@gmod/bbi 7.0.5 → 8.0.0

package/dist/block-view.js

@@ -9,7 +9,7 @@ const quick_lru_1 = __importDefault(require("quick-lru"));
 const range_ts_1 = __importDefault(require("./range.js"));
 const unzip_ts_1 = require("./unzip.js");
 const util_ts_1 = require("./util.js");
-const decoder = typeof TextDecoder !== 'undefined' ? new TextDecoder('utf8') : undefined;
+const decoder = new TextDecoder('utf8');
 function coordFilter(s1, e1, s2, e2) {
     return s1 < e2 && e1 >= s2;
 }
@@ -20,18 +20,30 @@ function coordFilter(s1, e1, s2, e2) {
  * Genome Explorer by Thomas Down.
  */
 class BlockView {
-    constructor(bbi, refsByName, cirTreeOffset, isCompressed, blockType) {
+    bbi;
+    refsByName;
+    rTreeOffset;
+    uncompressBufSize;
+    blockType;
+    // R-tree index header cache - R-trees are spatial data structures used to
+    // efficiently query genomic intervals by chromosome and position
+    rTreePromise;
+    featureCache = new abortable_promise_cache_1.default({
+        cache: new quick_lru_1.default({ maxSize: 1000 }),
+        fill: async ({ length, offset }, signal) => this.bbi.read(length, offset, { signal }),
+    });
+    constructor(bbi, refsByName, 
+    // Offset to the R-tree index in the file - this is part of the "cirTree"
+    // (combined ID R-tree), which combines a B+ tree for chromosome names
+    // with an R-tree for efficient spatial queries
+    rTreeOffset, uncompressBufSize, blockType) {
         this.bbi = bbi;
         this.refsByName = refsByName;
-        this.cirTreeOffset = cirTreeOffset;
-        this.isCompressed = isCompressed;
+        this.rTreeOffset = rTreeOffset;
+        this.uncompressBufSize = uncompressBufSize;
         this.blockType = blockType;
-        this.featureCache = new abortable_promise_cache_1.default({
-            cache: new quick_lru_1.default({ maxSize: 1000 }),
-            fill: async ({ length, offset }, signal) => this.bbi.read(length, offset, { signal }),
-        });
-        if (!(cirTreeOffset >= 0)) {
-            throw new Error('invalid cirTreeOffset!');
+        if (!(rTreeOffset >= 0)) {
+            throw new Error('invalid rTreeOffset!');
         }
     }
     async readWigData(chrName, start, end, observer, opts) {
@@ -39,105 +51,98 @@ class BlockView {
             const chrId = this.refsByName[chrName];
             if (chrId === undefined) {
                 observer.complete();
+                return;
             }
             const request = { chrId, start, end };
-            if (!this.cirTreePromise) {
-                this.cirTreePromise = this.bbi.read(48, this.cirTreeOffset, opts);
+            if (!this.rTreePromise) {
+                this.rTreePromise = this.bbi.read(48, this.rTreeOffset, opts);
             }
-            const buffer = await this.cirTreePromise;
-            const dataView = new DataView(buffer.buffer);
-            const cirBlockSize = dataView.getUint32(4, true);
-            let blocksToFetch = [];
+            const buffer = await this.rTreePromise;
+            const dataView = new DataView(buffer.buffer, buffer.byteOffset, buffer.length);
+            // Maximum number of children per R-tree node - used to calculate memory bounds
+            const rTreeBlockSize = dataView.getUint32(4, true);
+            const blocksToFetch = [];
             let outstanding = 0;
-            const cirFobRecur2 = (cirBlockData, offset2, level) => {
+            // R-tree leaf nodes contain the actual data blocks to fetch
+            const processLeafNode = (dataView, startOffset, count) => {
+                let offset = startOffset;
+                for (let i = 0; i < count; i++) {
+                    const startChrom = dataView.getUint32(offset, true);
+                    offset += 4;
+                    const startBase = dataView.getUint32(offset, true);
+                    offset += 4;
+                    const endChrom = dataView.getUint32(offset, true);
+                    offset += 4;
+                    const endBase = dataView.getUint32(offset, true);
+                    offset += 4;
+                    const blockOffset = Number(dataView.getBigUint64(offset, true));
+                    offset += 8;
+                    const blockSize = Number(dataView.getBigUint64(offset, true));
+                    offset += 8;
+                    if (blockIntersectsQuery({ startChrom, startBase, endBase, endChrom })) {
+                        blocksToFetch.push({
+                            offset: blockOffset,
+                            length: blockSize,
+                        });
+                    }
+                }
+            };
+            // R-tree non-leaf nodes contain pointers to child nodes
