@databio/gtars 0.8.0 → 0.8.1

package/gtars_js.d.ts

@@ -184,23 +184,74 @@ export class RegionSet {
  * A collection of RegionSets — the gtars equivalent of GRangesList.
  */
 export class RegionSetList {
-    private constructor();
     free(): void;
     [Symbol.dispose](): void;
+    /**
+     * Add a RegionSet to this list, with an optional name.
+     */
+    add(set: RegionSet, name?: string | null): void;
+    /**
+     * Compute all N union-except results in O(n) via prefix/suffix.
+     * Returns { union: RegionSet, excepts: RegionSet[] }.
+     */
+    bulkUnionExcept(): any;
     /**
      * Flatten all region sets into a single RegionSet (no merging).
      */
     concat(): RegionSet;
+    /**
+     * Build a RegionSetList directly from arrays of BED entries.
+     *
+     * @param entries - Array of arrays: [[[chr, start, end, rest], ...], ...]
+     * @param names - Optional array of names, one per set
+     */
+    static fromEntries(entries: any, names: any): RegionSetList;
     /**
      * Get a region set by 0-based index.
      */
     get(index: number): RegionSet;
+    /**
+     * Intersection of all sets.
+     */
+    intersectAll(): RegionSet;
+    /**
+     * Jaccard similarity between two sets by index.
+     */
+    jaccardAt(i: number, j: number): number;
+    /**
+     * Create an empty RegionSetList. Use `add()` to populate it.
+     */
+    constructor();
     /**
      * Compute pairwise Jaccard similarity for all pairs of region sets.
      *
      * Returns { matrix: number[][], names: string[] | null }.
      */
     pairwiseJaccard(): any;
+    /**
+     * Number of overlapping regions between two sets by index.
+     */
+    pintersectCount(i: number, j: number): number;
+    /**
+     * Number of regions in the set at the given index.
+     */
+    regionCount(index: number): number;
+    /**
+     * Setdiff of two sets by index (set[i] minus set[j]).
+     */
+    setdiffAt(i: number, j: number): RegionSet;
+    /**
+     * Union of all sets.
+     */
+    unionAll(): RegionSet;
+    /**
+     * Union of two sets by index.
+     */
+    unionAt(i: number, j: number): RegionSet;
+    /**
+     * Union of all sets except the one at the given index.
+     */
+    unionExcept(skip: number): RegionSet;
     /**
      * Number of region sets in this list.
      */
@@ -469,8 +520,6 @@ export function fastaHasherProgress(handle: number): any;
  */
 export function fastaHasherUpdate(handle: number, chunk: Uint8Array): void;
 
-export function greet(name: string): void;
-
 /**
  * Run LOLA enrichment analysis.
  *
@@ -520,30 +569,6 @@ 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;
@@ -591,17 +616,67 @@ export interface InitOutput {
     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_add: (a: number, b: number, c: number, d: number) => void;
+    readonly regionsetlist_bulkUnionExcept: (a: number) => [number, number, number];
     readonly regionsetlist_concat: (a: number) => number;
+    readonly regionsetlist_fromEntries: (a: any, b: any) => [number, number, number];
     readonly regionsetlist_get: (a: number, b: number) => [number, number, number];
+    readonly regionsetlist_intersectAll: (a: number) => [number, number, number];
+    readonly regionsetlist_jaccardAt: (a: number, b: number, c: number) => [number, number, number];
     readonly regionsetlist_length: (a: number) => number;
     readonly regionsetlist_names: (a: number) => any;
+    readonly regionsetlist_new: () => number;
     readonly regionsetlist_pairwiseJaccard: (a: number) => [number, number, number];
+    readonly regionsetlist_pintersectCount: (a: number, b: number, c: number) => [number, number, number];
+    readonly regionsetlist_regionCount: (a: number, b: number) => [number, number, number];
+    readonly regionsetlist_setdiffAt: (a: number, b: number, c: number) => [number, number, number];
+    readonly regionsetlist_unionAll: (a: number) => [number, number, number];
+    readonly regionsetlist_unionAt: (a: number, b: number, c: number) => [number, number, number];
+    readonly regionsetlist_unionExcept: (a: number, b: number) => [number, number, number];
     readonly chromosomestatistics_minimum_region_length: (a: 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_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_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 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 __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];
@@ -624,21 +699,6 @@ export interface InitOutput {
     readonly tokenizer_unkToken: (a: number) => [number, number];
     readonly tokenizer_unkTokenId: (a: number) => number;
     readonly tokenizer_vocabSize: (a: number) => number;
-    readonly __wbg_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;

