@gmod/bbi 7.0.5 → 8.0.0

package/esm/bigbed.js

@@ -3,17 +3,113 @@ import QuickLRU from 'quick-lru';
 import { Observable, firstValueFrom, merge } from 'rxjs';
 import { map, reduce } from 'rxjs/operators';
 import { BBI } from "./bbi.js";
+const decoder = new TextDecoder('utf8');
 export function filterUndef(ts) {
     return ts.filter((t) => !!t);
 }
-export class BigBed extends BBI {
-    constructor() {
-        super(...arguments);
-        this.readIndicesCache = new AbortablePromiseCache({
-            cache: new QuickLRU({ maxSize: 1 }),
-            fill: (args, signal) => this._readIndices({ ...args, signal }),
-        });
+function getTabField(str, fieldIndex) {
+    if (fieldIndex < 0) {
+        return undefined;
+    }
+    let start = 0;
+    for (let i = 0; i < fieldIndex; i++) {
+        start = str.indexOf('\t', start);
+        if (start === -1) {
+            return undefined;
+        }
+        start++;
+    }
+    const end = str.indexOf('\t', start);
+    return end === -1 ? str.slice(start) : str.slice(start, end);
+}
+// 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));
+}
+// 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
+async function readBPlusTreeNode(bbi, nodeOffset, blockSize, keySize, valSize, name, field, opts) {
+    const len = 4 + blockSize * (keySize + valSize);
+    const buffer = await bbi.read(len, nodeOffset, opts);
+    const dataView = new DataView(buffer.buffer, buffer.byteOffset, buffer.length);
+    let offset = 0;
+    const nodeType = dataView.getInt8(offset);
+    offset += 2; // skip nodeType byte + 1 reserved byte
+    const cnt = dataView.getInt16(offset, true);
+    offset += 2;
+    // Non-leaf node (nodeType === 0): contains keys and child node pointers for navigation
+    if (nodeType === 0) {
+        const leafkeys = [];
+        for (let i = 0; i < cnt; i++) {
+            const key = parseKey(buffer, offset, keySize);
+            offset += keySize;
+            const dataOffset = Number(dataView.getBigUint64(offset, true));
+            offset += 8;
+            leafkeys.push({
+                key,
+                offset: dataOffset,
+            });
+        }
+        // Binary search to find the appropriate child node
+        let left = 0;
+        let right = leafkeys.length - 1;
+        let targetIndex = leafkeys.length - 1;
+        while (left <= right) {
+            const mid = Math.floor((left + right) / 2);
+            const cmp = name.localeCompare(leafkeys[mid].key);
+            if (cmp < 0) {
+                targetIndex = mid - 1;
+                right = mid - 1;
+            }
+            else {
+                left = mid + 1;
+            }
+        }
+        const childOffset = targetIndex >= 0 ? leafkeys[targetIndex].offset : leafkeys[0].offset;
+        return readBPlusTreeNode(bbi, childOffset, blockSize, keySize, valSize, name, field, opts);
+    }
+    else if (nodeType === 1) {
+        // Leaf node (nodeType === 1): contains actual key-value data
+        const keys = [];
+        for (let i = 0; i < cnt; i++) {
+            const key = parseKey(buffer, offset, keySize);
+            offset += keySize;
+            const dataOffset = Number(dataView.getBigUint64(offset, true));
+            offset += 8;
+            const length = dataView.getUint32(offset, true);
+            offset += 4;
+            offset += 4; // skip reserved
