@databio/gtars 0.7.1 → 0.8.0

package/gtars_js.d.ts

@@ -57,6 +57,70 @@ export class GeneModel {
     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;
@@ -92,13 +156,20 @@ export class RegionSet {
     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;
@@ -109,9 +180,44 @@ 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.
      *
@@ -206,6 +312,15 @@ export function calcSummarySignal(region_set: RegionSet, signal_matrix: SignalMa
  */
 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.
  *
@@ -356,6 +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.
  *
@@ -393,11 +520,36 @@ export type InitInput = RequestInfo | URL | Response | BufferSource | WebAssembl
 
 export interface InitOutput {
     readonly memory: WebAssembly.Memory;
+    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];
@@ -416,12 +568,17 @@ export interface InitOutput {
     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;
@@ -429,40 +586,22 @@ export interface InitOutput {
     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_signalmatrix_free: (a: number, b: number) => void;
-    readonly calcSummarySignal: (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 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_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_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_tokenizer_free: (a: number, b: number) => void;
-    readonly greet: (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];
@@ -485,6 +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 __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;
@@ -492,6 +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;
 }
 

package/gtars_js.js

@@ -193,6 +193,13 @@ export class ConsensusBuilder {
 if (Symbol.dispose) ConsensusBuilder.prototype[Symbol.dispose] = ConsensusBuilder.prototype.free;
 
 export class GeneModel {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(GeneModel.prototype);
+        obj.__wbg_ptr = ptr;
+        GeneModelFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
     __destroy_into_raw() {
         const ptr = this.__wbg_ptr;
         this.__wbg_ptr = 0;
@@ -225,6 +232,158 @@ export class GeneModel {
 }
 if (Symbol.dispose) GeneModel.prototype[Symbol.dispose] = GeneModel.prototype.free;
 
