    for (let i = 0; i < itemCount; i++) {
+                        const start = blockStart + i * itemStep;
+                        starts[i] = start;
+                        ends[i] = start + itemSpan;
+                        scores[i] = dataView.getFloat32(offset, true);
+                        offset += 4;
+                    }
+                    return { starts, ends, scores };
+                }
+            }
+            return { starts, ends, scores };
+        }
+        const reqStart = req.start;
+        const reqEnd = req.end;
+        let idx = 0;
+        switch (blockType) {
+            case 1: {
+                let offset = 24;
+                for (let i = 0; i < itemCount; i++) {
+                    const start = dataView.getInt32(offset, true);
+                    const end = dataView.getInt32(offset + 4, true);
+                    if (start < reqEnd && end >= reqStart) {
+                        starts[idx] = start;
+                        ends[idx] = end;
+                        scores[idx] = dataView.getFloat32(offset + 8, true);
+                        idx++;
+                    }
+                    offset += 12;
+                }
+                break;
+            }
+            case 2: {
+                let offset = 24;
+                for (let i = 0; i < itemCount; i++) {
+                    const start = dataView.getInt32(offset, true);
+                    const end = start + itemSpan;
+                    if (start < reqEnd && end >= reqStart) {
+                        starts[idx] = start;
+                        ends[idx] = end;
+                        scores[idx] = dataView.getFloat32(offset + 4, true);
+                        idx++;
+                    }
+                    offset += 8;
+                }
+                break;
+            }
+            case 3: {
+                let offset = 24;
+                for (let i = 0; i < itemCount; i++) {
+                    const start = blockStart + i * itemStep;
+                    const end = start + itemSpan;
+                    if (start < reqEnd && end >= reqStart) {
+                        starts[idx] = start;
+                        ends[idx] = end;
+                        scores[idx] = dataView.getFloat32(offset, true);
+                        idx++;
+                    }
+                    offset += 4;
+                }
+                break;
+            }
+        }
+        if (idx < itemCount) {
+            return {
+                starts: starts.subarray(0, idx),
+                ends: ends.subarray(0, idx),
+                scores: scores.subarray(0, idx),
+            };
+        }
+        return { starts, ends, scores };
+    }
     async readFeatures(observer, blocks, opts = {}) {
         try {
             const { blockType, uncompressBufSize } = this;
@@ -410,21 +516,12 @@ export class BlockView {
             else {
                 for (const block of localBlocks) {
                     const blockData = data.subarray(block.offset, block.offset + block.length);
-                    const features = this.parseBigWigBlock(blockData, 0, request);
-                    if (features.length > 0) {
-                        const starts = new Int32Array(features.length);
-                        const ends = new Int32Array(features.length);
-                        const scores = new Float32Array(features.length);
-                        for (let i = 0; i < features.length; i++) {
-                            const f = features[i];
-                            starts[i] = f.start;
-                            ends[i] = f.end;
-                            scores[i] = f.score;
-                        }
-                        allStarts.push(starts);
-                        allEnds.push(ends);
-                        allScores.push(scores);
-                        totalCount += features.length;
+                    const result = this.parseBigWigBlockAsArrays(blockData, 0, request);
+                    if (result.starts.length > 0) {
+                        allStarts.push(result.starts);
+                        allEnds.push(result.ends);
+                        allScores.push(result.scores);
+                        totalCount += result.starts.length;
                     }
                 }
             }

package/esm/block-view.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/esm/unzip.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/esm/wasm/inflate-wasm-inlined.d.ts CHANGED Viewed

@@ -1,19 +1,18 @@
-declare function d(A: any, Q: any, I: any, g: any, C: any, B: any): Promise<{
+export function decompressAndParseBigWig(inputs: any, inputOffsets: any, inputLengths: any, maxBlockSize: any, reqStart: any, reqEnd: any): Promise<{
     starts: Int32Array<any>;
     ends: Int32Array<any>;
     scores: Float32Array<any>;
 }>;
-declare function r(A: any, Q: any, I: any, g: any, C: any, B: any, E: any): Promise<{
+export function decompressAndParseSummary(inputs: any, inputOffsets: any, inputLengths: any, maxBlockSize: any, reqChrId: any, reqStart: any, reqEnd: any): Promise<{
     starts: Int32Array<any>;
     ends: Int32Array<any>;
     scores: Float32Array<any>;
     minScores: Float32Array<any>;
     maxScores: Float32Array<any>;
 }>;
-declare function n(A: any, Q: any): Promise<any>;
-declare function e(A: any, Q: any, I: any, g: any): Promise<{
-    data: any;
+export function inflateRaw(input: any, outputSize: any): Promise<Uint8Array<ArrayBufferLike>>;
+export function inflateRawBatch(inputs: any, inputOffsets: any, inputLengths: any, maxOutputSize: any): Promise<{
+    data: Uint8Array<ArrayBufferLike>;
     offsets: any[];
 }>;
-declare function H(A: any): Promise<any>;
-export { d as decompressAndParseBigWig, r as decompressAndParseSummary, n as inflateRaw, e as inflateRawBatch, H as inflateRawUnknownSize };
+export function inflateRawUnknownSize(input: any): Promise<Uint8Array<ArrayBufferLike>>;