+            keys.push({
+                key,
+                offset: dataOffset,
+                length,
+            });
+        }
+        // Binary search for exact key match in sorted leaf node
+        let left = 0;
+        let right = keys.length - 1;
+        while (left <= right) {
+            const mid = Math.floor((left + right) / 2);
+            const cmp = name.localeCompare(keys[mid].key);
+            if (cmp === 0) {
+                return { ...keys[mid], field };
+            }
+            else if (cmp < 0) {
+                right = mid - 1;
+            }
+            else {
+                left = mid + 1;
+            }
+        }
+        return undefined;
     }
+}
+export class BigBed extends BBI {
+    readIndicesCache = new AbortablePromiseCache({
+        cache: new QuickLRU({ maxSize: 1 }),
+        fill: (args, signal) => this._readIndices({ ...args, signal }),
+    });
     readIndices(opts = {}) {
         const { signal, ...rest } = opts;
         return this.readIndicesCache.get(JSON.stringify(rest), opts, signal);
@@ -33,7 +129,7 @@ export class BigBed extends BBI {
      */
     async _readIndices(opts) {
         const { extHeaderOffset } = await this.getHeader(opts);
-        const b = await this.bbi.read(64, Number(extHeaderOffset));
+        const b = await this.bbi.read(64, extHeaderOffset);
         const dataView = new DataView(b.buffer, b.byteOffset, b.length);
         let offset = 0;
         // const _size = dataView.getUint16(offset, true)
@@ -48,7 +144,7 @@ export class BigBed extends BBI {
         }
         const blocklen = 20;
         const len = blocklen * count;
-        const buffer = await this.bbi.read(len, Number(dataOffset));
+        const buffer = await this.bbi.read(len, dataOffset);
         const indices = [];
         for (let i = 0; i < count; i += 1) {
             const b = buffer.subarray(i * blocklen);
@@ -59,9 +155,14 @@ export class BigBed extends BBI {
             const fieldcount = dataView.getInt16(offset, true);
             offset += 2;
             const dataOffset = Number(dataView.getBigUint64(offset, true));
-            offset += 8 + 4; //4 skip
+            offset += 8 + 4; // skip 8-byte offset + 4 reserved bytes
             const field = dataView.getInt16(offset, true);
-            indices.push({ type, fieldcount, offset: Number(dataOffset), field });
+            indices.push({
+                type,
+                fieldcount,
+                offset: dataOffset,
+                field,
+            });
         }
         return indices;
     }
@@ -80,7 +181,6 @@ export class BigBed extends BBI {
         if (indices.length === 0) {
             return [];
         }
-        const decoder = new TextDecoder('utf8');
         const locs = indices.map(async (index) => {
             const { offset: offset2, field } = index;
             const b = await this.bbi.read(32, offset2, opts);
@@ -96,72 +196,7 @@ export class BigBed extends BBI {
             offset += 4;
             // const _itemCount = Number(dataView.getBigUint64(offset, true))
             offset += 8;
-            const bptReadNode = async (nodeOffset) => {
-                const val = Number(nodeOffset);
-                const len = 4 + blockSize * (keySize + valSize);
-                const buffer = await this.bbi.read(len, val, opts);
-                const b = buffer;
