supercat666's picture
add igv
78c921d
raw
history blame
14.2 kB
// Licensed to the Apache Software Foundation (ASF) under one
// or more contributor license agreements. See the NOTICE file
// distributed with this work for additional information
// regarding copyright ownership. The ASF licenses this file
// to you under the Apache License, Version 2.0 (the
// "License"); you may not use this file except in compliance
// with the License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing,
// software distributed under the License is distributed on an
// "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
// KIND, either express or implied. See the License for the
// specific language governing permissions and limitations
// under the License.
import { encodeUtf8 } from '../util/utf8.js';
import { TypedArray, TypedArrayConstructor, BigIntArrayConstructor } from '../interfaces.js';
import { isPromise, isIterable, isAsyncIterable, isIteratorResult, isFlatbuffersByteBuffer, BigInt64Array, BigUint64Array } from './compat.js';
import { ByteBuffer } from 'flatbuffers';
/** @ignore */
const SharedArrayBuf = (typeof SharedArrayBuffer !== 'undefined' ? SharedArrayBuffer : ArrayBuffer);
/** @ignore */
function collapseContiguousByteRanges(chunks: Uint8Array[]) {
const result = chunks[0] ? [chunks[0]] : [];
let xOffset: number, yOffset: number, xLen: number, yLen: number;
for (let x, y, i = 0, j = 0, n = chunks.length; ++i < n;) {
x = result[j];
y = chunks[i];
// continue if x and y don't share the same underlying ArrayBuffer, or if x isn't before y
if (!x || !y || x.buffer !== y.buffer || y.byteOffset < x.byteOffset) {
y && (result[++j] = y);
continue;
}
({ byteOffset: xOffset, byteLength: xLen } = x);
({ byteOffset: yOffset, byteLength: yLen } = y);
// continue if the byte ranges of x and y aren't contiguous
if ((xOffset + xLen) < yOffset || (yOffset + yLen) < xOffset) {
y && (result[++j] = y);
continue;
}
result[j] = new Uint8Array(x.buffer, xOffset, yOffset - xOffset + yLen);
}
return result;
}
/** @ignore */
export function memcpy<TTarget extends ArrayBufferView, TSource extends ArrayBufferView>(target: TTarget, source: TSource, targetByteOffset = 0, sourceByteLength = source.byteLength) {
const targetByteLength = target.byteLength;
const dst = new Uint8Array(target.buffer, target.byteOffset, targetByteLength);
const src = new Uint8Array(source.buffer, source.byteOffset, Math.min(sourceByteLength, targetByteLength));
dst.set(src, targetByteOffset);
return target;
}
/** @ignore */
export function joinUint8Arrays(chunks: Uint8Array[], size?: number | null): [Uint8Array, Uint8Array[], number] {
// collapse chunks that share the same underlying ArrayBuffer and whose byte ranges overlap,
// to avoid unnecessarily copying the bytes to do this buffer join. This is a common case during
// streaming, where we may be reading partial byte ranges out of the same underlying ArrayBuffer
const result = collapseContiguousByteRanges(chunks);
const byteLength = result.reduce((x, b) => x + b.byteLength, 0);
let source: Uint8Array, sliced: Uint8Array, buffer: Uint8Array | void;
let offset = 0, index = -1;
const length = Math.min(size || Number.POSITIVE_INFINITY, byteLength);
for (const n = result.length; ++index < n;) {
source = result[index];
sliced = source.subarray(0, Math.min(source.length, length - offset));
if (length <= (offset + sliced.length)) {
if (sliced.length < source.length) {
result[index] = source.subarray(sliced.length);
} else if (sliced.length === source.length) { index++; }
buffer ? memcpy(buffer, sliced, offset) : (buffer = sliced);
break;
}
memcpy(buffer || (buffer = new Uint8Array(length)), sliced, offset);
offset += sliced.length;
}
return [buffer || new Uint8Array(0), result.slice(index), byteLength - (buffer ? buffer.byteLength : 0)];
}
/** @ignore */
export type ArrayBufferViewInput = ArrayBufferView | ArrayBufferLike | ArrayBufferView | Iterable<number> | ArrayLike<number> | ByteBuffer | string | null | undefined |
IteratorResult<ArrayBufferView | ArrayBufferLike | ArrayBufferView | Iterable<number> | ArrayLike<number> | ByteBuffer | string | null | undefined> |
ReadableStreamReadResult<ArrayBufferView | ArrayBufferLike | ArrayBufferView | Iterable<number> | ArrayLike<number> | ByteBuffer | string | null | undefined>;
/** @ignore */
export function toArrayBufferView<
T extends TypedArrayConstructor<any> | BigIntArrayConstructor<any>
