@databio/gtars 0.6.1 → 0.7.1

package/gtars_js.d.ts

@@ -25,6 +25,38 @@ 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 Overlapper {
     free(): void;
     [Symbol.dispose](): void;
@@ -33,6 +65,19 @@ 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 +87,20 @@ export class RegionDistribution {
 export class RegionSet {
     free(): void;
     [Symbol.dispose](): void;
+    calcNearestNeighbors(): any;
+    calcNeighborDistances(): any;
+    calcWidths(): Uint32Array;
     chromosomeStatistics(): any;
+    concat(other: RegionSet): RegionSet;
+    jaccard(other: RegionSet): number;
     constructor(regions: any);
+    pintersect(other: RegionSet): RegionSet;
+    promoters(upstream: number, downstream: number): RegionSet;
+    reduce(): RegionSet;
     regionDistribution(n_bins: number): any;
+    setdiff(other: RegionSet): RegionSet;
+    trim(chrom_sizes: any): RegionSet;
+    union(other: RegionSet): RegionSet;
     readonly classify: BedClassificationOutput;
     readonly firstRegion: string;
     readonly identifier: string;
@@ -53,6 +109,21 @@ export class RegionSet {
     readonly numberOfRegions: number;
 }
 
+export class SignalMatrix {
+    free(): void;
+    [Symbol.dispose](): void;
+    /**
+     * 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 +151,48 @@ 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.
  *
@@ -280,9 +393,9 @@ export type InitInput = RequestInfo | URL | Response | BufferSource | WebAssembl
 
 export interface InitOutput {
     readonly memory: WebAssembly.Memory;
-    readonly greet: (a: number, b: number) => void;
     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 bedclassificationoutput_bed_compliance: (a: number) => [number, number];
@@ -296,17 +409,60 @@ 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_concat: (a: number, b: number) => number;
     readonly regionset_firstRegion: (a: number) => [number, number];
     readonly regionset_identifier: (a: number) => [number, number];
+    readonly regionset_jaccard: (a: number, b: number) => number;
     readonly regionset_meanRegionWidth: (a: 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_setdiff: (a: number, b: number) => number;
+    readonly regionset_trim: (a: number, b: any) => [number, number, number];
+    readonly regionset_union: (a: number, b: 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 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];
@@ -329,21 +485,6 @@ export interface InitOutput {
     readonly tokenizer_unkToken: (a: number) => [number, number];
     readonly tokenizer_unkTokenId: (a: number) => number;
     readonly tokenizer_vocabSize: (a: number) => number;
-    readonly __wbg_overlapper_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 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 __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;

package/gtars_js.js

@@ -123,7 +123,7 @@ export class ChromosomeStatistics {
      * @returns {number}
      */
     get minimum_region_length() {
-        const ret = wasm.bedclassificationoutput_compliant_columns(this.__wbg_ptr);
+        const ret = wasm.chromosomestatistics_minimum_region_length(this.__wbg_ptr);
         return ret >>> 0;
     }
     /**
@@ -143,6 +143,88 @@ export class ChromosomeStatistics {
 }
 if (Symbol.dispose) ChromosomeStatistics.prototype[Symbol.dispose] = ChromosomeStatistics.prototype.free;
 