+export class GenomicDistAnnotation {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(GenomicDistAnnotation.prototype);
+        obj.__wbg_ptr = ptr;
+        GenomicDistAnnotationFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        GenomicDistAnnotationFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_genomicdistannotation_free(ptr, 0);
+    }
+    /**
+     * Load a GenomicDistAnnotation from GDA binary bytes.
+     * @param {Uint8Array} bytes
+     * @returns {GenomicDistAnnotation}
+     */
+    static fromBin(bytes) {
+        const ptr0 = passArray8ToWasm0(bytes, wasm.__wbindgen_malloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.genomicdistannotation_fromBin(ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return GenomicDistAnnotation.__wrap(ret[0]);
+    }
+    /**
+     * Get the gene model as a JsGeneModel.
+     *
+     * Note: this clones the gene model data since WASM ownership requires it.
+     * @returns {GeneModel}
+     */
+    geneModel() {
+        const ret = wasm.genomicdistannotation_geneModel(this.__wbg_ptr);
+        return GeneModel.__wrap(ret);
+    }
+    /**
+     * Build a PartitionList from the gene model and provided chrom sizes.
+     *
+     * `chrom_sizes` should be a JS object like `{"chr1": 249250621, ...}`.
+     * @param {number} core_prom_size
+     * @param {number} prox_prom_size
+     * @param {any} chrom_sizes
+     * @returns {PartitionList}
+     */
+    partitionList(core_prom_size, prox_prom_size, chrom_sizes) {
+        const ret = wasm.genomicdistannotation_partitionList(this.__wbg_ptr, core_prom_size, prox_prom_size, chrom_sizes);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return PartitionList.__wrap(ret[0]);
+    }
+    /**
+     * Derive a TssIndex from gene starts + strand.
+     *
+     * Plus/Unstranded genes → TSS at start, Minus genes → TSS at end.
+     * @returns {TssIndex}
+     */
+    tssIndex() {
+        const ret = wasm.genomicdistannotation_tssIndex(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return TssIndex.__wrap(ret[0]);
+    }
+}
+if (Symbol.dispose) GenomicDistAnnotation.prototype[Symbol.dispose] = GenomicDistAnnotation.prototype.free;
+
+/**
+ * A LOLA region database for enrichment testing.
+ *
+ * Built in-memory from region data — no filesystem needed.
+ */
+export class LolaRegionDB {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        LolaRegionDBFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_lolaregiondb_free(ptr, 0);
+    }
+    /**
+     * Collection-level annotations from the RegionDB.
+     *
+     * @returns Array of objects with keys: collectionname, collector, date, source, description
+     * @returns {any}
+     */
+    get collectionAnno() {
+        const ret = wasm.lolaregiondb_collectionAnno(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    /**
+     * Extract region sets by 0-based indices as a RegionSetList.
+     *
+     * @param indices - Optional array of 0-based indices. If omitted, returns all.
+     * @param {Uint32Array | null} [indices]
+     * @returns {RegionSetList}
+     */
+    getRegionSets(indices) {
+        var ptr0 = isLikeNone(indices) ? 0 : passArray32ToWasm0(indices, wasm.__wbindgen_malloc);
+        var len0 = WASM_VECTOR_LEN;
+        const ret = wasm.lolaregiondb_getRegionSets(this.__wbg_ptr, ptr0, len0);
+        return RegionSetList.__wrap(ret);
+    }
+    /**
+     * List region set filenames.
+     * @returns {string[]}
+     */
+    listRegionSets() {
+        const ret = wasm.lolaregiondb_listRegionSets(this.__wbg_ptr);
+        var v1 = getArrayJsValueFromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
+    /**
+     * Create a LolaRegionDB from an array of {regions, name} objects.
+     *
+     * @param entries - Array of { regions: [["chr1", 100, 200], ...], name: "filename.bed" }
+     * @param {any} entries
+     */
+    constructor(entries) {
+        const ret = wasm.lolaregiondb_new(entries);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        this.__wbg_ptr = ret[0] >>> 0;
+        LolaRegionDBFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+    /**
+     * Number of region sets in this database.
+     * @returns {number}
+     */
+    get numRegionSets() {
+        const ret = wasm.lolaregiondb_numRegionSets(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+}
+if (Symbol.dispose) LolaRegionDB.prototype[Symbol.dispose] = LolaRegionDB.prototype.free;
+
 export class Overlapper {
     __destroy_into_raw() {
         const ptr = this.__wbg_ptr;
@@ -396,7 +555,10 @@ export class RegionSet {
      */
     get classify() {
         const ret = wasm.regionset_classify(this.__wbg_ptr);
-        return BedClassificationOutput.__wrap(ret);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return BedClassificationOutput.__wrap(ret[0]);
     }
     /**
      * @param {RegionSet} other
@@ -407,6 +569,13 @@ export class RegionSet {
         const ret = wasm.regionset_concat(this.__wbg_ptr, other.__wbg_ptr);
         return RegionSet.__wrap(ret);
     }
+    /**
+     * @returns {RegionSet}
+     */
+    disjoin() {
+        const ret = wasm.regionset_disjoin(this.__wbg_ptr);
+        return RegionSet.__wrap(ret);
+    }
     /**
      * @returns {string}
      */
@@ -422,6 +591,23 @@ export class RegionSet {
             wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
         }
     }
+    /**
+     * @param {number} width
+     * @param {boolean} use_start
+     * @param {boolean} both
+     * @returns {RegionSet}
+     */
+    flank(width, use_start, both) {
+        const ret = wasm.regionset_flank(this.__wbg_ptr, width, use_start, both);
+        return RegionSet.__wrap(ret);
+    }
+    /**
+     * @returns {RegionSet}
+     */
+    gaps() {
+        const ret = wasm.regionset_gaps(this.__wbg_ptr);
+        return RegionSet.__wrap(ret);
+    }
     /**
      * @returns {string}
      */
@@ -437,6 +623,15 @@ export class RegionSet {
             wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
         }
     }
+    /**
+     * @param {RegionSet} other
+     * @returns {RegionSet}
+     */
+    intersect(other) {
+        _assertClass(other, RegionSet);
+        const ret = wasm.regionset_intersect(this.__wbg_ptr, other.__wbg_ptr);
+        return RegionSet.__wrap(ret);
+    }
     /**
      * @param {RegionSet} other
      * @returns {number}
@@ -453,6 +648,16 @@ export class RegionSet {
         const ret = wasm.regionset_meanRegionWidth(this.__wbg_ptr);
         return ret;
     }
+    /**
+     * @param {number | null} [start]
+     * @param {number | null} [end]
+     * @param {number | null} [width]
+     * @returns {RegionSet}
+     */
+    narrow(start, end, width) {
+        const ret = wasm.regionset_narrow(this.__wbg_ptr, isLikeNone(start) ? 0x100000001 : (start) >>> 0, isLikeNone(end) ? 0x100000001 : (end) >>> 0, isLikeNone(width) ? 0x100000001 : (width) >>> 0);
+        return RegionSet.__wrap(ret);
+    }
     /**
      * @param {any} regions
      */
@@ -515,6 +720,17 @@ export class RegionSet {
         }
         return takeFromExternrefTable0(ret[0]);
     }
+    /**
+     * @param {number} width
+     * @param {string} fix
+     * @returns {RegionSet}
+     */
+    resize(width, fix) {
+        const ptr0 = passStringToWasm0(fix, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.regionset_resize(this.__wbg_ptr, width, ptr0, len0);
+        return RegionSet.__wrap(ret);
+    }
     /**
      * @param {RegionSet} other
      * @returns {RegionSet}
@@ -524,6 +740,14 @@ export class RegionSet {
         const ret = wasm.regionset_setdiff(this.__wbg_ptr, other.__wbg_ptr);
         return RegionSet.__wrap(ret);
     }
+    /**
+     * @param {bigint} offset
+     * @returns {RegionSet}
+     */
+    shift(offset) {
+        const ret = wasm.regionset_shift(this.__wbg_ptr, offset);
+        return RegionSet.__wrap(ret);
+    }
     /**
      * @param {any} chrom_sizes
      * @returns {RegionSet}
@@ -547,7 +771,87 @@ export class RegionSet {
 }
 if (Symbol.dispose) RegionSet.prototype[Symbol.dispose] = RegionSet.prototype.free;
 
