@databio/gtars 0.7.0 → 0.8.0

package/gtars_js.d.ts

@@ -25,6 +25,102 @@ export class ChromosomeStatistics {
     readonly start_nucleotide_position: number;
 }
 
+/**
+ * Builder for computing consensus regions from multiple RegionSet objects.
+ *
+ * Usage from JS:
+ * ```js
+ * const cb = new ConsensusBuilder();
+ * cb.add(rs1);
+ * cb.add(rs2);
+ * cb.add(rs3);
+ * const result = cb.compute(); // [{chr, start, end, count}, ...]
+ * ```
+ */
+export class ConsensusBuilder {
+    free(): void;
+    [Symbol.dispose](): void;
+    add(set: RegionSet): void;
+    compute(): any;
+    constructor();
+}
+
+export class GeneModel {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Construct a GeneModel from JS arrays of region tuples.
+     *
+     * Each array contains `[chr, start, end]` or `[chr, start, end, strand]` tuples.
+     * `threeUtr` and `fiveUtr` are optional (pass `null`/`undefined`).
+     */
+    constructor(genes: any, exons: any, three_utr: any, five_utr: any);
+}
+
+export class GenomicDistAnnotation {
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Load a GenomicDistAnnotation from GDA binary bytes.
+     */
+    static fromBin(bytes: Uint8Array): GenomicDistAnnotation;
+    /**
+     * Get the gene model as a JsGeneModel.
+     *
+     * Note: this clones the gene model data since WASM ownership requires it.
+     */
+    geneModel(): GeneModel;
+    /**
+     * Build a PartitionList from the gene model and provided chrom sizes.
+     *
+     * `chrom_sizes` should be a JS object like `{"chr1": 249250621, ...}`.
+     */
+    partitionList(core_prom_size: number, prox_prom_size: number, chrom_sizes: any): PartitionList;
+    /**
+     * Derive a TssIndex from gene starts + strand.
+     *
+     * Plus/Unstranded genes → TSS at start, Minus genes → TSS at end.
+     */
+    tssIndex(): TssIndex;
+}
+
+/**
+ * A LOLA region database for enrichment testing.
+ *
+ * Built in-memory from region data — no filesystem needed.
+ */
+export class LolaRegionDB {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Extract region sets by 0-based indices as a RegionSetList.
+     *
+     * @param indices - Optional array of 0-based indices. If omitted, returns all.
+     */
+    getRegionSets(indices?: Uint32Array | null): RegionSetList;
+    /**
+     * List region set filenames.
+     */
+    listRegionSets(): string[];
+    /**
+     * Create a LolaRegionDB from an array of {regions, name} objects.
+     *
+     * @param entries - Array of { regions: [["chr1", 100, 200], ...], name: "filename.bed" }
+     */
+    constructor(entries: any);
+    /**
+     * Collection-level annotations from the RegionDB.
+     *
+     * @returns Array of objects with keys: collectionname, collector, date, source, description
+     */
+    readonly collectionAnno: any;
+    /**
+     * Number of region sets in this database.
+     */
+    readonly numRegionSets: number;
+}
+
 export class Overlapper {
     free(): void;
     [Symbol.dispose](): void;
@@ -33,6 +129,19 @@ export class Overlapper {
     constructor(universe: any, backend: string);
 }
 
+export class PartitionList {
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Build a PartitionList from a GeneModel.
+     *
+     * `chromSizes` is an optional JS object `{"chr1": 249250621, ...}` for
+     * trimming promoters at chromosome boundaries.
+     */
+    static fromGeneModel(model: GeneModel, core_prom_size: number, prox_prom_size: number, chrom_sizes: any): PartitionList;
+}
+
 export class RegionDistribution {
     private constructor();
     free(): void;
@@ -42,9 +151,27 @@ export class RegionDistribution {
 export class RegionSet {
     free(): void;
     [Symbol.dispose](): void;
+    calcNearestNeighbors(): any;
+    calcNeighborDistances(): any;
+    calcWidths(): Uint32Array;
     chromosomeStatistics(): any;
+    concat(other: RegionSet): RegionSet;
+    disjoin(): RegionSet;
+    flank(width: number, use_start: boolean, both: boolean): RegionSet;
+    gaps(): RegionSet;
+    intersect(other: RegionSet): RegionSet;
+    jaccard(other: RegionSet): number;
+    narrow(start?: number | null, end?: number | null, width?: number | null): RegionSet;
     constructor(regions: any);
+    pintersect(other: RegionSet): RegionSet;
+    promoters(upstream: number, downstream: number): RegionSet;
+    reduce(): RegionSet;
     regionDistribution(n_bins: number): any;
+    resize(width: number, fix: string): RegionSet;
+    setdiff(other: RegionSet): RegionSet;
+    shift(offset: bigint): RegionSet;
+    trim(chrom_sizes: any): RegionSet;
+    union(other: RegionSet): RegionSet;
     readonly classify: BedClassificationOutput;
     readonly firstRegion: string;
     readonly identifier: string;
@@ -53,6 +180,56 @@ export class RegionSet {
     readonly numberOfRegions: number;
 }
 
