scran.js
Version:
Single cell RNA-seq analysis in Javascript
782 lines (695 loc) • 30.1 kB
JavaScript
import * as gc from "./gc.js";
import * as wasm from "./wasm.js";
import * as utils from "./utils.js";
import { ScranMatrix } from "./ScranMatrix.js";
import * as wa from "wasmarrays.js";
import * as init from "./initializeMatrixFromArrays.js";
/**************************************************
**************************************************/
/**
* Wrapper around a labelled reference dataset on the Wasm heap, typically produced by {@linkcode loadLabelCellsReferenceFromBuffers}.
* @hideconstructor
*/
class LoadedLabelCellsReference {
#id;
#reference;
constructor(id, raw) {
this.#id = id;
this.#reference = raw;
return;
}
// Internal use only, not documented.
get reference() {
return this.#reference;
}
/**
* @return {number} Number of samples in this dataset.
*/
numberOfSamples() {
return this.#reference.num_samples();
}
/**
* @return {number} Number of features in this dataset.
*/
numberOfFeatures() {
return this.#reference.num_features();
}
/**
* @return {number} Number of labels in this dataset.
*/
numberOfLabels() {
return this.#reference.num_labels();
}
/**
* @return Frees the memory allocated on the Wasm heap for this object.
* This invalidates this object and all references to it.
*/
free() {
if (this.#reference !== null) {
gc.release(this.#id);
this.#reference = null;
}
}
}
/**
* Load a reference dataset for annotation in {@linkecode labelCells}.
* The reference should be represented by several files, the contents of which are described in the [**singlepp_loaders** documentation](https://github.com/SingleR-inc/singlepp_loaders).
*
* @param {Uint8Array|Uint8WasmArray} ranks - Buffer containing the Gzipped CSV file containing a matrix of ranks.
* Each line corresponds to a sample and contains a comma-separated vector of ranks across all features.
* All lines should contain the same number of entries.
* This is effectively a row-major matrix where rows are samples and columns are features.
* (Advanced users may note that this is transposed in C++.)
* @param {Uint8Array|Uint8WasmArray} markers - Buffer containing the Gzipped GMT file containing the markers for each pairwise comparison between labels.
* For `markers`, the GMT format is a tab-separated file with possibly variable numbers of fields for each line.
* Each line corresponds to a pairwise comparison between labels, defined by the first two fields.
* The remaining fields should contain indices of marker features (referring to columns of `matrix`) that are upregulated in the first label when compared to the second.
* Markers should be sorted in order of decreasing strength.
* @param {Uint8Array|Uint8WasmArray} labels - Buffer containing the Gzipped text file containing the label for each sample.
* Each line should contain an integer representing a particular label, from `[0, N)` where `N` is the number of unique labels.
* The number of lines should be equal to the number of rows in `matrix`.
* The actual names of the labels are usually held elsewhere.
*
* @return {LoadedLabelCellsReference} Object containing the reference dataset.
*/
export function loadLabelCellsReferenceFromBuffers(ranks, markers, labels) {
var output;
var matbuf;
var markbuf;
var labbuf;
try {
matbuf = utils.wasmifyArray(ranks, "Uint8WasmArray");
markbuf = utils.wasmifyArray(markers, "Uint8WasmArray");
labbuf = utils.wasmifyArray(labels, "Uint8WasmArray");
output = gc.call(
module => module.load_singlepp_reference(labbuf.offset, labbuf.length, markbuf.offset, markbuf.length, matbuf.offset, matbuf.length),
LoadedLabelCellsReference
);
} catch (e) {
utils.free(output);
throw e;
} finally {
utils.free(matbuf);
utils.free(markbuf);
utils.free(labbuf);
}
return output;
}
/**************************************************
**************************************************/
/**
* Wrapper around a built labelled reference dataset on the Wasm heap, typically produced by {@linkcode trainLabelCellsReference}.
* @hideconstructor
*/
class TrainedLabelCellsReference {
#id;
#reference;
constructor(id, raw, expected_features) {
this.#id = id;
this.#reference = raw;
this.expectedNumberOfFeatures = expected_features;
return;
}
// internal use only.
get reference() {
return this.#reference;
}
/**
* @return {number} Number of shared features between the test and reference datasets.
*/
numberOfFeatures() {
return this.#reference.num_features();
}
/**
* @return {number} Number of labels in this dataset.