+/**
+ * A collection of RegionSets — the gtars equivalent of GRangesList.
+ */
+export class RegionSetList {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(RegionSetList.prototype);
+        obj.__wbg_ptr = ptr;
+        RegionSetListFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        RegionSetListFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_regionsetlist_free(ptr, 0);
+    }
+    /**
+     * Flatten all region sets into a single RegionSet (no merging).
+     * @returns {RegionSet}
+     */
+    concat() {
+        const ret = wasm.regionsetlist_concat(this.__wbg_ptr);
+        return RegionSet.__wrap(ret);
+    }
+    /**
+     * Get a region set by 0-based index.
+     * @param {number} index
+     * @returns {RegionSet}
+     */
+    get(index) {
+        const ret = wasm.regionsetlist_get(this.__wbg_ptr, index);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return RegionSet.__wrap(ret[0]);
+    }
+    /**
+     * Number of region sets in this list.
+     * @returns {number}
+     */
+    get length() {
+        const ret = wasm.regionsetlist_length(this.__wbg_ptr);
+        return ret >>> 0;
+    }
+    /**
+     * Get the names of the region sets, or null if unnamed.
+     * @returns {any}
+     */
+    get names() {
+        const ret = wasm.regionsetlist_names(this.__wbg_ptr);
+        return ret;
+    }
+    /**
+     * Compute pairwise Jaccard similarity for all pairs of region sets.
+     *
+     * Returns { matrix: number[][], names: string[] | null }.
+     * @returns {any}
+     */
+    pairwiseJaccard() {
+        const ret = wasm.regionsetlist_pairwiseJaccard(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+}
+if (Symbol.dispose) RegionSetList.prototype[Symbol.dispose] = RegionSetList.prototype.free;
+
 export class SignalMatrix {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(SignalMatrix.prototype);
+        obj.__wbg_ptr = ptr;
+        SignalMatrixFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
     __destroy_into_raw() {
         const ptr = this.__wbg_ptr;
         this.__wbg_ptr = 0;
@@ -558,6 +862,20 @@ export class SignalMatrix {
         const ptr = this.__destroy_into_raw();
         wasm.__wbg_signalmatrix_free(ptr, 0);
     }
+    /**
+     * Load a SignalMatrix from packed binary bytes.
+     * @param {Uint8Array} bytes
+     * @returns {SignalMatrix}
+     */
+    static fromBin(bytes) {
+        const ptr0 = passArray8ToWasm0(bytes, wasm.__wbindgen_malloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.signalmatrix_fromBin(ptr0, len0);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return SignalMatrix.__wrap(ret[0]);
+    }
     /**
      * Construct a SignalMatrix from JS data.
      *
@@ -837,6 +1155,13 @@ export class Tokenizer {
 if (Symbol.dispose) Tokenizer.prototype[Symbol.dispose] = Tokenizer.prototype.free;
 