-                const dataView = new DataView(b.buffer, b.byteOffset, b.length);
-                let offset = 0;
-                const nodeType = dataView.getInt8(offset);
-                offset += 2; //skip 1
-                const cnt = dataView.getInt16(offset, true);
-                offset += 2;
-                const keys = [];
-                if (nodeType === 0) {
-                    const leafkeys = [];
-                    for (let i = 0; i < cnt; i++) {
-                        const key = decoder
-                            .decode(b.subarray(offset, offset + keySize))
-                            .replaceAll('\0', '');
-                        offset += keySize;
-                        const dataOffset = Number(dataView.getBigUint64(offset, true));
-                        offset += 8;
-                        leafkeys.push({
-                            key,
-                            offset: dataOffset,
-                        });
-                    }
-                    let lastOffset = 0;
-                    for (const { key, offset } of leafkeys) {
-                        if (name.localeCompare(key) < 0 && lastOffset) {
-                            return bptReadNode(lastOffset);
-                        }
-                        lastOffset = offset;
-                    }
-                    return bptReadNode(lastOffset);
-                }
-                else if (nodeType === 1) {
-                    for (let i = 0; i < cnt; i++) {
-                        const key = decoder
-                            .decode(b.subarray(offset, offset + keySize))
-                            .replaceAll('\0', '');
-                        offset += keySize;
-                        const dataOffset = Number(dataView.getBigUint64(offset, true));
-                        offset += 8;
-                        const length = dataView.getUint32(offset, true);
-                        offset += 4;
-                        const reserved = dataView.getUint32(offset, true);
-                        offset += 4;
-                        keys.push({
-                            key,
-                            offset: dataOffset,
-                            length,
-                            reserved,
-                        });
-                    }
-                    for (const n of keys) {
-                        if (n.key === name) {
-                            return {
-                                ...n,
-                                field,
-                            };
-                        }
-                    }
-                    return undefined;
-                }
-            };
-            return bptReadNode(offset2 + 32);
+            return readBPlusTreeNode(this.bbi, offset2 + 32, blockSize, keySize, valSize, name, field, opts);
         });
         return filterUndef(await Promise.all(locs));
     }
@@ -172,7 +207,7 @@ export class BigBed extends BBI {
      *
      * @param name - the name to search for
      *
-     * @param opts - options object with optional AboutSignal
+     * @param opts - options object with optional AbortSignal
      *
      * @return array of Feature
      */
@@ -187,15 +222,21 @@ export class BigBed extends BBI {
                 view.readFeatures(observer, [block], opts).catch((e) => {
                     observer.error(e);
                 });