+/**
+ * A collection of RegionSets — the gtars equivalent of GRangesList.
+ */
+export class RegionSetList {
+    private constructor();
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Flatten all region sets into a single RegionSet (no merging).
+     */
+    concat(): RegionSet;
+    /**
+     * Get a region set by 0-based index.
+     */
+    get(index: number): RegionSet;
+    /**
+     * Compute pairwise Jaccard similarity for all pairs of region sets.
+     *
+     * Returns { matrix: number[][], names: string[] | null }.
+     */
+    pairwiseJaccard(): any;
+    /**
+     * Number of region sets in this list.
+     */
+    readonly length: number;
+    /**
+     * Get the names of the region sets, or null if unnamed.
+     */
+    readonly names: any;
+}
+
+export class SignalMatrix {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Load a SignalMatrix from packed binary bytes.
+     */
+    static fromBin(bytes: Uint8Array): SignalMatrix;
+    /**
+     * Construct a SignalMatrix from JS data.
+     *
+     * - `regionIds`: array of strings in `"chr_start_end"` format
+     * - `conditionNames`: array of condition/cell-type names
+     * - `values`: flat row-major array of signal values
+     * - `nRegions`: number of rows (regions)
+     * - `nConditions`: number of columns (conditions)
+     */
+    constructor(region_ids: any, condition_names: any, values: Float64Array, n_regions: number, n_conditions: number);
+}
+
 export class Tokenizer {
     free(): void;
     [Symbol.dispose](): void;
@@ -80,6 +257,48 @@ export class Tokenizer {
     readonly vocabSize: number;
 }
 
+export class TssIndex {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * Calculate signed distance from each query region to its nearest feature.
+     *
+     * Positive = feature is downstream, negative = feature is upstream.
+     * Returns an array where `null` indicates no features on that chromosome
+     * (sentinel `i64::MAX` in Rust → `null` in JS).
+     */
+    calcFeatureDistances(query: RegionSet): any;
+    /**
+     * Calculate unsigned distance from each query region to its nearest feature midpoint.
+     *
+     * Returns an array where `null` indicates no features on that chromosome
+     * (sentinel `u32::MAX` in Rust → `null` in JS).
+     */
+    calcTssDistances(query: RegionSet): any;
+    /**
+     * Build a TssIndex from a RegionSet of features (e.g. TSS sites).
+     *
+     * Clones the inner RegionSet and computes sorted midpoints per chromosome.
+     */
+    constructor(features: RegionSet);
+}
+
+/**
+ * Compute observed vs expected partition enrichment.
+ */
+export function calcExpectedPartitions(region_set: RegionSet, partition_list: PartitionList, chrom_sizes: any, bp_proportion: boolean): any;
+
+/**
+ * Classify query regions into partitions.
+ */
+export function calcPartitions(region_set: RegionSet, partition_list: PartitionList, bp_proportion: boolean): any;
+
+/**
+ * Compute summary signal: overlap query regions with a signal matrix,
+ * take MAX per condition, and compute boxplot statistics.
+ */
+export function calcSummarySignal(region_set: RegionSet, signal_matrix: SignalMatrix): any;
+
 /**
  * Canonicalize a JSON string according to RFC-8785.
  *
@@ -93,6 +312,15 @@ export class Tokenizer {
  */
 export function canonicalizeJsonString(json_str: string): string;
 
+/**
+ * Check whether the universe is appropriate for the given user sets.
+ *
+ * @param userSets - Array of arrays of [chr, start, end] tuples
+ * @param universe - Array of [chr, start, end] tuples
+ * @returns Object with column arrays: userSet, totalRegions, regionsInUniverse, coverage, manyToMany, warnings
+ */
+export function checkUniverseAppropriateness(user_sets: any, universe_regions: any): any;
+
 /**
  * Compute the MD5 digest of a string.
  *
@@ -243,6 +471,18 @@ export function fastaHasherUpdate(handle: number, chunk: Uint8Array): void;
 
 export function greet(name: string): void;
 