+/**
+ * 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 {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        ConsensusBuilderFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_consensusbuilder_free(ptr, 0);
+    }
+    /**
+     * @param {RegionSet} set
+     */
+    add(set) {
+        _assertClass(set, RegionSet);
+        wasm.consensusbuilder_add(this.__wbg_ptr, set.__wbg_ptr);
+    }
+    /**
+     * @returns {any}
+     */
+    compute() {
+        const ret = wasm.consensusbuilder_compute(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    constructor() {
+        const ret = wasm.consensusbuilder_new();
+        this.__wbg_ptr = ret >>> 0;
+        ConsensusBuilderFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+}
+if (Symbol.dispose) ConsensusBuilder.prototype[Symbol.dispose] = ConsensusBuilder.prototype.free;
+
+export class GeneModel {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        GeneModelFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_genemodel_free(ptr, 0);
+    }
+    /**
+     * 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`).
+     * @param {any} genes
+     * @param {any} exons
+     * @param {any} three_utr
+     * @param {any} five_utr
+     */
+    constructor(genes, exons, three_utr, five_utr) {
+        const ret = wasm.genemodel_new(genes, exons, three_utr, five_utr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        this.__wbg_ptr = ret[0] >>> 0;
+        GeneModelFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+}
+if (Symbol.dispose) GeneModel.prototype[Symbol.dispose] = GeneModel.prototype.free;
+
 export class Overlapper {
     __destroy_into_raw() {
         const ptr = this.__wbg_ptr;
@@ -198,6 +280,46 @@ export class Overlapper {
 }
 if (Symbol.dispose) Overlapper.prototype[Symbol.dispose] = Overlapper.prototype.free;
 
+export class PartitionList {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(PartitionList.prototype);
+        obj.__wbg_ptr = ptr;
+        PartitionListFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        PartitionListFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_partitionlist_free(ptr, 0);
+    }
+    /**
+     * Build a PartitionList from a GeneModel.
+     *
+     * `chromSizes` is an optional JS object `{"chr1": 249250621, ...}` for
+     * trimming promoters at chromosome boundaries.
+     * @param {GeneModel} model
+     * @param {number} core_prom_size
+     * @param {number} prox_prom_size
+     * @param {any} chrom_sizes
+     * @returns {PartitionList}
+     */
+    static fromGeneModel(model, core_prom_size, prox_prom_size, chrom_sizes) {
+        _assertClass(model, GeneModel);
+        const ret = wasm.partitionlist_fromGeneModel(model.__wbg_ptr, core_prom_size, prox_prom_size, chrom_sizes);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return PartitionList.__wrap(ret[0]);
+    }
+}
+if (Symbol.dispose) PartitionList.prototype[Symbol.dispose] = PartitionList.prototype.free;
+
 export class RegionDistribution {
     __destroy_into_raw() {
         const ptr = this.__wbg_ptr;
@@ -213,6 +335,13 @@ export class RegionDistribution {
 if (Symbol.dispose) RegionDistribution.prototype[Symbol.dispose] = RegionDistribution.prototype.free;
 