*/
numberOfLabels() {
return this.#reference.num_labels();
}
/**
* @return Frees the memory allocated on the Wasm heap for this object.
* This invalidates this object and all references to it.
*/
free() {
if (this.#reference !== null) {
gc.release(this.#id);
this.#reference = null;
}
}
}
/**
* @ignore
*/
export function intersectFeatures(testFeatures, referenceFeatures) { // exported only for testing purposes.
let registry = new Map;
for (var i = 0; i < testFeatures.length; i++) {
let id = testFeatures[i];
if (id !== null && !registry.has(id)) { // first hit gets the preference.
registry.set(id, i);
}
}
let tkeep = [], rkeep = [];
for (var i = 0; i < referenceFeatures.length; i++) {
let id = referenceFeatures[i];
if (id == null) {
continue;
}
if (!Array.isArray(id)) {
if (registry.has(id)) {
tkeep.push(registry.get(id));
registry.delete(id); // deleting to avoid a future match to the same ID, as the intersection must be unique in its first/second hits.
rkeep.push(i);
}
} else { // otherwise, it's an array of multiple synonymous gene names.
for (const xid of id) {
if (registry.has(xid)) {
tkeep.push(registry.get(xid));
registry.delete(xid);
rkeep.push(i);
break;
}
}
}
}
return { "test": tkeep, "reference": rkeep };
}
/**
* Train a reference dataset for annotation in {@linkcode labelCells}.
* The build process involves harmonizing the identities of the features available in the test dataset compared to the reference.
* Specifically, a feature must be present in both datasets in order to be retained.
* Of those features in the intersection, only the `top` markers from each pairwise comparison are ultimately used for classification.
*
* Needless to say, `testFeatures` should match up to the rows of the {@linkplain ScranMatrix} that is actually used for annotation in {@linkcode labelCells}.
*
* @param {Array} testFeatures - An array of feature identifiers (usually strings) of length equal to the number of rows in the test matrix.
* Each entry should contain the identifier for the corresponding row of the test matrix.
* Any `null` entries are considered to be incomparable.
* @param {LoadedLabelCellsReference} loadedReference - A reference dataset, typically loaded with {@linkcode loadLabelCellsReferenceFromBuffers}.
* @param {Array} referenceFeatures - An array of feature identifiers (usually strings) of length equal to the number of features in `reference`.
* Each entry may also be an array of synonymous identifiers, in which case the first identifier that matches to an entry of `features` is used.
* Contents of `referenceFeatures` are expected to exhibit some overlap with identifiers in `testFeatures`.
* Any `null` entries are considered to be incomparable.
* If multiple entries of `referenceFeatures` match to the same feature in `features`, only the first matching entry is used and the rest are ignored.
* @param {object} [options={}] - Optional parameters.
* @param {number} [options.top=20] - Number of top marker features to use.
* These features are taken from each pairwise comparison between labels.
* @param {?number} [options.numberOfThreads=null] - Number of threads to use.
* If `null`, defaults to {@linkcode maximumThreads}.
*
* @return {TrainedLabelCellsReference} Object containing the built reference dataset.
*/
export function trainLabelCellsReference(testFeatures, loadedReference, referenceFeatures, options = {}) {
const { top = 20, numberOfThreads = null, ...others } = options;
utils.checkOtherOptions(others);
var test_id_buffer;
var ref_id_buffer;
var output;
let nthreads = utils.chooseNumberOfThreads(numberOfThreads);
if (referenceFeatures.length != loadedReference.numberOfFeatures()) {
throw new Error("length of 'referenceFeatures' should be equal to the number of features in 'loadedReference'");
}
const intersection = intersectFeatures(testFeatures, referenceFeatures);
try {
test_id_buffer = utils.wasmifyArray(intersection.test, "Int32WasmArray");
ref_id_buffer = utils.wasmifyArray(intersection.reference, "Int32WasmArray");
output = gc.call(
module => module.train_singlepp_reference(
test_id_buffer.length,
test_id_buffer.offset,
ref_id_buffer.offset,
loadedReference.reference,
top,
nthreads
),
TrainedLabelCellsReference,
testFeatures.length
);
} catch (e) {
utils.free(output);
throw e;
} finally {
utils.free(test_id_buffer);
utils.free(ref_id_buffer);
}
return output;
}
/**************************************************
**************************************************/
/**
* Wrapper around the cell labelling results on the Wasm heap, typically produced by {@linkcode labelCells}.