-            }).pipe(reduce((acc, curr) => acc.concat(curr)), map(x => {
-                for (const element of x) {
-                    element.field = block.field;
-                }
-                return x;
-            }));
+            }).pipe(reduce((acc, curr) => {
+                acc.push(...curr);
+                return acc;
+            }, []), map(features => features.map(f => ({ ...f, field: block.field }))));
         });
         const ret = await firstValueFrom(merge(...res));
-        return ret.filter(f => f.rest?.split('\t')[(f.field || 0) - 3] === name);
+        // Filter to features where the indexed field matches the search name
+        // field offset is adjusted by -3 to account for chrom, chromStart, chromEnd columns
+        return ret.filter(f => {
+            if (!f.rest) {
+                return false;
+            }
+            const fieldIndex = (f.field || 0) - 3;
+            return getTabField(f.rest, fieldIndex) === name;
+        });
     }
 }
 //# sourceMappingURL=bigbed.js.map

package/esm/bigbed.js.map

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+{"version":3,"file":"bigbed.js","sourceRoot":"","sources":["../src/bigbed.ts"],"names":[],"mappings":"AAAA,OAAO,qBAAqB,MAAM,+BAA+B,CAAA;AACjE,OAAO,QAAQ,MAAM,WAAW,CAAA;AAChC,OAAO,EAAE,UAAU,EAAE,cAAc,EAAE,KAAK,EAAE,MAAM,MAAM,CAAA;AACxD,OAAO,EAAE,GAAG,EAAE,MAAM,EAAE,MAAM,gBAAgB,CAAA;AAE5C,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAK9B,MAAM,OAAO,GAAG,IAAI,WAAW,CAAC,MAAM,CAAC,CAAA;AAgBvC,MAAM,UAAU,WAAW,CAAI,EAAqB;IAClD,OAAO,EAAE,CAAC,MAAM,CAAC,CAAC,CAAgB,EAAU,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAA;AACrD,CAAC;AAED,SAAS,WAAW,CAAC,GAAW,EAAE,UAAkB;IAClD,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;QACnB,OAAO,SAAS,CAAA;IAClB,CAAC;IACD,IAAI,KAAK,GAAG,CAAC,CAAA;IACb,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,EAAE,CAAC,EAAE,EAAE,CAAC;QACpC,KAAK,GAAG,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,KAAK,CAAC,CAAA;QAChC,IAAI,KAAK,KAAK,CAAC,CAAC,EAAE,CAAC;YACjB,OAAO,SAAS,CAAA;QAClB,CAAC;QACD,KAAK,EAAE,CAAA;IACT,CAAC;IACD,MAAM,GAAG,GAAG,GAAG,CAAC,OAAO,CAAC,IAAI,EAAE,KAAK,CAAC,CAAA;IACpC,OAAO,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,EAAE,GAAG,CAAC,CAAA;AAC9D,CAAC;AAED,0DAA0D;AAC1D,SAAS,QAAQ,CAAC,MAAkB,EAAE,MAAc,EAAE,OAAe;IACnE,MAAM,MAAM,GAAG,MAAM,CAAC,OAAO,CAAC,CAAC,EAAE,MAAM,CAAC,CAAA;IACxC,OAAO,OAAO,CAAC,MAAM,CACnB,MAAM,CAAC,QAAQ,CAAC,MAAM,EAAE,MAAM,KAAK,CAAC,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,GAAG,OAAO,CAAC,CACnE,CAAA;AACH,CAAC;AAED,yFAAyF;AACzF,0EAA0E;AAC1E,KAAK,UAAU,iBAAiB,CAC9B,GAAsB,EACtB,UAAkB,EAClB,SAAiB,EACjB,OAAe,EACf,OAAe,EACf,IAAY,EACZ,KAAa,EACb,IAAoB;IAEpB,MAAM,GAAG,GAAG,CAAC,GAAG,SAAS,GAAG,CAAC,OAAO,GAAG,OAAO,CAAC,CAAA;IAC/C,MAAM,MAAM,GAAG,MAAM,GAAG,CAAC,IAAI,CAAC,GAAG,EAAE,UAAU,EAAE,IAAI,CAAC,CAAA;IACpD,MAAM,QAAQ,GAAG,IAAI,QAAQ,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,UAAU,EAAE,MAAM,CAAC,MAAM,CAAC,CAAA;IAC9E,IAAI,MAAM,GAAG,CAAC,CAAA;IACd,MAAM,QAAQ,GAAG,QAAQ,CAAC,OAAO,CAAC,MAAM,CAAC,CAAA;IACzC,MAAM,IAAI,CAAC,CAAA,CAAC,uCAAuC;IACnD,MAAM,GAAG,GAAG,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;IAC3C,MAAM,IAAI,CAAC,CAAA;IAEX,uFAAuF;IACvF,IAAI,QAAQ,KAAK,CAAC,EAAE,CAAC;QACnB,MAAM,QAAQ,GAAG,EAAE,CAAA;QACnB,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;YAC7B,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YAC7C,MAAM,IAAI,OAAO,CAAA;YACjB,MAAM,UAAU,GAAG,