 export class RegionSet {
+    static __wrap(ptr) {
+        ptr = ptr >>> 0;
+        const obj = Object.create(RegionSet.prototype);
+        obj.__wbg_ptr = ptr;
+        RegionSetFinalization.register(obj, obj.__wbg_ptr, obj);
+        return obj;
+    }
     __destroy_into_raw() {
         const ptr = this.__wbg_ptr;
         this.__wbg_ptr = 0;
@@ -223,6 +352,35 @@ export class RegionSet {
         const ptr = this.__destroy_into_raw();
         wasm.__wbg_regionset_free(ptr, 0);
     }
+    /**
+     * @returns {any}
+     */
+    calcNearestNeighbors() {
+        const ret = wasm.regionset_calcNearestNeighbors(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    /**
+     * @returns {any}
+     */
+    calcNeighborDistances() {
+        const ret = wasm.regionset_calcNeighborDistances(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    /**
+     * @returns {Uint32Array}
+     */
+    calcWidths() {
+        const ret = wasm.regionset_calcWidths(this.__wbg_ptr);
+        var v1 = getArrayU32FromWasm0(ret[0], ret[1]).slice();
+        wasm.__wbindgen_free(ret[0], ret[1] * 4, 4);
+        return v1;
+    }
     /**
      * @returns {any}
      */
@@ -240,6 +398,15 @@ export class RegionSet {
         const ret = wasm.regionset_classify(this.__wbg_ptr);
         return BedClassificationOutput.__wrap(ret);
     }
+    /**
+     * @param {RegionSet} other
+     * @returns {RegionSet}
+     */
+    concat(other) {
+        _assertClass(other, RegionSet);
+        const ret = wasm.regionset_concat(this.__wbg_ptr, other.__wbg_ptr);
+        return RegionSet.__wrap(ret);
+    }
     /**
      * @returns {string}
      */
@@ -270,6 +437,15 @@ export class RegionSet {
             wasm.__wbindgen_free(deferred1_0, deferred1_1, 1);
         }
     }
+    /**
+     * @param {RegionSet} other
+     * @returns {number}
+     */
+    jaccard(other) {
+        _assertClass(other, RegionSet);
+        const ret = wasm.regionset_jaccard(this.__wbg_ptr, other.__wbg_ptr);
+        return ret;
+    }
     /**
      * @returns {number}
      */
@@ -303,6 +479,31 @@ export class RegionSet {
         const ret = wasm.regionset_numberOfRegions(this.__wbg_ptr);
         return ret;
     }
+    /**
+     * @param {RegionSet} other
+     * @returns {RegionSet}
+     */
+    pintersect(other) {
+        _assertClass(other, RegionSet);
+        const ret = wasm.regionset_pintersect(this.__wbg_ptr, other.__wbg_ptr);
+        return RegionSet.__wrap(ret);
+    }
+    /**
+     * @param {number} upstream
+     * @param {number} downstream
+     * @returns {RegionSet}
+     */
+    promoters(upstream, downstream) {
+        const ret = wasm.regionset_promoters(this.__wbg_ptr, upstream, downstream);
+        return RegionSet.__wrap(ret);
+    }
+    /**
+     * @returns {RegionSet}
+     */
+    reduce() {
+        const ret = wasm.regionset_reduce(this.__wbg_ptr);
+        return RegionSet.__wrap(ret);
+    }
     /**
      * @param {number} n_bins
      * @returns {any}
@@ -314,9 +515,77 @@ export class RegionSet {
         }
         return takeFromExternrefTable0(ret[0]);
     }
+    /**
+     * @param {RegionSet} other
+     * @returns {RegionSet}
+     */
+    setdiff(other) {
+        _assertClass(other, RegionSet);
+        const ret = wasm.regionset_setdiff(this.__wbg_ptr, other.__wbg_ptr);
+        return RegionSet.__wrap(ret);
+    }
+    /**
+     * @param {any} chrom_sizes
+     * @returns {RegionSet}
+     */
+    trim(chrom_sizes) {
+        const ret = wasm.regionset_trim(this.__wbg_ptr, chrom_sizes);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return RegionSet.__wrap(ret[0]);
+    }
+    /**
+     * @param {RegionSet} other
+     * @returns {RegionSet}
+     */
+    union(other) {
+        _assertClass(other, RegionSet);
+        const ret = wasm.regionset_union(this.__wbg_ptr, other.__wbg_ptr);
+        return RegionSet.__wrap(ret);
+    }
 }
 if (Symbol.dispose) RegionSet.prototype[Symbol.dispose] = RegionSet.prototype.free;
 
+export class SignalMatrix {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        SignalMatrixFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_signalmatrix_free(ptr, 0);
+    }
+    /**
+     * 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)
+     * @param {any} region_ids
+     * @param {any} condition_names
+     * @param {Float64Array} values
+     * @param {number} n_regions
+     * @param {number} n_conditions
+     */
+    constructor(region_ids, condition_names, values, n_regions, n_conditions) {
+        const ptr0 = passArrayF64ToWasm0(values, wasm.__wbindgen_malloc);
+        const len0 = WASM_VECTOR_LEN;
+        const ret = wasm.signalmatrix_new(region_ids, condition_names, ptr0, len0, n_regions, n_conditions);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        this.__wbg_ptr = ret[0] >>> 0;
+        SignalMatrixFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+}
+if (Symbol.dispose) SignalMatrix.prototype[Symbol.dispose] = SignalMatrix.prototype.free;
+
 export class Tokenizer {
     __destroy_into_raw() {
         const ptr = this.__wbg_ptr;
@@ -561,12 +830,127 @@ export class Tokenizer {
      * @returns {number}
      */
     get vocabSize() {
-        const ret = wasm.tokenizer_length(this.__wbg_ptr);
+        const ret = wasm.tokenizer_vocabSize(this.__wbg_ptr);
         return ret >>> 0;
     }
 }
 if (Symbol.dispose) Tokenizer.prototype[Symbol.dispose] = Tokenizer.prototype.free;
 