* @hideconstructor
*/
class LabelCellsResults {
#id;
#results;
constructor(id, raw) {
this.#id = id;
this.#results = raw;
return;
}
/**
* @return {number} Number of labels used in {@linkcode labelCells}.
*/
numberOfLabels() {
return this.#results.num_labels();
}
/**
* @return {number} Number of cells that were labelled.
*/
numberOfCells() {
return this.#results.num_samples();
}
/**
* @param {object} [options={}] - Optional parameters.
* @param {boolean|string} [options.copy=true] - Copying mode, see {@linkcode possibleCopy} for details.
* @return {Int32Array|Int32WasmArray} Array of length equal to the number of cells,
* containing the index of the best label for each cell.
*/
predicted(options = {}) {
const { copy = true, ...others } = options;
utils.checkOtherOptions(others);
return utils.possibleCopy(this.#results.best(), copy);
}
/**
* @param {number} i - Index of the cell of interest.
* @param {object} [options={}] - Optional parameters.
* @param {boolean} [options.asTypedArray=true] - Whether to return a Float64Array.
* If `false`, a Float64WasmArray is returned instead.
* @param {?Float64WasmArray} [options.buffer=null] - Buffer in which to store the output.
* This should have the same length as the {@linkcode LabelCellsResults#numberOfLabels numberOfLabels}.
*
* @return {Float64Array|Float64WasmArray} Array containing the scores for this cell across all labels.
* If `buffer` is supplied, the function returns `buffer` if `asTypedArray = false`, or a view on `buffer` if `asTypedArray = true`.
*/
scoreForCell(i, options = {}) {
let { asTypedArray = true, buffer = null, ...others } = options;
utils.checkOtherOptions(others);
let tmp = null;
try {
if (buffer == null) {
tmp = utils.createFloat64WasmArray(this.#results.num_labels());
buffer = tmp;
}
this.#results.score_for_sample(i, buffer.offset);
} catch (e) {
utils.free(tmp);
throw e;
}
return utils.toTypedArray(buffer, tmp == null, asTypedArray);
}
/**
* @param {number} i - Index of the label of interest.
* @param {object} [options={}] - Optional parameters.
* @param {boolean|string} [options.copy=true] - Copying mode, see {@linkcode possibleCopy} for details.
* Only used if `buffer` is not supplied.
* @return {Float64Array|Float64WasmArray} Array containing the scores across all cells for this label.
*/
scoreForLabel(i, options = {}) {
const { copy = true, ...others } = options;
utils.checkOtherOptions(others);
return utils.possibleCopy(this.#results.score_for_label(i), copy);
}
/**
* @param {object} [options={}] - Optional parameters.
* @param {boolean|string} [options.copy=true] - Copying mode, see {@linkcode possibleCopy} for details.
* @return {Float64Array|Float64WasmArray} Array of length equal to the number of cells,
* containing the difference in scores between the best and second-best labels.
*/
delta(options = {}) {
const { copy = true, ...others } = options;
utils.checkOtherOptions(others);
return utils.possibleCopy(this.#results.delta(), copy);
}
/**
* @return Frees the memory allocated on the Wasm heap for this object.
* This invalidates this object and all references to it.
*/
free() {
if (this.#results !== null) {
gc.release(this.#id);
this.#results = null;
}
}
}
/**
* Label cells based on similarity in expression to a reference dataset.
* This uses the [**SingleR** algorithm](https://github.com/SingleR-inc/singlepp) for cell type annotation.
*
* @param {ScranMatrix} x - The count matrix, or log-normalized matrix, containing features in the rows and cells in the columns.
* @param {BuildLabelledReferenceResults} reference - A built reference dataset, typically generated by {@linkcode buildLabelledReference}.
* @param {object} [options={}] - Optional parameters.
* @param {number} [options.quantile=0.8] - Quantile on the correlations to use to compute the score for each label.
* @param {?number} [options.numberOfThreads=null] - Number of threads to use.
* If `null`, defaults to {@linkcode maximumThreads}.
*
* @return {LabelCellsResults} Labelling results for each cell in `x`.