>(ArrayBufferViewCtor: any, input: ArrayBufferViewInput): InstanceType<T> {
let value: any = isIteratorResult(input) ? input.value : input;
if (value instanceof ArrayBufferViewCtor) {
if (ArrayBufferViewCtor === Uint8Array) {
// Node's `Buffer` class passes the `instanceof Uint8Array` check, but we need
// a real Uint8Array, since Buffer#slice isn't the same as Uint8Array#slice :/
return new ArrayBufferViewCtor(value.buffer, value.byteOffset, value.byteLength);
}
return value;
}
if (!value) { return new ArrayBufferViewCtor(0); }
if (typeof value === 'string') { value = encodeUtf8(value); }
if (value instanceof ArrayBuffer) { return new ArrayBufferViewCtor(value); }
if (value instanceof SharedArrayBuf) { return new ArrayBufferViewCtor(value); }
if (isFlatbuffersByteBuffer(value)) { return toArrayBufferView(ArrayBufferViewCtor, value.bytes()); }
return !ArrayBuffer.isView(value) ? ArrayBufferViewCtor.from(value) : (value.byteLength <= 0 ? new ArrayBufferViewCtor(0)
: new ArrayBufferViewCtor(value.buffer, value.byteOffset, value.byteLength / ArrayBufferViewCtor.BYTES_PER_ELEMENT));
}
/** @ignore */ export const toInt8Array = (input: ArrayBufferViewInput) => toArrayBufferView(Int8Array, input);
/** @ignore */ export const toInt16Array = (input: ArrayBufferViewInput) => toArrayBufferView(Int16Array, input);
/** @ignore */ export const toInt32Array = (input: ArrayBufferViewInput) => toArrayBufferView(Int32Array, input);
/** @ignore */ export const toBigInt64Array = (input: ArrayBufferViewInput) => toArrayBufferView(BigInt64Array, input);
/** @ignore */ export const toUint8Array = (input: ArrayBufferViewInput) => toArrayBufferView(Uint8Array, input);
/** @ignore */ export const toUint16Array = (input: ArrayBufferViewInput) => toArrayBufferView(Uint16Array, input);
/** @ignore */ export const toUint32Array = (input: ArrayBufferViewInput) => toArrayBufferView(Uint32Array, input);
/** @ignore */ export const toBigUint64Array = (input: ArrayBufferViewInput) => toArrayBufferView(BigUint64Array, input);
/** @ignore */ export const toFloat32Array = (input: ArrayBufferViewInput) => toArrayBufferView(Float32Array, input);
/** @ignore */ export const toFloat64Array = (input: ArrayBufferViewInput) => toArrayBufferView(Float64Array, input);
/** @ignore */ export const toUint8ClampedArray = (input: ArrayBufferViewInput) => toArrayBufferView(Uint8ClampedArray, input);
/** @ignore */
type ArrayBufferViewIteratorInput = Iterable<ArrayBufferViewInput> | ArrayBufferViewInput;
/** @ignore */
const pump = <T extends Iterator<any> | AsyncIterator<any>>(iterator: T) => { iterator.next(); return iterator; };
/** @ignore */
export function* toArrayBufferViewIterator<T extends TypedArray>(ArrayCtor: TypedArrayConstructor<T>, source: ArrayBufferViewIteratorInput) {
const wrap = function*<T>(x: T) { yield x; };
const buffers: Iterable<ArrayBufferViewInput> =
(typeof source === 'string') ? wrap(source)
: (ArrayBuffer.isView(source)) ? wrap(source)
: (source instanceof ArrayBuffer) ? wrap(source)
: (source instanceof SharedArrayBuf) ? wrap(source)
: !isIterable<ArrayBufferViewInput>(source) ? wrap(source) : source;
yield* pump((function* (it: Iterator<ArrayBufferViewInput, any, number | undefined>): Generator<T, void, number | undefined> {
let r: IteratorResult<any> = <any>null;
do {
r = it.next(yield toArrayBufferView(ArrayCtor, r));
} while (!r.done);
})(buffers[Symbol.iterator]()));
return new ArrayCtor();
}
/** @ignore */ export const toInt8ArrayIterator = (input: ArrayBufferViewIteratorInput) => toArrayBufferViewIterator(Int8Array, input);
/** @ignore */ export const toInt16ArrayIterator = (input: ArrayBufferViewIteratorInput) => toArrayBufferViewIterator(Int16Array, input);
/** @ignore */ export const toInt32ArrayIterator = (input: ArrayBufferViewIteratorInput) => toArrayBufferViewIterator(Int32Array, input);
/** @ignore */ export const toUint8ArrayIterator = (input: ArrayBufferViewIteratorInput) => toArrayBufferViewIterator(Uint8Array, input);
/** @ignore */ export const toUint16ArrayIterator = (input: ArrayBufferViewIteratorInput) => toArrayBufferViewIterator(Uint16Array, input);
/** @ignore */ export const toUint32ArrayIterator = (input: ArrayBufferViewIteratorInput) => toArrayBufferViewIterator(Uint32Array, input);
/** @ignore */ export const toFloat32ArrayIterator = (input: ArrayBufferViewIteratorInput) => toArrayBufferViewIterator(Float32Array, input);