 export class TssIndex {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(TssIndex.prototype);
+        obj.__wbg_ptr = ptr;
+        TssIndexFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
     __destroy_into_raw() {
         const ptr = this.__wbg_ptr;
         this.__wbg_ptr = 0;
@@ -985,6 +1310,24 @@ export function canonicalizeJsonString(json_str) {
     }
 }
 
+/**
+ * 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
+ * @param {any} user_sets
+ * @param {any} universe_regions
+ * @returns {any}
+ */
+export function checkUniverseAppropriateness(user_sets, universe_regions) {
+    const ret = wasm.checkUniverseAppropriateness(user_sets, universe_regions);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return takeFromExternrefTable0(ret[0]);
+}
+
 /**
  * Compute the MD5 digest of a string.
  *
@@ -1216,6 +1559,33 @@ export function greet(name) {
     wasm.greet(ptr0, len0);
 }
 
+/**
+ * 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.
+ * @param {any} user_sets
+ * @param {any} universe_regions
+ * @param {LolaRegionDB} region_db
+ * @param {number | null} [min_overlap]
+ * @param {string | null} [direction]
+ * @returns {any}
+ */
+export function runLOLA(user_sets, universe_regions, region_db, min_overlap, direction) {
+    _assertClass(region_db, LolaRegionDB);
+    var ptr0 = isLikeNone(direction) ? 0 : passStringToWasm0(direction, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+    var len0 = WASM_VECTOR_LEN;
+    const ret = wasm.runLOLA(user_sets, universe_regions, region_db.__wbg_ptr, isLikeNone(min_overlap) ? 0x100000001 : (min_overlap) >> 0, ptr0, len0);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return takeFromExternrefTable0(ret[0]);
+}
+
 /**
  * Compute a sequence digest (sha512t24u) from raw sequence data.
  *
@@ -1282,7 +1652,7 @@ export function sequenceMd5(sequence) {
 function __wbg_get_imports() {
     const import0 = {
         __proto__: null,
-        __wbg_Error_dbcd8782dbb273a2: function(arg0, arg1) {
+        __wbg_Error_83742b46f01ce22d: function(arg0, arg1) {
             const ret = Error(getStringFromWasm0(arg0, arg1));
             return ret;
         },
@@ -1293,68 +1663,68 @@ function __wbg_get_imports() {
             getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
             getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
         },
-        __wbg___wbindgen_bigint_get_as_i64_25c638f64ce0e2e0: function(arg0, arg1) {
+        __wbg___wbindgen_bigint_get_as_i64_447a76b5c6ef7bda: function(arg0, arg1) {
             const v = arg1;
             const ret = typeof(v) === 'bigint' ? v : undefined;
             getDataViewMemory0().setBigInt64(arg0 + 8 * 1, isLikeNone(ret) ? BigInt(0) : ret, true);
             getDataViewMemory0().setInt32(arg0 + 4 * 0, !isLikeNone(ret), true);
         },
-        __wbg___wbindgen_boolean_get_7f1c4dd217655ab6: function(arg0) {
+        __wbg___wbindgen_boolean_get_c0f3f60bac5a78d1: function(arg0) {
             const v = arg0;
             const ret = typeof(v) === 'boolean' ? v : undefined;
             return isLikeNone(ret) ? 0xFFFFFF : ret ? 1 : 0;
         },
-        __wbg___wbindgen_debug_string_6cf0badf0b90f6ef: function(arg0, arg1) {
+        __wbg___wbindgen_debug_string_5398f5bb970e0daa: function(arg0, arg1) {
             const ret = debugString(arg1);
             const ptr1 = passStringToWasm0(ret, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
             const len1 = WASM_VECTOR_LEN;
             getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
             getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
         },
-        __wbg___wbindgen_in_e32cbbbf71fdc915: function(arg0, arg1) {
+        __wbg___wbindgen_in_41dbb8413020e076: function(arg0, arg1) {
             const ret = arg0 in arg1;
             return ret;
         },
-        __wbg___wbindgen_is_bigint_95f22c948ca1bbe1: function(arg0) {
+        __wbg___wbindgen_is_bigint_e2141d4f045b7eda: function(arg0) {
             const ret = typeof(arg0) === 'bigint';
             return ret;
         },
-        __wbg___wbindgen_is_function_4500d4795b15e70b: function(arg0) {
+        __wbg___wbindgen_is_function_3c846841762788c1: function(arg0) {
             const ret = typeof(arg0) === 'function';
             return ret;
         },
-        __wbg___wbindgen_is_null_5467e07e008308e7: function(arg0) {
+        __wbg___wbindgen_is_null_0b605fc6b167c56f: function(arg0) {
             const ret = arg0 === null;
             return ret;
         },