+            const processNonLeafNode = (dataView, startOffset, count, level) => {
+                const recurOffsets = [];
+                let offset = startOffset;
+                for (let i = 0; i < count; i++) {
+                    const startChrom = dataView.getUint32(offset, true);
+                    offset += 4;
+                    const startBase = dataView.getUint32(offset, true);
+                    offset += 4;
+                    const endChrom = dataView.getUint32(offset, true);
+                    offset += 4;
+                    const endBase = dataView.getUint32(offset, true);
+                    offset += 4;
+                    const blockOffset = Number(dataView.getBigUint64(offset, true));
+                    offset += 8;
+                    if (blockIntersectsQuery({ startChrom, startBase, endChrom, endBase })) {
+                        recurOffsets.push(blockOffset);
+                    }
+                }
+                if (recurOffsets.length > 0) {
+                    traverseRTree(recurOffsets, level + 1);
+                }
+            };
+            const processRTreeNode = (rTreeBlockData, offset2, level) => {
                 try {
-                    const data = cirBlockData.subarray(offset2);
-                    const b = data;
-                    const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+                    const data = rTreeBlockData.subarray(offset2);
+                    const dataView = new DataView(data.buffer, data.byteOffset, data.length);
                     let offset = 0;
                     const isLeaf = dataView.getUint8(offset);
-                    offset += 2; // 1 skip
-                    const cnt = dataView.getUint16(offset, true);
+                    offset += 2; // 1 skip for reserved byte
+                    const count = dataView.getUint16(offset, true);
                     offset += 2;
                     if (isLeaf === 1) {
-                        const blocksToFetch2 = [];
-                        for (let i = 0; i < cnt; i++) {
-                            const startChrom = dataView.getUint32(offset, true);
-                            offset += 4;
-                            const startBase = dataView.getUint32(offset, true);
-                            offset += 4;
-                            const endChrom = dataView.getUint32(offset, true);
-                            offset += 4;
-                            const endBase = dataView.getUint32(offset, true);
-                            offset += 4;
-                            const blockOffset = Number(dataView.getBigUint64(offset, true));
-                            offset += 8;
-                            const blockSize = Number(dataView.getBigUint64(offset, true));
-                            offset += 8;
-                            blocksToFetch2.push({
-                                startChrom,
-                                startBase,
-                                endBase,
-                                endChrom,
-                                blockOffset,
-                                blockSize,
-                                offset,
-                            });
-                        }
-                        blocksToFetch = blocksToFetch.concat(blocksToFetch2
-                            .filter(f => filterFeats(f))
-                            .map(l => ({
-                            offset: l.blockOffset,
-                            length: l.blockSize,
-                        })));
+                        processLeafNode(dataView, offset, count);
                     }
                     else if (isLeaf === 0) {
-                        const recurOffsets = [];
-                        for (let i = 0; i < cnt; i++) {
-                            const startChrom = dataView.getUint32(offset, true);
-                            offset += 4;
-                            const startBase = dataView.getUint32(offset, true);
-                            offset += 4;
-                            const endChrom = dataView.getUint32(offset, true);
-                            offset += 4;
-                            const endBase = dataView.getUint32(offset, true);
-                            offset += 4;
-                            const blockOffset = Number(dataView.getBigUint64(offset, true));
-                            offset += 8;
-                            recurOffsets.push({
-                                startChrom,
-                                startBase,
-                                endChrom,
-                                endBase,
-                                blockOffset,