+export class TssIndex {
+    __destroy_into_raw() {
+        const ptr = this.__wbg_ptr;
+        this.__wbg_ptr = 0;
+        TssIndexFinalization.unregister(this);
+        return ptr;
+    }
+    free() {
+        const ptr = this.__destroy_into_raw();
+        wasm.__wbg_tssindex_free(ptr, 0);
+    }
+    /**
+     * 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).
+     * @param {RegionSet} query
+     * @returns {any}
+     */
+    calcFeatureDistances(query) {
+        _assertClass(query, RegionSet);
+        const ret = wasm.tssindex_calcFeatureDistances(this.__wbg_ptr, query.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    /**
+     * 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).
+     * @param {RegionSet} query
+     * @returns {any}
+     */
+    calcTssDistances(query) {
+        _assertClass(query, RegionSet);
+        const ret = wasm.tssindex_calcTssDistances(this.__wbg_ptr, query.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
+    /**
+     * Build a TssIndex from a RegionSet of features (e.g. TSS sites).
+     *
+     * Clones the inner RegionSet and computes sorted midpoints per chromosome.
+     * @param {RegionSet} features
+     */
+    constructor(features) {
+        _assertClass(features, RegionSet);
+        const ret = wasm.tssindex_new(features.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        this.__wbg_ptr = ret[0] >>> 0;
+        TssIndexFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
+}
+if (Symbol.dispose) TssIndex.prototype[Symbol.dispose] = TssIndex.prototype.free;
+
+/**
+ * Compute observed vs expected partition enrichment.
+ * @param {RegionSet} region_set
+ * @param {PartitionList} partition_list
+ * @param {any} chrom_sizes
+ * @param {boolean} bp_proportion
+ * @returns {any}
+ */
+export function calcExpectedPartitions(region_set, partition_list, chrom_sizes, bp_proportion) {
+    _assertClass(region_set, RegionSet);
+    _assertClass(partition_list, PartitionList);
+    const ret = wasm.calcExpectedPartitions(region_set.__wbg_ptr, partition_list.__wbg_ptr, chrom_sizes, bp_proportion);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return takeFromExternrefTable0(ret[0]);
+}
+
+/**
+ * Classify query regions into partitions.
+ * @param {RegionSet} region_set
+ * @param {PartitionList} partition_list
+ * @param {boolean} bp_proportion
+ * @returns {any}
+ */
+export function calcPartitions(region_set, partition_list, bp_proportion) {
+    _assertClass(region_set, RegionSet);
+    _assertClass(partition_list, PartitionList);
+    const ret = wasm.calcPartitions(region_set.__wbg_ptr, partition_list.__wbg_ptr, bp_proportion);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return takeFromExternrefTable0(ret[0]);
+}
+
+/**
+ * Compute summary signal: overlap query regions with a signal matrix,
+ * take MAX per condition, and compute boxplot statistics.
+ * @param {RegionSet} region_set
+ * @param {SignalMatrix} signal_matrix
+ * @returns {any}
+ */
+export function calcSummarySignal(region_set, signal_matrix) {
+    _assertClass(region_set, RegionSet);
+    _assertClass(signal_matrix, SignalMatrix);
+    const ret = wasm.calcSummarySignal(region_set.__wbg_ptr, signal_matrix.__wbg_ptr);
+    if (ret[2]) {
+        throw takeFromExternrefTable0(ret[1]);
+    }
+    return takeFromExternrefTable0(ret[0]);
+}
+
 /**
  * Canonicalize a JSON string according to RFC-8785.
  *
@@ -898,53 +1282,79 @@ export function sequenceMd5(sequence) {
 function __wbg_get_imports() {
     const import0 = {
         __proto__: null,
-        __wbg_Error_8c4e43fe74559d73: function(arg0, arg1) {
+        __wbg_Error_dbcd8782dbb273a2: function(arg0, arg1) {