/** @ignore */ export const toFloat64ArrayIterator = (input: ArrayBufferViewIteratorInput) => toArrayBufferViewIterator(Float64Array, input);
/** @ignore */ export const toUint8ClampedArrayIterator = (input: ArrayBufferViewIteratorInput) => toArrayBufferViewIterator(Uint8ClampedArray, input);
/** @ignore */
type ArrayBufferViewAsyncIteratorInput = AsyncIterable<ArrayBufferViewInput> | Iterable<ArrayBufferViewInput> | PromiseLike<ArrayBufferViewInput> | ArrayBufferViewInput;
/** @ignore */
export async function* toArrayBufferViewAsyncIterator<T extends TypedArray>(ArrayCtor: TypedArrayConstructor<T>, source: ArrayBufferViewAsyncIteratorInput): AsyncGenerator<T, T, number | undefined> {
// if a Promise, unwrap the Promise and iterate the resolved value
if (isPromise<ArrayBufferViewInput>(source)) {
return yield* toArrayBufferViewAsyncIterator(ArrayCtor, await source);
}
const wrap = async function*<T>(x: T) { yield await x; };
const emit = async function* <T extends Iterable<any>>(source: T) {
yield* pump((function* (it: Iterator<any>) {
let r: IteratorResult<any> = <any>null;
do {
r = it.next(yield r?.value);
} while (!r.done);
})(source[Symbol.iterator]()));
};
const buffers: AsyncIterable<ArrayBufferViewInput> =
(typeof source === 'string') ? wrap(source) // if string, wrap in an AsyncIterableIterator
: (ArrayBuffer.isView(source)) ? wrap(source) // if TypedArray, wrap in an AsyncIterableIterator
: (source instanceof ArrayBuffer) ? wrap(source) // if ArrayBuffer, wrap in an AsyncIterableIterator
: (source instanceof SharedArrayBuf) ? wrap(source) // if SharedArrayBuffer, wrap in an AsyncIterableIterator
: isIterable<ArrayBufferViewInput>(source) ? emit(source) // If Iterable, wrap in an AsyncIterableIterator and compose the `next` values
: !isAsyncIterable<ArrayBufferViewInput>(source) ? wrap(source) // If not an AsyncIterable, treat as a sentinel and wrap in an AsyncIterableIterator
: source; // otherwise if AsyncIterable, use it
yield* pump((async function* (it: AsyncIterator<ArrayBufferViewInput, any, number | undefined>): AsyncGenerator<T, void, number | undefined> {
let r: IteratorResult<any> = <any>null;
do {
r = await it.next(yield toArrayBufferView(ArrayCtor, r));
} while (!r.done);
})(buffers[Symbol.asyncIterator]()));
return new ArrayCtor();
}
/** @ignore */ export const toInt8ArrayAsyncIterator = (input: ArrayBufferViewAsyncIteratorInput) => toArrayBufferViewAsyncIterator(Int8Array, input);
/** @ignore */ export const toInt16ArrayAsyncIterator = (input: ArrayBufferViewAsyncIteratorInput) => toArrayBufferViewAsyncIterator(Int16Array, input);
/** @ignore */ export const toInt32ArrayAsyncIterator = (input: ArrayBufferViewAsyncIteratorInput) => toArrayBufferViewAsyncIterator(Int32Array, input);
/** @ignore */ export const toUint8ArrayAsyncIterator = (input: ArrayBufferViewAsyncIteratorInput) => toArrayBufferViewAsyncIterator(Uint8Array, input);
/** @ignore */ export const toUint16ArrayAsyncIterator = (input: ArrayBufferViewAsyncIteratorInput) => toArrayBufferViewAsyncIterator(Uint16Array, input);
/** @ignore */ export const toUint32ArrayAsyncIterator = (input: ArrayBufferViewAsyncIteratorInput) => toArrayBufferViewAsyncIterator(Uint32Array, input);
/** @ignore */ export const toFloat32ArrayAsyncIterator = (input: ArrayBufferViewAsyncIteratorInput) => toArrayBufferViewAsyncIterator(Float32Array, input);
/** @ignore */ export const toFloat64ArrayAsyncIterator = (input: ArrayBufferViewAsyncIteratorInput) => toArrayBufferViewAsyncIterator(Float64Array, input);
/** @ignore */ export const toUint8ClampedArrayAsyncIterator = (input: ArrayBufferViewAsyncIteratorInput) => toArrayBufferViewAsyncIterator(Uint8ClampedArray, input);
/** @ignore */
export function rebaseValueOffsets(offset: number, length: number, valueOffsets: Int32Array) {
// If we have a non-zero offset, create a new offsets array with the values
// shifted by the start offset, such that the new start offset is 0
if (offset !== 0) {
valueOffsets = valueOffsets.slice(0, length + 1);
for (let i = -1; ++i <= length;) {
valueOffsets[i] += offset;
}
}
return valueOffsets;
}
/** @ignore */
export function compareArrayLike<T extends ArrayLike<any>>(a: T, b: T) {
let i = 0;
const n = a.length;
if (n !== b.length) { return false; }
if (n > 0) {
do { if (a[i] !== b[i]) { return false; } } while (++i < n);
}
return true;
}