-                                offset,
-                            });
-                        }
-                        const recurOffsets2 = recurOffsets
-                            .filter(f => filterFeats(f))
-                            .map(l => l.blockOffset);
-                        if (recurOffsets2.length > 0) {
-                            cirFobRecur(recurOffsets2, level + 1);
-                        }
+                        processNonLeafNode(dataView, offset, count, level);
                     }
                 }
                 catch (e) {
                     observer.error(e);
                 }
             };
-            const filterFeats = (b) => {
+            const blockIntersectsQuery = (b) => {
                 const { startChrom, startBase, endChrom, endBase } = b;
                 return ((startChrom < chrId || (startChrom === chrId && startBase <= end)) &&
                     (endChrom > chrId || (endChrom === chrId && endBase >= start)));
             };
-            const cirFobStartFetch = async (off, fr, level) => {
+            const fetchAndProcessRTreeBlocks = async (offsets, range, level) => {
                 try {
-                    const length = fr.max - fr.min;
-                    const offset = fr.min;
+                    const length = range.max - range.min;
+                    const offset = range.min;
                     const resultBuffer = await this.featureCache.get(`${length}_${offset}`, { length, offset }, opts?.signal);
-                    for (const element of off) {
-                        if (fr.contains(element)) {
-                            cirFobRecur2(resultBuffer, element - offset, level);
+                    for (const element of offsets) {
+                        if (range.contains(element)) {
+                            processRTreeNode(resultBuffer, element - offset, level);
                             outstanding -= 1;
                             if (outstanding === 0) {
                                 this.readFeatures(observer, blocksToFetch, {
@@ -154,34 +159,37 @@ class BlockView {
                     observer.error(e);
                 }
             };
-            const cirFobRecur = (offset, level) => {
+            const traverseRTree = (offsets, level) => {
                 try {
-                    outstanding += offset.length;
+                    outstanding += offsets.length;
                     // Upper bound on size, based on a completely full leaf node.
-                    const maxCirBlockSpan = 4 + cirBlockSize * 32;
+                    const maxRTreeBlockSpan = 4 + rTreeBlockSize * 32;
                     let spans = new range_ts_1.default([
                         {
-                            min: offset[0],
-                            max: offset[0] + maxCirBlockSpan,
+                            min: offsets[0],
+                            max: offsets[0] + maxRTreeBlockSpan,
                         },
                     ]);
-                    for (let i = 1; i < offset.length; i += 1) {
+                    for (let i = 1; i < offsets.length; i += 1) {
                         const blockSpan = new range_ts_1.default([
                             {
-                                min: offset[i],
-                                max: offset[i] + maxCirBlockSpan,
+                                min: offsets[i],
+                                max: offsets[i] + maxRTreeBlockSpan,
                             },
                         ]);
                         spans = spans.union(blockSpan);
                     }
-                    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-                    spans.getRanges().map(fr => cirFobStartFetch(offset, fr, level));
+                    spans.getRanges().forEach(range => {
+                        fetchAndProcessRTreeBlocks(offsets, range, level).catch((e) => {
+                            observer.error(e);
+                        });
+                    });
                 }
                 catch (e) {
                     observer.error(e);
                 }
             };
-            cirFobRecur([Number(this.cirTreeOffset) + 48], 1);
+            traverseRTree([this.rTreeOffset + 48], 1);
             return;
         }
         catch (e) {
@@ -193,8 +201,6 @@ class BlockView {
         let offset = startOffset;
         const dataView = new DataView(b.buffer, b.byteOffset, b.length);
         while (offset < b.byteLength) {
-            // this was extracted from looking at the runtime code generated by
-            // binary-parser
             const chromId = dataView.getUint32(offset, true);
             offset += 4;