+/**
+ * Run LOLA enrichment analysis.
+ *
+ * @param userSets - Array of arrays of [chr, start, end] tuples
+ * @param universe - Array of [chr, start, end] tuples
+ * @param regionDb - A LolaRegionDB object
+ * @param minOverlap - Minimum bp overlap (default 1)
+ * @param direction - "enrichment" or "depletion" (default "enrichment")
+ * @returns Object with column arrays: userSet, dbSet, pValueLog, oddsRatio, support, etc.
+ */
+export function runLOLA(user_sets: any, universe_regions: any, region_db: LolaRegionDB, min_overlap?: number | null, direction?: string | null): any;
+
 /**
  * Compute a sequence digest (sha512t24u) from raw sequence data.
  *
@@ -280,11 +520,36 @@ export type InitInput = RequestInfo | URL | Response | BufferSource | WebAssembl
 
 export interface InitOutput {
     readonly memory: WebAssembly.Memory;
-    readonly greet: (a: number, b: number) => void;
+    readonly __wbg_genomicdistannotation_free: (a: number, b: number) => void;
+    readonly canonicalizeJsonString: (a: number, b: number) => [number, number, number, number];
+    readonly computeMd5: (a: number, b: number) => [number, number];
+    readonly computeSha512t24u: (a: number, b: number) => [number, number];
+    readonly digestSeqcol: (a: number, b: number) => [number, number, number];
+    readonly fastaHasherFinish: (a: number) => [number, number, number];
+    readonly fastaHasherFree: (a: number) => number;
+    readonly fastaHasherNew: () => number;
+    readonly fastaHasherProgress: (a: number) => [number, number, number];
+    readonly fastaHasherUpdate: (a: number, b: number, c: number) => [number, number];
+    readonly genomicdistannotation_fromBin: (a: number, b: number) => [number, number, number];
+    readonly genomicdistannotation_geneModel: (a: number) => number;
+    readonly genomicdistannotation_partitionList: (a: number, b: number, c: number, d: any) => [number, number, number];
+    readonly genomicdistannotation_tssIndex: (a: number) => [number, number, number];
+    readonly sequenceDigest: (a: number, b: number) => [number, number];
+    readonly sequenceMd5: (a: number, b: number) => [number, number];
+    readonly __wbg_lolaregiondb_free: (a: number, b: number) => void;
+    readonly checkUniverseAppropriateness: (a: any, b: any) => [number, number, number];
+    readonly lolaregiondb_collectionAnno: (a: number) => [number, number, number];
+    readonly lolaregiondb_getRegionSets: (a: number, b: number, c: number) => number;
+    readonly lolaregiondb_listRegionSets: (a: number) => [number, number];
+    readonly lolaregiondb_new: (a: any) => [number, number, number];
+    readonly lolaregiondb_numRegionSets: (a: number) => number;
+    readonly runLOLA: (a: any, b: any, c: number, d: number, e: number, f: number) => [number, number, number];
     readonly __wbg_bedclassificationoutput_free: (a: number, b: number) => void;
     readonly __wbg_chromosomestatistics_free: (a: number, b: number) => void;
+    readonly __wbg_consensusbuilder_free: (a: number, b: number) => void;
     readonly __wbg_regiondistribution_free: (a: number, b: number) => void;
     readonly __wbg_regionset_free: (a: number, b: number) => void;
+    readonly __wbg_regionsetlist_free: (a: number, b: number) => void;
     readonly bedclassificationoutput_bed_compliance: (a: number) => [number, number];
     readonly bedclassificationoutput_compliant_columns: (a: number) => number;
     readonly bedclassificationoutput_data_format: (a: number) => [number, number];
@@ -296,21 +561,47 @@ export interface InitOutput {
     readonly chromosomestatistics_median_region_length: (a: number) => number;
     readonly chromosomestatistics_number_of_regions: (a: number) => number;
     readonly chromosomestatistics_start_nucleotide_position: (a: number) => number;
+    readonly consensusbuilder_add: (a: number, b: number) => void;
+    readonly consensusbuilder_compute: (a: number) => [number, number, number];
+    readonly consensusbuilder_new: () => number;
+    readonly regionset_calcNearestNeighbors: (a: number) => [number, number, number];
+    readonly regionset_calcNeighborDistances: (a: number) => [number, number, number];
+    readonly regionset_calcWidths: (a: number) => [number, number];
     readonly regionset_chromosomeStatistics: (a: number) => [number, number, number];
-    readonly regionset_classify: (a: number) => number;
+    readonly regionset_classify: (a: number) => [number, number, number];
+    readonly regionset_concat: (a: number, b: number) => number;
+    readonly regionset_disjoin: (a: number) => number;
     readonly regionset_firstRegion: (a: number) => [number, number];
+    readonly regionset_flank: (a: number, b: number, c: number, d: number) => number;
+    readonly regionset_gaps: (a: number) => number;
     readonly regionset_identifier: (a: number) => [number, number];
+    readonly regionset_intersect: (a: number, b: number) => number;
+    readonly regionset_jaccard: (a: number, b: number) => number;