             const ret = Error(getStringFromWasm0(arg0, arg1));
             return ret;
         },
-        __wbg_String_fed4d24b68977888: function(arg0, arg1) {
+        __wbg_String_11905339415cf58e: function(arg0, arg1) {
             const ret = String(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_boolean_get_bbbb1c18aa2f5e25: function(arg0) {
+        __wbg___wbindgen_bigint_get_as_i64_25c638f64ce0e2e0: 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) {
             const v = arg0;
             const ret = typeof(v) === 'boolean' ? v : undefined;
             return isLikeNone(ret) ? 0xFFFFFF : ret ? 1 : 0;
         },
-        __wbg___wbindgen_debug_string_0bc8482c6e3508ae: function(arg0, arg1) {
+        __wbg___wbindgen_debug_string_6cf0badf0b90f6ef: 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_is_function_0095a73b8b156f76: function(arg0) {
+        __wbg___wbindgen_in_e32cbbbf71fdc915: function(arg0, arg1) {
+            const ret = arg0 in arg1;
+            return ret;
+        },
+        __wbg___wbindgen_is_bigint_95f22c948ca1bbe1: function(arg0) {
+            const ret = typeof(arg0) === 'bigint';
+            return ret;
+        },
+        __wbg___wbindgen_is_function_4500d4795b15e70b: function(arg0) {
             const ret = typeof(arg0) === 'function';
             return ret;
         },
-        __wbg___wbindgen_is_object_5ae8e5880f2c1fbd: function(arg0) {
+        __wbg___wbindgen_is_null_5467e07e008308e7: function(arg0) {
+            const ret = arg0 === null;
+            return ret;
+        },
+        __wbg___wbindgen_is_object_f8b6723c60349a13: function(arg0) {
             const val = arg0;
             const ret = typeof(val) === 'object' && val !== null;
             return ret;
         },
-        __wbg___wbindgen_is_string_cd444516edc5b180: function(arg0) {
+        __wbg___wbindgen_is_string_89134e23eba104e4: function(arg0) {
             const ret = typeof(arg0) === 'string';
             return ret;
         },
-        __wbg___wbindgen_jsval_loose_eq_9dd77d8cd6671811: function(arg0, arg1) {
+        __wbg___wbindgen_is_undefined_1296fcc83c2da07a: function(arg0) {
+            const ret = arg0 === undefined;
+            return ret;
+        },
+        __wbg___wbindgen_jsval_eq_39cab0b49f8188e9: function(arg0, arg1) {
+            const ret = arg0 === arg1;
+            return ret;
+        },
+        __wbg___wbindgen_jsval_loose_eq_3173dea557396a92: function(arg0, arg1) {
             const ret = arg0 == arg1;
             return ret;
         },
-        __wbg___wbindgen_number_get_8ff4255516ccad3e: function(arg0, arg1) {
+        __wbg___wbindgen_number_get_3330675b4e5c3680: 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_72fb696202c56729: function(arg0, arg1) {
+        __wbg___wbindgen_string_get_7b8bc463f6cbeefe: 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);
@@ -952,29 +1362,37 @@ function __wbg_get_imports() {
             getDataViewMemory0().setInt32(arg0 + 4 * 1, len1, true);
             getDataViewMemory0().setInt32(arg0 + 4 * 0, ptr1, true);
         },
-        __wbg___wbindgen_throw_be289d5034ed271b: function(arg0, arg1) {
+        __wbg___wbindgen_throw_89ca9e2c67795ec1: function(arg0, arg1) {
             throw new Error(getStringFromWasm0(arg0, arg1));
         },
-        __wbg_alert_1e3e10e7a5109f8f: function(arg0, arg1) {
+        __wbg_alert_54562c808bfe0277: function(arg0, arg1) {
             alert(getStringFromWasm0(arg0, arg1));
         },
-        __wbg_call_389efe28435a9388: function() { return handleError(function (arg0, arg1) {
+        __wbg_call_eb691bc2f5533064: function() { return handleError(function (arg0, arg1) {