             const start = dataView.getUint32(offset, true);
@@ -208,14 +214,10 @@ class BlockView {
             const maxScore = dataView.getFloat32(offset, true);
             offset += 4;
             const sumData = dataView.getFloat32(offset, true);
-            offset += 4;
-            // unused
-            // const sumSqData = dataView.getFloat32(offset, true)
-            offset += 4;
-            if (request
-                ? chromId === request.chrId &&
-                    coordFilter(start, end, request.start, request.end)
-                : true) {
+            offset += 8;
+            if (!request ||
+                (chromId === request.chrId &&
+                    coordFilter(start, end, request.start, request.end))) {
                 features.push({
                     start,
                     end,
@@ -231,8 +233,7 @@ class BlockView {
     parseBigBedBlock(data, startOffset, offset, request) {
         const items = [];
         let currOffset = startOffset;
-        const b = data;
-        const dataView = new DataView(b.buffer, b.byteOffset, b.length);
+        const dataView = new DataView(data.buffer, data.byteOffset, data.length);
         while (currOffset < data.byteLength) {
             const c2 = currOffset;
             const chromId = dataView.getUint32(currOffset, true);
@@ -248,19 +249,20 @@ class BlockView {
                 }
             }
             const b = data.subarray(currOffset, i);
-            const rest = decoder?.decode(b) ?? b.toString();
+            const rest = decoder.decode(b);
             currOffset = i + 1;
-            items.push({
-                chromId,
-                start,
-                end,
-                rest,
-                uniqueId: `bb-${offset + c2}`,
-            });
+            if (!request ||
+                (chromId === request.chrId &&
+                    coordFilter(start, end, request.start, request.end))) {
+                items.push({
+                    start,
+                    end,
+                    rest,
+                    uniqueId: `bb-${offset + c2}`,
+                });
+            }
         }
-        return request
-            ? items.filter((f) => coordFilter(f.start, f.end, request.start, request.end))
-            : items;
+        return items;
     }
     parseBigWigBlock(buffer, startOffset, req) {
         const b = buffer.subarray(startOffset);
@@ -277,7 +279,7 @@ class BlockView {
         offset += 2;
         const itemCount = dataView.getUint16(offset, true);
         offset += 2;
-        const items = new Array(itemCount);
+        const items = [];
         switch (blockType) {
             case 1: {
                 for (let i = 0; i < itemCount; i++) {
@@ -287,11 +289,13 @@ class BlockView {
                     offset += 4;
                     const score = dataView.getFloat32(offset, true);
                     offset += 4;
-                    items[i] = {
-                        start,
-                        end,
-                        score,
-                    };
+                    if (!req || coordFilter(start, end, req.start, req.end)) {
+                        items.push({
+                            start,
+                            end,
+                            score,
+                        });
+                    }
                 }
                 break;
             }
@@ -301,11 +305,14 @@ class BlockView {
                     offset += 4;
                     const score = dataView.getFloat32(offset, true);
                     offset += 4;
-                    items[i] = {
-                        score,
-                        start,
-                        end: start + itemSpan,
-                    };
+                    const end = start + itemSpan;
+                    if (!req || coordFilter(start, end, req.start, req.end)) {
+                        items.push({
+                            score,
+                            start,
+                            end,
+                        });
+                    }
                 }
                 break;
             }
@@ -314,36 +321,49 @@ class BlockView {
                     const score = dataView.getFloat32(offset, true);
                     offset += 4;
                     const start = blockStart + i * itemStep;
-                    items[i] = {
-                        score,
-                        start,
-                        end: start + itemSpan,
-                    };
+                    const end = start + itemSpan;
+                    if (!req || coordFilter(start, end, req.start, req.end)) {
+                        items.push({
+                            score,
