@gmod/bbi 8.1.1 → 9.0.0

package/src/bigbed.ts

@@ -1,11 +1,9 @@
 import AbortablePromiseCache from '@gmod/abortable-promise-cache'
 import QuickLRU from '@jbrowse/quick-lru'
-import { Observable, firstValueFrom, merge } from 'rxjs'
-import { map, reduce } from 'rxjs/operators'
 
 import { BBI } from './bbi.ts'
 
-import type { Feature, RequestOptions } from './types.ts'
+import type { RequestOptions } from './types.ts'
 import type { GenericFilehandle } from 'generic-filehandle2'
 
 const decoder = new TextDecoder('utf8')
@@ -24,10 +22,6 @@ interface Index {
   field: number
 }
 
-export function filterUndef<T>(ts: (T | undefined)[]): T[] {
-  return ts.filter((t: T | undefined): t is T => !!t)
-}
-
 function getTabField(str: string, fieldIndex: number) {
   if (fieldIndex < 0) {
     return undefined
@@ -67,11 +61,9 @@ async function readBPlusTreeNode(
   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
+  const nodeType = dataView.getInt8(0)
+  const cnt = dataView.getInt16(2, true)
+  let offset = 4
 
   // Non-leaf node (nodeType === 0): contains keys and child node pointers for navigation
   if (nodeType === 0) {
@@ -186,13 +178,8 @@ export class BigBed extends BBI {
     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)
-    offset += 2
-    const count = dataView.getUint16(offset, true)
-    offset += 2
-    const dataOffset = Number(dataView.getBigUint64(offset, true))
-    offset += 8
+    const count = dataView.getUint16(2, true)
+    const dataOffset = Number(dataView.getBigUint64(4, true))
 
     // no extra index is defined if count==0
     if (count === 0) {
@@ -208,14 +195,10 @@ export class BigBed extends BBI {
     for (let i = 0; i < count; i += 1) {
       const b = buffer.subarray(i * blocklen)
       const dataView = new DataView(b.buffer, b.byteOffset, b.length)
-      let offset = 0
-      const type = dataView.getInt16(offset, true)
-      offset += 2
-      const fieldcount = dataView.getInt16(offset, true)
-      offset += 2
-      const dataOffset = Number(dataView.getBigUint64(offset, true))
-      offset += 8 + 4 // skip 8-byte offset + 4 reserved bytes
-      const field = dataView.getInt16(offset, true)
+      const type = dataView.getInt16(0, true)
+      const fieldcount = dataView.getInt16(2, true)
+      const dataOffset = Number(dataView.getBigUint64(4, true))
+      const field = dataView.getInt16(16, true)
       indices.push({
         type,
         fieldcount,
@@ -249,17 +232,9 @@ export class BigBed extends BBI {
       const b = await this.bbi.read(32, offset2, opts)
 
       const dataView = new DataView(b.buffer, b.byteOffset, b.length)
-      let offset = 0
-      // const _magic = dataView.getInt32(offset, true)
-      offset += 4
-      const blockSize = dataView.getInt32(offset, true)
-      offset += 4
-      const keySize = dataView.getInt32(offset, true)
-      offset += 4
-      const valSize = dataView.getInt32(offset, true)
-      offset += 4
-      // const _itemCount = Number(dataView.getBigUint64(offset, true))
-      offset += 8
+      const blockSize = dataView.getInt32(4, true)
+      const keySize = dataView.getInt32(8, true)
+      const valSize = dataView.getInt32(12, true)
 
       return readBPlusTreeNode(
         this.bbi,
@@ -272,7 +247,8 @@ export class BigBed extends BBI {
         opts,
       )
     })
-    return filterUndef(await Promise.all(locs))
+    const results = await Promise.all(locs)
+    return results.filter((l): l is Loc => l !== undefined)
   }
 
   /*
@@ -292,23 +268,14 @@ export class BigBed extends BBI {
       return []
     }
     const view = await this.getUnzoomedView(opts)
-    const res = blocks.map(block => {
-      return new Observable<Feature[]>(observer => {
-        view.readFeatures(observer, [block], opts).catch((e: unknown) => {
-          observer.error(e)
-        })
-      }).pipe(
-        reduce((acc, curr) => {
-          acc.push(...curr)
-          return acc
-        }, [] as Feature[]),
-        map(features => features.map(f => ({ ...f, field: block.field }))),
-      )
-    })
-    const ret = await firstValueFrom(merge(...res))
-    // Filter to features where the indexed field matches the search name
+    const results = await Promise.all(
+      blocks.map(async block => {
+        const features = await view.readFeatures([block], opts)
+        return features.map(f => ({ ...f, field: block.field }))
+      }),
+    )
     // field offset is adjusted by -3 to account for chrom, chromStart, chromEnd columns
-    return ret.filter(f => {
+    return results.flat().filter(f => {
       if (!f.rest) {
         return false
       }

package/src/bigwig.ts

@@ -1,5 +1,4 @@
 import { BBI } from './bbi.ts'
-import { BlockView } from './block-view.ts'
 
 import type { RequestOptions } from './types.ts'
 
@@ -21,8 +20,7 @@ export class BigWig extends BBI {
     for (let i = maxLevel; i >= 0; i -= 1) {
       const zh = zoomLevels[i]
       if (zh && zh.reductionLevel <= 2 * basesPerPx) {
-        return new BlockView(
-          this.bbi,
+        return this.getOrCreateBlockView(
           refsByName,
           zh.indexOffset,
           uncompressBufSize,