             const ret = arg0.call(arg1);
             return ret;
         }, arguments); },
-        __wbg_done_57b39ecd9addfe81: function(arg0) {
+        __wbg_done_82b14aeb31e98db6: function(arg0) {
             const ret = arg0.done;
             return ret;
         },
-        __wbg_get_9b94d73e6221f75c: function(arg0, arg1) {
+        __wbg_entries_46c64fadfaa3b525: function(arg0) {
+            const ret = Object.entries(arg0);
+            return ret;
+        },
+        __wbg_get_229657ec2da079cd: function(arg0, arg1) {
             const ret = arg0[arg1 >>> 0];
             return ret;
         },
-        __wbg_get_b3ed3ad4be2bc8ac: function() { return handleError(function (arg0, arg1) {
+        __wbg_get_ed44f5f876f22351: function() { return handleError(function (arg0, arg1) {
             const ret = Reflect.get(arg0, arg1);
             return ret;
         }, arguments); },
-        __wbg_instanceof_ArrayBuffer_c367199e2fa2aa04: function(arg0) {
+        __wbg_get_unchecked_ae4d1600970be7c3: function(arg0, arg1) {
+            const ret = arg0[arg1 >>> 0];
+            return ret;
+        },
+        __wbg_instanceof_ArrayBuffer_4f2b9b5ed416155d: function(arg0) {
             let result;
             try {
                 result = arg0 instanceof ArrayBuffer;
@@ -984,7 +1402,7 @@ function __wbg_get_imports() {
             const ret = result;
             return ret;
         },
-        __wbg_instanceof_Uint8Array_9b9075935c74707c: function(arg0) {
+        __wbg_instanceof_Uint8Array_6482c66fce35827d: function(arg0) {
             let result;
             try {
                 result = arg0 instanceof Uint8Array;
@@ -994,64 +1412,64 @@ function __wbg_get_imports() {
             const ret = result;
             return ret;
         },
-        __wbg_isArray_d314bb98fcf08331: function(arg0) {
+        __wbg_isArray_fe5201bfdab7e39d: function(arg0) {
             const ret = Array.isArray(arg0);
             return ret;
         },
-        __wbg_isSafeInteger_bfbc7332a9768d2a: function(arg0) {
+        __wbg_isSafeInteger_d6215c7562dbc4db: function(arg0) {
             const ret = Number.isSafeInteger(arg0);
             return ret;
         },
-        __wbg_iterator_6ff6560ca1568e55: function() {
+        __wbg_iterator_63c3a1857203cf2f: function() {
             const ret = Symbol.iterator;
             return ret;
         },
-        __wbg_length_32ed9a279acd054c: function(arg0) {
+        __wbg_length_f875d3a041bab91a: function(arg0) {
             const ret = arg0.length;
             return ret;
         },
-        __wbg_length_35a7bace40f36eac: function(arg0) {
+        __wbg_length_feaf2a40e5f9755a: function(arg0) {
             const ret = arg0.length;
             return ret;
         },
-        __wbg_new_361308b2356cecd0: function() {
-            const ret = new Object();
+        __wbg_new_5947ca72f3fee3e6: function() {
+            const ret = new Map();
             return ret;
         },
-        __wbg_new_3eb36ae241fe6f44: function() {
-            const ret = new Array();
+        __wbg_new_6e7681a5f6f98ceb: function(arg0) {
+            const ret = new Uint8Array(arg0);
             return ret;
         },
-        __wbg_new_dca287b076112a51: function() {
-            const ret = new Map();
+        __wbg_new_6feff3e11e4d0799: function() {
+            const ret = new Object();
             return ret;
         },
-        __wbg_new_dd2b680c8bf6ae29: function(arg0) {
-            const ret = new Uint8Array(arg0);
+        __wbg_new_ff7f9cc4c9a4a0cf: function() {
+            const ret = new Array();
             return ret;
         },
-        __wbg_next_3482f54c49e8af19: function() { return handleError(function (arg0) {