+                            start,
+                            end,
+                        });
+                    }
                 }
                 break;
             }
         }
-        return req
-            ? items.filter(f => coordFilter(f.start, f.end, req.start, req.end))
-            : items;
+        return items;
     }
     async readFeatures(observer, blocks, opts = {}) {
         try {
-            const { blockType, isCompressed } = this;
+            const { blockType, uncompressBufSize } = this;
             const { signal, request } = opts;
             const blockGroupsToFetch = (0, util_ts_1.groupBlocks)(blocks);
-            (0, util_ts_1.checkAbortSignal)(signal);
             await Promise.all(blockGroupsToFetch.map(async (blockGroup) => {
-                (0, util_ts_1.checkAbortSignal)(signal);
                 const { length, offset } = blockGroup;
                 const data = await this.featureCache.get(`${length}_${offset}`, blockGroup, signal);
-                for (const block of blockGroup.blocks) {
-                    (0, util_ts_1.checkAbortSignal)(signal);
-                    let resultData = data.subarray(Number(block.offset) - Number(blockGroup.offset));
-                    if (isCompressed) {
-                        resultData = (0, unzip_ts_1.unzip)(resultData);
-                    }
-                    (0, util_ts_1.checkAbortSignal)(signal);
+                const localBlocks = blockGroup.blocks.map(block => ({
+                    offset: block.offset - blockGroup.offset,
+                    length: block.length,
+                }));
+                let decompressedData;
+                let decompressedOffsets;
+                if (uncompressBufSize > 0) {
+                    const result = await (0, unzip_ts_1.unzipBatch)(data, localBlocks, uncompressBufSize);
+                    decompressedData = result.data;
+                    decompressedOffsets = result.offsets;
+                }
+                else {
+                    decompressedData = data;
+                    decompressedOffsets = localBlocks.map(b => b.offset);
+                    decompressedOffsets.push(data.length);
+                }
+                for (let i = 0; i < blockGroup.blocks.length; i++) {
+                    const block = blockGroup.blocks[i];
+                    const start = decompressedOffsets[i];
+                    const end = decompressedOffsets[i + 1];
+                    const resultData = decompressedData.subarray(start, end);
                     switch (blockType) {
                         case 'summary': {
                             observer.next(this.parseSummaryBlock(resultData, 0, request));
@@ -354,7 +374,7 @@ class BlockView {
                             break;
                         }
                         case 'bigbed': {
-                            observer.next(this.parseBigBedBlock(resultData, 0, Number(block.offset) * (1 << 8), request));
+                            observer.next(this.parseBigBedBlock(resultData, 0, block.offset * (1 << 8), request));
                             break;
                         }
                         default: {
@@ -369,6 +389,168 @@ class BlockView {
             observer.error(e);
         }
     }
+    async readBigWigFeaturesAsArrays(blocks, opts = {}) {
+        const { uncompressBufSize } = this;
+        const { signal, request } = opts;
+        const blockGroupsToFetch = (0, util_ts_1.groupBlocks)(blocks);
+        const allStarts = [];
+        const allEnds = [];
+        const allScores = [];
+        let totalCount = 0;
+        await Promise.all(blockGroupsToFetch.map(async (blockGroup) => {
+            const { length, offset } = blockGroup;
+            const data = await this.featureCache.get(`${length}_${offset}`, blockGroup, signal);
+            const localBlocks = blockGroup.blocks.map(block => ({
+                offset: block.offset - blockGroup.offset,
+                length: block.length,
+            }));
+            if (uncompressBufSize > 0) {
+                const result = await (0, unzip_ts_1.decompressAndParseBigWigBlocks)(data, localBlocks, uncompressBufSize, request?.start ?? 0, request?.end ?? 0);
+                if (result.starts.length > 0) {
+                    allStarts.push(result.starts);
+                    allEnds.push(result.ends);
+                    allScores.push(result.scores);
+                    totalCount += result.starts.length;
+                }
+            }
+            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;
+                    }
+                }
+            }
+        }));
+        if (allStarts.length === 0) {