*/
export function labelCells(x, reference, options = {}) {
const { numberOfFeatures = null, numberOfCells = null, quantile = 0.8, numberOfThreads = null, ...others } = options;
utils.checkOtherOptions(others);
var output = null;
var matbuf;
var tempmat;
let nthreads = utils.chooseNumberOfThreads(numberOfThreads);
try {
let target;
if (x instanceof ScranMatrix) {
target = x.matrix;
} else if (x instanceof wa.Float64WasmArray) {
// Back-compatibility only.
tempmat = init.initializeDenseMatrixFromDenseArray(numberOfFeatures, numberOfCells, x, { forceInteger: false });
target = tempmat.matrix;
} else {
throw new Error("unknown type for 'x'");
}
if (target.nrow() != reference.expectedNumberOfFeatures) {
throw new Error("number of rows in 'x' should be equal to length of 'features' used to build 'reference'");
}
output = gc.call(
module => module.run_singlepp(target, reference.reference, quantile, nthreads),
LabelCellsResults
);
} finally {
utils.free(matbuf);
utils.free(tempmat);
}
return output;
}
/**************************************************
**************************************************/
/**
* Wrapper around integrated reference datasets on the Wasm heap, typically produced by {@linkcode integrateLabelledReferences}.
* @hideconstructor
*/
class IntegratedLabelCellsReferences {
#id;
#integrated;
constructor(id, raw, expected_features) {
this.#id = id;
this.#integrated = raw;
this.expectedNumberOfFeatures = expected_features;
return;
}
// Internal use only, not documented.
get integrated() {
return this.#integrated;
}
/**
* @return {number} Number of reference datasets.
*/
numberOfReferences() {
return this.#integrated.num_references();
}
/**
* @return Frees the memory allocated on the Wasm heap for this object.
* This invalidates this object and all references to it.
*/
free() {
if (this.#integrated !== null) {
gc.release(this.#id);
this.#integrated = null;
}
}
}
/**
* Prepare a classifier that integrates multiple reference datasets.
* This allows users to choose the best label for a test cell based on its classifications in multiple references.
*
* @param {Array} testFeatures - An array of feature identifiers (usually strings) of length equal to the number of rows in the test matrix.
* Each entry should contain a single identifier for the corresponding row of the test matrix.
* Any `null` entries are considered to be incomparable.
* If any entries are duplicated, only the first occurrence is used and the rest are ignored.
* @param {Array} loadedReferences - Array of {@linkplain LoadedLabelCellsReference} objects, typically created with {@linkcode loadLabelCellsReferenceFromBuffers}.
* @param {Array} referenceFeatures - Array of length equal to `loadedReferences`,
* containing arrays of feature identifiers (usually strings) of length equal to the number of features the corresponding entry of `loadedReferences`.
* Each entry may also be an array of synonymous identifiers, in which case the first identifier that matches to an entry of `testFeatures` is used.
* Contents of `referenceFeatures` are expected to exhibit some overlap with identifiers in `testFeatures`.
* Any `null` entries are considered to be incomparable.
* If multiple entries of `referenceFeatures` match to the same feature in `testFeatures`, only the first matching entry is used and the rest are ignored.
* @param {Array} trainedReferences - Array of {@linkplain TrainedLabelCellsReference} objects, typically generated by calling {@linkcode trainLabelCellsReference}
* on the same `testFeatures` and the corresponding entries of `loadedReferences` and `referenceFeatures`.
* This should have length equal to that of `loadedReferences`.
* @param {object} [options={}] - Optional parameters.
* @param {?number} [options.numberOfThreads=null] - Number of threads to use.
* If `null`, defaults to {@linkcode maximumThreads}.
*
* @return {IntegratedLabelCellsReference} Object containing the integrated references.
*/
export function integrateLabelCellsReferences(testFeatures, loadedReferences, referenceFeatures, trainedReferences, options = {}) {
const { numberOfThreads = null, ...others } = options;
utils.checkOtherOptions(others);
let interlen_arr;
let test_id_arr = [];
let test_id_ptr_arr;
let ref_id_arr = [];
let ref_id_ptr_arr;
let loaded_arr;
let trained_arr;
let output;
let nthreads = utils.chooseNumberOfThreads(numberOfThreads);
// Checking the inputs.