+        __wbg_next_ae5b710aea83f41e: function() { return handleError(function (arg0) {
             const ret = arg0.next();
             return ret;
         }, arguments); },
-        __wbg_next_418f80d8f5303233: function(arg0) {
+        __wbg_next_f577b3e02c9be709: function(arg0) {
             const ret = arg0.next;
             return ret;
         },
-        __wbg_prototypesetcall_bdcdcc5842e4d77d: function(arg0, arg1, arg2) {
+        __wbg_prototypesetcall_37f00e1be5c4015a: function(arg0, arg1, arg2) {
             Uint8Array.prototype.set.call(getArrayU8FromWasm0(arg0, arg1), arg2);
         },
-        __wbg_set_1eb0999cf5d27fc8: function(arg0, arg1, arg2) {
+        __wbg_set_601f3e1d081df3ac: function(arg0, arg1, arg2) {
+            arg0[arg1 >>> 0] = arg2;
+        },
+        __wbg_set_b1226382f10be917: function(arg0, arg1, arg2) {
             const ret = arg0.set(arg1, arg2);
             return ret;
         },
-        __wbg_set_3fda3bac07393de4: function(arg0, arg1, arg2) {
+        __wbg_set_d1cb61e9f39c870f: function(arg0, arg1, arg2) {
             arg0[arg1] = arg2;
         },
-        __wbg_set_f43e577aea94465b: function(arg0, arg1, arg2) {
-            arg0[arg1 >>> 0] = arg2;
-        },
-        __wbg_value_0546255b415e96c1: function(arg0) {
+        __wbg_value_3e1fdb73e1353fb3: function(arg0) {
             const ret = arg0.value;
             return ret;
         },
@@ -1060,12 +1478,17 @@ function __wbg_get_imports() {
             const ret = arg0;
             return ret;
         },
-        __wbindgen_cast_0000000000000002: function(arg0, arg1) {
+        __wbindgen_cast_0000000000000002: function(arg0) {
+            // Cast intrinsic for `I64 -> Externref`.
+            const ret = arg0;
+            return ret;
+        },
+        __wbindgen_cast_0000000000000003: function(arg0, arg1) {
             // Cast intrinsic for `Ref(String) -> Externref`.
             const ret = getStringFromWasm0(arg0, arg1);
             return ret;
         },
-        __wbindgen_cast_0000000000000003: function(arg0) {
+        __wbindgen_cast_0000000000000004: function(arg0) {
             // Cast intrinsic for `U64 -> Externref`.
             const ret = BigInt.asUintN(64, arg0);
             return ret;
@@ -1092,18 +1515,33 @@ const BedClassificationOutputFinalization = (typeof FinalizationRegistry === 'un
 const ChromosomeStatisticsFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_chromosomestatistics_free(ptr >>> 0, 1));
+const ConsensusBuilderFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_consensusbuilder_free(ptr >>> 0, 1));
+const GeneModelFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_genemodel_free(ptr >>> 0, 1));
 const OverlapperFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_overlapper_free(ptr >>> 0, 1));
+const PartitionListFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_partitionlist_free(ptr >>> 0, 1));
 const RegionDistributionFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_regiondistribution_free(ptr >>> 0, 1));
 const RegionSetFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_regionset_free(ptr >>> 0, 1));
+const SignalMatrixFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_signalmatrix_free(ptr >>> 0, 1));
 const TokenizerFinalization = (typeof FinalizationRegistry === 'undefined')
     ? { register: () => {}, unregister: () => {} }
     : new FinalizationRegistry(ptr => wasm.__wbg_tokenizer_free(ptr >>> 0, 1));
+const TssIndexFinalization = (typeof FinalizationRegistry === 'undefined')
+    ? { register: () => {}, unregister: () => {} }
+    : new FinalizationRegistry(ptr => wasm.__wbg_tssindex_free(ptr >>> 0, 1));
 