+            return {
+                starts: new Int32Array(0),
+                ends: new Int32Array(0),
+                scores: new Float32Array(0),
+            };
+        }
+        if (allStarts.length === 1) {
+            return {
+                starts: allStarts[0],
+                ends: allEnds[0],
+                scores: allScores[0],
+            };
+        }
+        const starts = new Int32Array(totalCount);
+        const ends = new Int32Array(totalCount);
+        const scores = new Float32Array(totalCount);
+        let offset = 0;
+        for (let i = 0; i < allStarts.length; i++) {
+            starts.set(allStarts[i], offset);
+            ends.set(allEnds[i], offset);
+            scores.set(allScores[i], offset);
+            offset += allStarts[i].length;
+        }
+        return { starts, ends, scores };
+    }
+    async readSummaryFeaturesAsArrays(blocks, opts = {}) {
+        const { uncompressBufSize } = this;
+        const { signal, request } = opts;
+        const blockGroupsToFetch = (0, util_ts_1.groupBlocks)(blocks);
+        const allStarts = [];
+        const allEnds = [];
+        const allScores = [];
+        const allMinScores = [];
+        const allMaxScores = [];
+        let totalCount = 0;
+        await Promise.all(blockGroupsToFetch.map(async (blockGroup) => {
+            const { length, offset } = blockGroup;
+            const data = await this.featureCache.get(`${length}_${offset}`, blockGroup, signal);
+            const localBlocks = blockGroup.blocks.map(block => ({
+                offset: block.offset - blockGroup.offset,
+                length: block.length,
+            }));
+            if (uncompressBufSize > 0) {
+                const result = await (0, unzip_ts_1.decompressAndParseSummaryBlocks)(data, localBlocks, uncompressBufSize, request?.chrId ?? 0, request?.start ?? 0, request?.end ?? 0);
+                if (result.starts.length > 0) {
+                    allStarts.push(result.starts);
+                    allEnds.push(result.ends);
+                    allScores.push(result.scores);
+                    allMinScores.push(result.minScores);
+                    allMaxScores.push(result.maxScores);
+                    totalCount += result.starts.length;
+                }
+            }
+            else {
+                for (const block of localBlocks) {
+                    const blockData = data.subarray(block.offset, block.offset + block.length);
+                    const features = this.parseSummaryBlock(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);
+                        const minScores = new Float32Array(features.length);
+                        const maxScores = 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 ?? 0;
+                            minScores[i] = f.minScore ?? 0;
+                            maxScores[i] = f.maxScore ?? 0;
+                        }
+                        allStarts.push(starts);
+                        allEnds.push(ends);
+                        allScores.push(scores);
+                        allMinScores.push(minScores);
+                        allMaxScores.push(maxScores);
+                        totalCount += features.length;
+                    }
+                }
+            }
+        }));
+        if (allStarts.length === 0) {
+            return {
+                starts: new Int32Array(0),
+                ends: new Int32Array(0),
+                scores: new Float32Array(0),
+                minScores: new Float32Array(0),
+                maxScores: new Float32Array(0),
+            };
+        }
+        if (allStarts.length === 1) {
+            return {
+                starts: allStarts[0],
+                ends: allEnds[0],
+                scores: allScores[0],
+                minScores: allMinScores[0],
+                maxScores: allMaxScores[0],
+            };
+        }
+        const starts = new Int32Array(totalCount);
+        const ends = new Int32Array(totalCount);
+        const scores = new Float32Array(totalCount);
+        const minScores = new Float32Array(totalCount);
+        const maxScores = new Float32Array(totalCount);
+        let offset = 0;
+        for (let i = 0; i < allStarts.length; i++) {
+            starts.set(allStarts[i], offset);
+            ends.set(allEnds[i], offset);
+            scores.set(allScores[i], offset);
+            minScores.set(allMinScores[i], offset);
+            maxScores.set(allMaxScores[i], offset);
+            offset += allStarts[i].length;
+        }
+        return { starts, ends, scores, minScores, maxScores };
+    }
 }
 exports.BlockView = BlockView;
 //# sourceMappingURL=block-view.js.map