let nrefs = loadedReferences.length;
if (referenceFeatures.length != nrefs) {
throw new Error("'loadedReferences' and 'referenceFeatures' should be of the same length");
}
if (trainedReferences.length != nrefs) {
throw new Error("'loadedReferences' and 'trainedReferences' should be of the same length");
}
for (var i = 0; i < nrefs; i++) {
if (loadedReferences[i].numberOfFeatures() != referenceFeatures[i].length) {
throw new Error("length of each 'referenceFeatures' should be equal to the number of features in the corresponding 'loadedReferences'");
}
}
try {
for (var i = 0; i < nrefs; i++) {
const intersection = intersectFeatures(testFeatures, referenceFeatures[i]);
test_id_arr.push(utils.wasmifyArray(intersection.test, "Int32WasmArray"));
ref_id_arr.push(utils.wasmifyArray(intersection.reference, "Int32WasmArray"));
}
loaded_arr = utils.createBigUint64WasmArray(nrefs);
trained_arr = utils.createBigUint64WasmArray(nrefs);
test_id_ptr_arr = utils.createBigUint64WasmArray(nrefs);
ref_id_ptr_arr = utils.createBigUint64WasmArray(nrefs);
interlen_arr = utils.createInt32WasmArray(nrefs);
{
let la = loaded_arr.array();
let ta = trained_arr.array();
let tia = test_id_ptr_arr.array();
let ria = ref_id_ptr_arr.array();
let ia = interlen_arr.array();
for (var i = 0; i < nrefs; i++) {
la[i] = BigInt(loadedReferences[i].reference.$$.ptr);
ta[i] = BigInt(trainedReferences[i].reference.$$.ptr);
tia[i] = BigInt(test_id_arr[i].offset);
ria[i] = BigInt(ref_id_arr[i].offset);
ia[i] = test_id_arr[i].length;
}
}
output = gc.call(
module => module.integrate_singlepp_references(
nrefs,
interlen_arr.offset,
test_id_ptr_arr.offset,
ref_id_ptr_arr.offset,
loaded_arr.offset,
trained_arr.offset,
nthreads
),
IntegratedLabelCellsReferences,
testFeatures.length
);
} catch (e) {
utils.free(output);
throw e;
} finally {
for (const x of test_id_arr) {
utils.free(x);
}
for (const x of ref_id_arr) {
utils.free(x);
}
utils.free(test_id_ptr_arr);
utils.free(ref_id_ptr_arr);
utils.free(loaded_arr);
utils.free(trained_arr);
}
return output;
}
/**************************************************
**************************************************/
/**
* Wrapper around the integrated cell labelling results on the Wasm heap, typically produced by {@linkcode integrateLabelCells}.
* @hideconstructor
*/
class IntegrateLabelCellsResults {
#id
#results;
constructor(id, raw) {
this.#id = id;
this.#results = raw;
return;
}
/**
* @return {number} Number of labels used in {@linkcode integratedLabelCells}.
*/
numberOfReferences() {
return this.#results.num_references();
}
/**
* @return {number} Number of cells that were labelled.
*/
numberOfCells() {
return this.#results.num_samples();
}
/**
* @param {object} [options={}] - Optional parameters.
* @param {boolean|string} [options.copy=true] - Copying mode, see {@linkcode possibleCopy} for details.
*
* @return {Int32Array|Int32WasmArray} Array of length equal to the number of cells,
* containing the index of the best reference for each cell.
*/
predicted(options = {}) {
const { copy = true, ...others } = options;
utils.checkOtherOptions(others);
return utils.possibleCopy(this.#results.best(), copy);
}
/**
* @param {number} i - Index of the cell of interest.
* @param {object} [options={}] - Optional parameters.
* @param {boolean} [options.asTypedArray=true] - Whether to return a Float64Array.
* If `false`, a Float64WasmArray is returned instead.
* @param {?Float64WasmArray} [options.buffer=null] - Buffer in which to store the output.
* This should have the same length as the {@linkcode IntegrateLabelCellsResults#numberOfReferences numberOfReferences}.
*
* @return {Float64Array|Float64WasmArray} Array containing the scores for this cell across all labels.
* If `buffer` is supplied, the function returns `buffer` if `asTypedArray = false`, or a view on `buffer` if `asTypedArray = true`.
*/
scoreForCell(i, options = {}) {
let { asTypedArray = true, buffer = null, ...others } = options;
utils.checkOtherOptions(others);
let tmp;
try {
if (buffer == null) {
tmp = utils.createFloat64WasmArray(this.#results.num_references());
buffer = tmp;
}
this.#results.score_for_sample(i, buffer.offset);
} catch (e) {
utils.free(tmp);
throw e;
}
return utils.toTypedArray(buffer, tmp == null, asTypedArray);
}
/**
* @param {number} i - Index of the reference of interest.