-        __wbg___wbindgen_is_object_f8b6723c60349a13: function(arg0) {
+        __wbg___wbindgen_is_object_781bc9f159099513: function(arg0) {
             const val = arg0;
             const ret = typeof(val) === 'object' && val !== null;
             return ret;
         },
-        __wbg___wbindgen_is_string_89134e23eba104e4: function(arg0) {
+        __wbg___wbindgen_is_string_7ef6b97b02428fae: function(arg0) {
             const ret = typeof(arg0) === 'string';
             return ret;
         },
-        __wbg___wbindgen_is_undefined_1296fcc83c2da07a: function(arg0) {
+        __wbg___wbindgen_is_undefined_52709e72fb9f179c: function(arg0) {
             const ret = arg0 === undefined;
             return ret;
         },
-        __wbg___wbindgen_jsval_eq_39cab0b49f8188e9: function(arg0, arg1) {
+        __wbg___wbindgen_jsval_eq_ee31bfad3e536463: function(arg0, arg1) {
             const ret = arg0 === arg1;
             return ret;
         },
-        __wbg___wbindgen_jsval_loose_eq_3173dea557396a92: function(arg0, arg1) {
+        __wbg___wbindgen_jsval_loose_eq_5bcc3bed3c69e72b: function(arg0, arg1) {
             const ret = arg0 == arg1;
             return ret;
         },
-        __wbg___wbindgen_number_get_3330675b4e5c3680: function(arg0, arg1) {
+        __wbg___wbindgen_number_get_34bb9d9dcfa21373: function(arg0, arg1) {
             const obj = arg1;
             const ret = typeof(obj) === 'number' ? obj : undefined;
             getDataViewMemory0().setFloat64(arg0 + 8 * 1, isLikeNone(ret) ? 0 : ret, true);
             getDataViewMemory0().setInt32(arg0 + 4 * 0, !isLikeNone(ret), true);
         },
-        __wbg___wbindgen_string_get_7b8bc463f6cbeefe: function(arg0, arg1) {
+        __wbg___wbindgen_string_get_395e606bd0ee4427: function(arg0, arg1) {
             const obj = arg1;
             const ret = typeof(obj) === 'string' ? obj : undefined;
             var ptr1 = isLikeNone(ret) ? 0 : passStringToWasm0(ret, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
@@ -1362,37 +1732,41 @@ function __wbg_get_imports() {
             getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
             getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
         },
-        __wbg___wbindgen_throw_89ca9e2c67795ec1: function(arg0, arg1) {
+        __wbg___wbindgen_throw_6ddd609b62940d55: function(arg0, arg1) {
             throw new Error(getStringFromWasm0(arg0, arg1));
         },
-        __wbg_alert_54562c808bfe0277: function(arg0, arg1) {
+        __wbg_alert_42dff0589bd812e0: function(arg0, arg1) {
             alert(getStringFromWasm0(arg0, arg1));
         },
-        __wbg_call_eb691bc2f5533064: function() { return handleError(function (arg0, arg1) {
+        __wbg_call_e133b57c9155d22c: function() { return handleError(function (arg0, arg1) {
             const ret = arg0.call(arg1);
             return ret;
         }, arguments); },
-        __wbg_done_82b14aeb31e98db6: function(arg0) {
+        __wbg_done_08ce71ee07e3bd17: function(arg0) {
             const ret = arg0.done;
             return ret;
         },
-        __wbg_entries_46c64fadfaa3b525: function(arg0) {
+        __wbg_entries_e8a20ff8c9757101: function(arg0) {
             const ret = Object.entries(arg0);
             return ret;
         },
-        __wbg_get_229657ec2da079cd: function(arg0, arg1) {
-            const ret = arg0[arg1 >>> 0];
-            return ret;
-        },
-        __wbg_get_ed44f5f876f22351: function() { return handleError(function (arg0, arg1) {
+        __wbg_get_326e41e095fb2575: function() { return handleError(function (arg0, arg1) {
             const ret = Reflect.get(arg0, arg1);
             return ret;
         }, arguments); },
-        __wbg_get_unchecked_ae4d1600970be7c3: function(arg0, arg1) {
+        __wbg_get_a8ee5c45dabc1b3b: function(arg0, arg1) {
             const ret = arg0[arg1 >>> 0];
             return ret;
         },
-        __wbg_instanceof_ArrayBuffer_4f2b9b5ed416155d: function(arg0) {
+        __wbg_get_unchecked_329cfe50afab7352: function(arg0, arg1) {
+            const ret = arg0[arg1 >>> 0];
+            return ret;
+        },
+        __wbg_get_with_ref_key_f38bf27dc398d91b: function(arg0, arg1) {
+            const ret = arg0[arg1];
+            return ret;
+        },
+        __wbg_instanceof_ArrayBuffer_101e2bf31071a9f6: function(arg0) {
             let result;
             try {
                 result = arg0 instanceof ArrayBuffer;
@@ -1402,7 +1776,7 @@ function __wbg_get_imports() {
             const ret = result;
             return ret;
         },