MAAM,CAAC,QAAQ,CAAC,YAAY,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC,CAAA;YAC9D,MAAM,IAAI,CAAC,CAAA;YACX,QAAQ,CAAC,IAAI,CAAC;gBACZ,GAAG;gBACH,MAAM,EAAE,UAAU;aACnB,CAAC,CAAA;QACJ,CAAC;QAED,mDAAmD;QACnD,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,KAAK,GAAG,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAA;QAC/B,IAAI,WAAW,GAAG,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAA;QAErC,OAAO,IAAI,IAAI,KAAK,EAAE,CAAC;YACrB,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAA;YAC1C,MAAM,GAAG,GAAG,IAAI,CAAC,aAAa,CAAC,QAAQ,CAAC,GAAG,CAAE,CAAC,GAAG,CAAC,CAAA;YAElD,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACZ,WAAW,GAAG,GAAG,GAAG,CAAC,CAAA;gBACrB,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;YACjB,CAAC;iBAAM,CAAC;gBACN,IAAI,GAAG,GAAG,GAAG,CAAC,CAAA;YAChB,CAAC;QACH,CAAC;QAED,MAAM,WAAW,GACf,WAAW,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,WAAW,CAAE,CAAC,MAAM,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAE,CAAC,MAAM,CAAA;QACxE,OAAO,iBAAiB,CACtB,GAAG,EACH,WAAW,EACX,SAAS,EACT,OAAO,EACP,OAAO,EACP,IAAI,EACJ,KAAK,EACL,IAAI,CACL,CAAA;IACH,CAAC;SAAM,IAAI,QAAQ,KAAK,CAAC,EAAE,CAAC;QAC1B,6DAA6D;QAC7D,MAAM,IAAI,GAAG,EAAE,CAAA;QACf,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,GAAG,EAAE,CAAC,EAAE,EAAE,CAAC;YAC7B,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,EAAE,MAAM,EAAE,OAAO,CAAC,CAAA;YAC7C,MAAM,IAAI,OAAO,CAAA;YACjB,MAAM,UAAU,GAAG,MAAM,CAAC,QAAQ,CAAC,YAAY,CAAC,MAAM,EAAE,IAAI,CAAC,CAAC,CAAA;YAC9D,MAAM,IAAI,CAAC,CAAA;YACX,MAAM,MAAM,GAAG,QAAQ,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,CAAC,CAAA;YAC/C,MAAM,IAAI,CAAC,CAAA;YACX,MAAM,IAAI,CAAC,CAAA,CAAC,gBAAgB;YAC5B,IAAI,CAAC,IAAI,CAAC;gBACR,GAAG;gBACH,MAAM,EAAE,UAAU;gBAClB,MAAM;aACP,CAAC,CAAA;QACJ,CAAC;QAED,wDAAwD;QACxD,IAAI,IAAI,GAAG,CAAC,CAAA;QACZ,IAAI,KAAK,GAAG,IAAI,CAAC,MAAM,GAAG,CAAC,CAAA;QAE3B,OAAO,IAAI,IAAI,KAAK,EAAE,CAAC;YACrB,MAAM,GAAG,GAAG,IAAI,CAAC,KAAK,CAAC,CAAC,IAAI,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,CAAA;YAC1C,MAAM,GAAG,GAAG,IAAI,CAAC,aAAa,CAAC,IAAI,CAAC,GAAG,CAAE,CAAC,GAAG,CAAC,CAAA;YAE9C,IAAI,GAAG,KAAK,CAAC,EAAE,CAAC;gBACd,OAAO,EAAE,GAAG,IAAI,CAAC,GAAG,CAAE,EAAE,KAAK,EAAE,CAAA;YACjC,CAAC;iBAAM,IAAI,GAAG,GAAG,CAAC,EAAE,CAAC;gBACnB,KAAK,GAAG,GAAG,GAAG,CAAC,CAAA;YACjB,CAAC;iBAAM,CAAC;gBACN,IAAI,GAAG,GAAG,GAAG,CAAC,CAAA;YAChB,CAAC;QACH,CAAC;QAED,OAAO,SAAS,CAAA;IAClB,CAAC;AACH,CAAC;AAED,MAAM,OAAO,MAAO,SAAQ,GAAG;IACtB,gBAAgB,GAAG,IAAI,qBAAqB,CAA0B;QAC3E,KAAK,EAAE,IAAI,QAAQ,CAAC,EAAE,OAAO,EAAE,CAAC,EAAE,CAAC;QACnC,IAAI,EAAE,CAAC,IAAoB,EAAE,MAAoB,EAAE,EAAE,CACnD,IAAI,CAAC,YAAY,CAAC,EAAE,GAAG,IAAI,EAAE,MAAM,EAAE,CAAC;KACzC,CAAC,CAAA;IAEK,WAAW,CAAC,OAAuB,EAAE;QAC1C,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,EAAE,GAAG,IAAI,CAAA;QAChC,OAAO,IAAI,CAAC,gBAAgB,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,MAAM,CAAC,CAAA;IACtE,CAAC;IAED;;OAEG;IACO,KAAK,CAAC,OAAO,CAAC,MAAc,EAAE,IAAqB;QAC3D,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;IAED;;;;;;OAMG;IACK,KAAK,CAAC,YAAY,CAAC,IAAoB;QAC7C,MAAM,EAAE,eAAe,EAAE,GAAG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package/esm/bigwig.js

@@ -15,9 +15,8 @@ export class BigWig extends BBI {
         const maxLevel = zoomLevels.length - 1;
         for (let i = maxLevel; i >= 0; i -= 1) {
             const zh = zoomLevels[i];
-            // eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
             if (zh && zh.reductionLevel <= 2 * basesPerPx) {