     readonly regionset_meanRegionWidth: (a: number) => number;
+    readonly regionset_narrow: (a: number, b: number, c: number, d: number) => number;
     readonly regionset_new: (a: any) => [number, number, number];
     readonly regionset_nucleotidesLength: (a: number) => number;
     readonly regionset_numberOfRegions: (a: number) => number;
+    readonly regionset_pintersect: (a: number, b: number) => number;
+    readonly regionset_promoters: (a: number, b: number, c: number) => number;
+    readonly regionset_reduce: (a: number) => number;
     readonly regionset_regionDistribution: (a: number, b: number) => [number, number, number];
+    readonly regionset_resize: (a: number, b: number, c: number, d: number) => number;
+    readonly regionset_setdiff: (a: number, b: number) => number;
+    readonly regionset_shift: (a: number, b: bigint) => number;
+    readonly regionset_trim: (a: number, b: any) => [number, number, number];
+    readonly regionset_union: (a: number, b: number) => number;
+    readonly regionsetlist_concat: (a: number) => number;
+    readonly regionsetlist_get: (a: number, b: number) => [number, number, number];
+    readonly regionsetlist_length: (a: number) => number;
+    readonly regionsetlist_names: (a: number) => any;
+    readonly regionsetlist_pairwiseJaccard: (a: number) => [number, number, number];
     readonly chromosomestatistics_minimum_region_length: (a: number) => number;
     readonly __wbg_overlapper_free: (a: number, b: number) => void;
+    readonly __wbg_tokenizer_free: (a: number, b: number) => void;
     readonly overlapper_find: (a: number, b: any) => [number, number, number];
     readonly overlapper_get_backend: (a: number) => [number, number];
     readonly overlapper_new: (a: any, b: number, c: number) => [number, number, number];
-    readonly __wbg_tokenizer_free: (a: number, b: number) => void;
     readonly tokenizer_bosToken: (a: number) => [number, number];
     readonly tokenizer_bosTokenId: (a: number) => number;
     readonly tokenizer_clsToken: (a: number) => [number, number];
@@ -333,17 +624,21 @@ export interface InitOutput {
     readonly tokenizer_unkToken: (a: number) => [number, number];
     readonly tokenizer_unkTokenId: (a: number) => number;
     readonly tokenizer_vocabSize: (a: number) => number;
-    readonly canonicalizeJsonString: (a: number, b: number) => [number, number, number, number];
-    readonly computeMd5: (a: number, b: number) => [number, number];
-    readonly computeSha512t24u: (a: number, b: number) => [number, number];
-    readonly digestSeqcol: (a: number, b: number) => [number, number, number];
-    readonly fastaHasherFinish: (a: number) => [number, number, number];
-    readonly fastaHasherFree: (a: number) => number;
-    readonly fastaHasherNew: () => number;
-    readonly fastaHasherProgress: (a: number) => [number, number, number];
-    readonly fastaHasherUpdate: (a: number, b: number, c: number) => [number, number];
-    readonly sequenceDigest: (a: number, b: number) => [number, number];
-    readonly sequenceMd5: (a: number, b: number) => [number, number];
+    readonly __wbg_genemodel_free: (a: number, b: number) => void;
+    readonly __wbg_partitionlist_free: (a: number, b: number) => void;
+    readonly __wbg_tssindex_free: (a: number, b: number) => void;
+    readonly calcExpectedPartitions: (a: number, b: number, c: any, d: number) => [number, number, number];
+    readonly calcPartitions: (a: number, b: number, c: number) => [number, number, number];
+    readonly genemodel_new: (a: any, b: any, c: any, d: any) => [number, number, number];
+    readonly partitionlist_fromGeneModel: (a: number, b: number, c: number, d: any) => [number, number, number];
+    readonly tssindex_calcFeatureDistances: (a: number, b: number) => [number, number, number];
+    readonly tssindex_calcTssDistances: (a: number, b: number) => [number, number, number];
+    readonly tssindex_new: (a: number) => [number, number, number];
+    readonly __wbg_signalmatrix_free: (a: number, b: number) => void;
+    readonly calcSummarySignal: (a: number, b: number) => [number, number, number];
+    readonly greet: (a: number, b: number) => void;
+    readonly signalmatrix_fromBin: (a: number, b: number) => [number, number, number];
+    readonly signalmatrix_new: (a: any, b: any, c: number, d: number, e: number, f: number) => [number, number, number];
     readonly __wbindgen_malloc: (a: number, b: number) => number;
     readonly __wbindgen_realloc: (a: number, b: number, c: number, d: number) => number;
     readonly __wbindgen_exn_store: (a: number) => void;
@@ -351,6 +646,7 @@ export interface InitOutput {
     readonly __wbindgen_externrefs: WebAssembly.Table;
     readonly __wbindgen_free: (a: number, b: number, c: number) => void;
     readonly __externref_table_dealloc: (a: number) => void;
+    readonly __externref_drop_slice: (a: number, b: number) => void;
     readonly __wbindgen_start: () => void;
 }