-        __wbg_instanceof_Uint8Array_6482c66fce35827d: function(arg0) {
+        __wbg_instanceof_Uint8Array_740438561a5b956d: function(arg0) {
             let result;
             try {
                 result = arg0 instanceof Uint8Array;
@@ -1412,64 +1786,64 @@ function __wbg_get_imports() {
             const ret = result;
             return ret;
         },
-        __wbg_isArray_fe5201bfdab7e39d: function(arg0) {
+        __wbg_isArray_33b91feb269ff46e: function(arg0) {
             const ret = Array.isArray(arg0);
             return ret;
         },
-        __wbg_isSafeInteger_d6215c7562dbc4db: function(arg0) {
+        __wbg_isSafeInteger_ecd6a7f9c3e053cd: function(arg0) {
             const ret = Number.isSafeInteger(arg0);
             return ret;
         },
-        __wbg_iterator_63c3a1857203cf2f: function() {
+        __wbg_iterator_d8f549ec8fb061b1: function() {
             const ret = Symbol.iterator;
             return ret;
         },
-        __wbg_length_f875d3a041bab91a: function(arg0) {
+        __wbg_length_b3416cf66a5452c8: function(arg0) {
             const ret = arg0.length;
             return ret;
         },
-        __wbg_length_feaf2a40e5f9755a: function(arg0) {
+        __wbg_length_ea16607d7b61445b: function(arg0) {
             const ret = arg0.length;
             return ret;
         },
-        __wbg_new_5947ca72f3fee3e6: function() {
+        __wbg_new_49d5571bd3f0c4d4: function() {
             const ret = new Map();
             return ret;
         },
-        __wbg_new_6e7681a5f6f98ceb: function(arg0) {
+        __wbg_new_5f486cdf45a04d78: function(arg0) {
             const ret = new Uint8Array(arg0);
             return ret;
         },
-        __wbg_new_6feff3e11e4d0799: function() {
-            const ret = new Object();
+        __wbg_new_a70fbab9066b301f: function() {
+            const ret = new Array();
             return ret;
         },
-        __wbg_new_ff7f9cc4c9a4a0cf: function() {
-            const ret = new Array();
+        __wbg_new_ab79df5bd7c26067: function() {
+            const ret = new Object();
             return ret;
         },
-        __wbg_next_ae5b710aea83f41e: function() { return handleError(function (arg0) {
+        __wbg_next_11b99ee6237339e3: function() { return handleError(function (arg0) {
             const ret = arg0.next();
             return ret;
         }, arguments); },
-        __wbg_next_f577b3e02c9be709: function(arg0) {
+        __wbg_next_e01a967809d1aa68: function(arg0) {
             const ret = arg0.next;
             return ret;
         },
-        __wbg_prototypesetcall_37f00e1be5c4015a: function(arg0, arg1, arg2) {
+        __wbg_prototypesetcall_d62e5099504357e6: function(arg0, arg1, arg2) {
             Uint8Array.prototype.set.call(getArrayU8FromWasm0(arg0, arg1), arg2);
         },
-        __wbg_set_601f3e1d081df3ac: function(arg0, arg1, arg2) {
+        __wbg_set_282384002438957f: function(arg0, arg1, arg2) {
             arg0[arg1 >>> 0] = arg2;
         },
-        __wbg_set_b1226382f10be917: function(arg0, arg1, arg2) {
+        __wbg_set_bf7251625df30a02: function(arg0, arg1, arg2) {
             const ret = arg0.set(arg1, arg2);
             return ret;
         },
         __wbg_set_d1cb61e9f39c870f: function(arg0, arg1, arg2) {
             arg0[arg1] = arg2;
         },
-        __wbg_value_3e1fdb73e1353fb3: function(arg0) {
+        __wbg_value_21fc78aab0322612: function(arg0) {
             const ret = arg0.value;
             return ret;
         },
@@ -1521,6 +1895,12 @@ const ConsensusBuilderFinalization = (typeof FinalizationRegistry === 'undefined
 const GeneModelFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_genemodel_free(ptr >>> 0, 1));
+const GenomicDistAnnotationFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_genomicdistannotation_free(ptr >>> 0, 1));
+const LolaRegionDBFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_lolaregiondb_free(ptr >>> 0, 1));
 const OverlapperFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_overlapper_free(ptr >>> 0, 1));
@@ -1533,6 +1913,9 @@ const RegionDistributionFinalization = (typeof FinalizationRegistry === 'undefin
 const RegionSetFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_regionset_free(ptr >>> 0, 1));
+const RegionSetListFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_regionsetlist_free(ptr >>> 0, 1));
 const SignalMatrixFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_signalmatrix_free(ptr >>> 0, 1));
@@ -1620,6 +2003,17 @@ function debugString(val) {
     return className;
 }
 