-                return new BlockView(this.bbi, refsByName, zh.indexOffset, uncompressBufSize > 0, 'summary');
+                return new BlockView(this.bbi, refsByName, zh.indexOffset, uncompressBufSize, 'summary');
             }
         }
         return this.getUnzoomedView(opts);

package/esm/bigwig.js.map

@@ -1 +1 @@
-{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAC9B,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAI3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,iBAAiB,EAAE,GACjD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,MAAM,QAAQ,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAEtC,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,uEAAuE;YACvE,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBAC9C,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,EAAE,CAAC,WAAW,EACd,iBAAiB,GAAG,CAAC,EACrB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}
+{"version":3,"file":"bigwig.js","sourceRoot":"","sources":["../src/bigwig.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,GAAG,EAAE,MAAM,UAAU,CAAA;AAC9B,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAA;AAI3C,MAAM,OAAO,MAAO,SAAQ,GAAG;IAC7B;;;;;;;OAOG;IACO,KAAK,CAAC,OAAO,CAAC,KAAa,EAAE,IAAoB;QACzD,MAAM,EAAE,UAAU,EAAE,UAAU,EAAE,iBAAiB,EAAE,GACjD,MAAM,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,CAAA;QAC5B,MAAM,UAAU,GAAG,CAAC,GAAG,KAAK,CAAA;QAC5B,MAAM,QAAQ,GAAG,UAAU,CAAC,MAAM,GAAG,CAAC,CAAA;QAEtC,KAAK,IAAI,CAAC,GAAG,QAAQ,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC,IAAI,CAAC,EAAE,CAAC;YACtC,MAAM,EAAE,GAAG,UAAU,CAAC,CAAC,CAAC,CAAA;YACxB,IAAI,EAAE,IAAI,EAAE,CAAC,cAAc,IAAI,CAAC,GAAG,UAAU,EAAE,CAAC;gBAC9C,OAAO,IAAI,SAAS,CAClB,IAAI,CAAC,GAAG,EACR,UAAU,EACV,EAAE,CAAC,WAAW,EACd,iBAAiB,EACjB,SAAS,CACV,CAAA;YACH,CAAC;QACH,CAAC;QACD,OAAO,IAAI,CAAC,eAAe,CAAC,IAAI,CAAC,CAAA;IACnC,CAAC;CACF"}

package/esm/block-view.d.ts

@@ -1,4 +1,5 @@
 import type { Feature } from './types.ts';
+import type { BigWigFeatureArrays, SummaryFeatureArrays } from './unzip.ts';
 import type { GenericFilehandle } from 'generic-filehandle2';
 import type { Observer } from 'rxjs';
 interface CoordRequest {
@@ -19,12 +20,12 @@ interface Options {
 export declare class BlockView {
     private bbi;
     private refsByName;
-    private cirTreeOffset;
-    private isCompressed;
+    private rTreeOffset;
+    private uncompressBufSize;
     private blockType;
-    private cirTreePromise?;
+    private rTreePromise?;
     private featureCache;
-    constructor(bbi: GenericFilehandle, refsByName: any, cirTreeOffset: number, isCompressed: boolean, blockType: string);
+    constructor(bbi: GenericFilehandle, refsByName: Record<string, number>, rTreeOffset: number, uncompressBufSize: number, blockType: string);
     readWigData(chrName: string, start: number, end: number, observer: Observer<Feature[]>, opts?: Options): Promise<void>;
     private parseSummaryBlock;
     private parseBigBedBlock;
@@ -33,5 +34,13 @@ export declare class BlockView {
         offset: number;
         length: number;
     }[], opts?: Options): Promise<void>;
+    readBigWigFeaturesAsArrays(blocks: {
+        offset: number;
+        length: number;
+    }[], opts?: Options): Promise<BigWigFeatureArrays>;
+    readSummaryFeaturesAsArrays(blocks: {
+        offset: number;
+        length: number;
+    }[], opts?: Options): Promise<SummaryFeatureArrays>;
 }
 export {};