* @param {object} [options={}] - Optional parameters.
* @param {boolean|string} [options.copy=true] - Copying mode, see {@linkcode possibleCopy} for details.
*
* @return {Float64Array|Float64WasmArray} Array containing the scores across all cells for this label.
*/
scoreForReference(i, options = {}) {
const { copy = true, ...others } = options;
utils.checkOtherOptions(others);
return utils.possibleCopy(this.#results.score_for_reference(i), copy);
}
/**
* @param {object} [options={}] - Optional parameters.
* @param {boolean|string} [options.copy=true] - Copying mode, see {@linkcode possibleCopy} for details.
*
* @return {Float64Array|Float64WasmArray} Array of length equal to the number of cells,
* containing the difference in scores between the best and second-best references.
*/
delta(options = {}) {
const { copy = true, ...others } = options;
utils.checkOtherOptions(others);
return utils.possibleCopy(this.#results.delta(), copy);
}
/**
* @return Frees the memory allocated on the Wasm heap for this object.
* This invalidates this object and all references to it.
*/
free() {
if (this.#results !== null) {
gc.release(this.#id);
this.#results = null;
}
}
}
/**
* Integrate cell labels across multiple reference datasets.
*
* @param {ScranMatrix} x - The count matrix, or log-normalized matrix, containing features in the rows and cells in the columns.
* @param {IntegratedLabelCellsReferences} integrated - An integrated set of reference datasets, typically generated by {@linkcode integrateLabelCellsReferences}.
* @param {Array} assigned - An array of length equal to the number of references in `integrated`.
* This should contain the result of classification of `x` with each individual reference via {@linkcode labelCells}.
* Each element should be a {@linkplain LabelCellsResults} object; or an Array, TypedArray or Int32WasmArray of length equal to the number of cells in `x`.
* @param {object} [options={}] - Optional parameters.
* @param {number} [options.quantile=0.8] - Quantile on the correlations to use to compute the score for each label.
* @param {?number} [options.numberOfThreads=null] - Number of threads to use.
* If `null`, defaults to {@linkcode maximumThreads}.
*
* @return {IntegrateLabelCellsResults} Integrated labelling results for each cell in `x`.
*/
export function integrateLabelCells(x, assigned, integrated, options = {}) {
const { numberOfFeatures = null, numberOfCells = null, quantile = 0.8, numberOfThreads = null, ...others } = options;
utils.checkOtherOptions(others);
let nrefs = integrated.numberOfReferences();
if (assigned.length != nrefs) {
throw new Error("length of 'assigned' should be equal to the number of references in 'integrated'");
}
let output;
var matbuf;
var tempmat;
let assigned_ptrs;
let assigned_arrs = new Array(nrefs);
let nthreads = utils.chooseNumberOfThreads(numberOfThreads);
try {
let target;
if (x instanceof ScranMatrix) {
target = x.matrix;
} else if (x instanceof wa.Float64WasmArray) {
// Back-compatibility only.
tempmat = init.initializeDenseMatrixFromDenseArray(numberOfFeatures, numberOfCells, x, { sparse: false, forceInteger: false });
target = tempmat.matrix;
} else {
throw new Error("unknown type for 'x'");
}
if (target.nrow() != integrated.expectedNumberOfFeatures) {
throw new Error("number of rows in 'x' should be equal to length of 'features' used to build 'reference'");
}
assigned_ptrs = utils.createBigUint64WasmArray(nrefs);
let assigned_ptr_arr = assigned_ptrs.array();
for (var i = 0; i < assigned.length; i++) {
let current = assigned[i];
if (current instanceof LabelCellsResults) {
current = current.predicted({ copy: "view" });
}
if (current.length != x.numberOfColumns()) {
throw new Error("length of each element in 'assigned' should be equal to number of columns in 'x'");
}
assigned_arrs[i] = utils.wasmifyArray(current, "Int32WasmArray");
assigned_ptr_arr[i] = BigInt(assigned_arrs[i].offset);
}
output = gc.call(
module => module.integrate_singlepp(
target,
assigned_ptrs.offset,
integrated.integrated,
quantile,
nthreads
),
IntegrateLabelCellsResults
);
} catch (e) {
utils.free(output);
throw e;
} finally{
utils.free(assigned_ptrs);
for (const x of assigned_arrs) {
utils.free(x);
}
utils.free(matbuf);
utils.free(tempmat);
}
return output;
}