 function addToExternrefTable0(obj) {
     const idx = wasm.__externref_table_alloc();
@@ -1111,6 +1549,12 @@ function addToExternrefTable0(obj) {
     return idx;
 }
 
+function _assertClass(instance, klass) {
+    if (!(instance instanceof klass)) {
+        throw new Error(`expected instance of ${klass.name}`);
+    }
+}
+
 function debugString(val) {
     // primitive types
     const type = typeof val;
@@ -1176,6 +1620,11 @@ function debugString(val) {
     return className;
 }
 
+function getArrayU32FromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    return getUint32ArrayMemory0().subarray(ptr / 4, ptr / 4 + len);
+}
+
 function getArrayU8FromWasm0(ptr, len) {
     ptr = ptr >>> 0;
     return getUint8ArrayMemory0().subarray(ptr / 1, ptr / 1 + len);
@@ -1189,11 +1638,27 @@ function getDataViewMemory0() {
     return cachedDataViewMemory0;
 }
 
+let cachedFloat64ArrayMemory0 = null;
+function getFloat64ArrayMemory0() {
+    if (cachedFloat64ArrayMemory0 === null || cachedFloat64ArrayMemory0.byteLength === 0) {
+        cachedFloat64ArrayMemory0 = new Float64Array(wasm.memory.buffer);
+    }
+    return cachedFloat64ArrayMemory0;
+}
+
 function getStringFromWasm0(ptr, len) {
     ptr = ptr >>> 0;
     return decodeText(ptr, len);
 }
 
+let cachedUint32ArrayMemory0 = null;
+function getUint32ArrayMemory0() {
+    if (cachedUint32ArrayMemory0 === null || cachedUint32ArrayMemory0.byteLength === 0) {
+        cachedUint32ArrayMemory0 = new Uint32Array(wasm.memory.buffer);
+    }
+    return cachedUint32ArrayMemory0;
+}
+
 let cachedUint8ArrayMemory0 = null;
 function getUint8ArrayMemory0() {
     if (cachedUint8ArrayMemory0 === null || cachedUint8ArrayMemory0.byteLength === 0) {
@@ -1222,6 +1687,13 @@ function passArray8ToWasm0(arg, malloc) {
     return ptr;
 }
 
+function passArrayF64ToWasm0(arg, malloc) {
+    const ptr = malloc(arg.length * 8, 8) >>> 0;
+    getFloat64ArrayMemory0().set(arg, ptr / 8);
+    WASM_VECTOR_LEN = arg.length;
+    return ptr;
+}
+
 function passStringToWasm0(arg, malloc, realloc) {
     if (realloc === undefined) {
         const buf = cachedTextEncoder.encode(arg);
@@ -1299,6 +1771,8 @@ function __wbg_finalize_init(instance, module) {
     wasm = instance.exports;
     wasmModule = module;
     cachedDataViewMemory0 = null;
+    cachedFloat64ArrayMemory0 = null;
+    cachedUint32ArrayMemory0 = null;
     cachedUint8ArrayMemory0 = null;
     wasm.__wbindgen_start();
     return wasm;

package/package.json

@@ -4,7 +4,7 @@
   "collaborators": [
     "Nathan LeRoy <NLeRoy917@gmail.com>"
   ],
-  "version": "0.6.1",
+  "version": "0.7.1",
   "files": [
     "gtars_js_bg.wasm",
     "gtars_js.js",