+function getArrayJsValueFromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    const mem = getDataViewMemory0();
+    const result = [];
+    for (let i = ptr; i < ptr + 4 * len; i += 4) {
+        result.push(wasm.__wbindgen_externrefs.get(mem.getUint32(i, true)));
+    }
+    wasm.__externref_drop_slice(ptr, len);
+    return result;
+}
+
 function getArrayU32FromWasm0(ptr, len) {
     ptr = ptr >>> 0;
     return getUint32ArrayMemory0().subarray(ptr / 4, ptr / 4 + len);
@@ -1680,6 +2074,13 @@ function isLikeNone(x) {
     return x === undefined || x === null;
 }
 
+function passArray32ToWasm0(arg, malloc) {
+    const ptr = malloc(arg.length * 4, 4) >>> 0;
+    getUint32ArrayMemory0().set(arg, ptr / 4);
+    WASM_VECTOR_LEN = arg.length;
+    return ptr;
+}
+
 function passArray8ToWasm0(arg, malloc) {
     const ptr = malloc(arg.length * 1, 1) >>> 0;
     getUint8ArrayMemory0().set(arg, ptr / 1);

package/package.json

@@ -4,7 +4,7 @@
   "collaborators": [
     "Nathan LeRoy <NLeRoy917@gmail.com>"
   ],
-  "version": "0.7.1",
+  "version": "0.8.0",
   "files": [
     "gtars_js_bg.wasm",
     "gtars_js.js",