package/gtars_js.js

@@ -792,6 +792,29 @@ export class RegionSetList {
         const ptr = this.__destroy_into_raw();
         wasm.__wbg_regionsetlist_free(ptr, 0);
     }
+    /**
+     * Add a RegionSet to this list, with an optional name.
+     * @param {RegionSet} set
+     * @param {string | null} [name]
+     */
+    add(set, name) {
+        _assertClass(set, RegionSet);
+        var ptr0 = isLikeNone(name) ? 0 : passStringToWasm0(name, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
+        var len0 = WASM_VECTOR_LEN;
+        wasm.regionsetlist_add(this.__wbg_ptr, set.__wbg_ptr, ptr0, len0);
+    }
+    /**
+     * Compute all N union-except results in O(n) via prefix/suffix.
+     * Returns { union: RegionSet, excepts: RegionSet[] }.
+     * @returns {any}
+     */
+    bulkUnionExcept() {
+        const ret = wasm.regionsetlist_bulkUnionExcept(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return takeFromExternrefTable0(ret[0]);
+    }
     /**
      * Flatten all region sets into a single RegionSet (no merging).
      * @returns {RegionSet}
@@ -800,6 +823,22 @@ export class RegionSetList {
         const ret = wasm.regionsetlist_concat(this.__wbg_ptr);
         return RegionSet.__wrap(ret);
     }
+    /**
+     * Build a RegionSetList directly from arrays of BED entries.
+     *
+     * @param entries - Array of arrays: [[[chr, start, end, rest], ...], ...]
+     * @param names - Optional array of names, one per set
+     * @param {any} entries
+     * @param {any} names
+     * @returns {RegionSetList}
+     */
+    static fromEntries(entries, names) {
+        const ret = wasm.regionsetlist_fromEntries(entries, names);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return RegionSetList.__wrap(ret[0]);
+    }
     /**
      * Get a region set by 0-based index.
      * @param {number} index
@@ -812,6 +851,30 @@ export class RegionSetList {
         }
         return RegionSet.__wrap(ret[0]);
     }
+    /**
+     * Intersection of all sets.
+     * @returns {RegionSet}
+     */
+    intersectAll() {
+        const ret = wasm.regionsetlist_intersectAll(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return RegionSet.__wrap(ret[0]);
+    }
+    /**
+     * Jaccard similarity between two sets by index.
+     * @param {number} i
+     * @param {number} j
+     * @returns {number}
+     */
+    jaccardAt(i, j) {
+        const ret = wasm.regionsetlist_jaccardAt(this.__wbg_ptr, i, j);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0];
+    }
     /**
      * Number of region sets in this list.
      * @returns {number}
@@ -828,6 +891,15 @@ export class RegionSetList {
         const ret = wasm.regionsetlist_names(this.__wbg_ptr);
         return ret;
     }
+    /**
+     * Create an empty RegionSetList. Use `add()` to populate it.
+     */
+    constructor() {
+        const ret = wasm.regionsetlist_new();
+        this.__wbg_ptr = ret >>> 0;
+        RegionSetListFinalization.register(this, this.__wbg_ptr, this);
+        return this;
+    }
     /**
      * Compute pairwise Jaccard similarity for all pairs of region sets.
      *
@@ -841,6 +913,80 @@ export class RegionSetList {
         }
         return takeFromExternrefTable0(ret[0]);
     }
+    /**
+     * Number of overlapping regions between two sets by index.
+     * @param {number} i
+     * @param {number} j
+     * @returns {number}
+     */
+    pintersectCount(i, j) {
+        const ret = wasm.regionsetlist_pintersectCount(this.__wbg_ptr, i, j);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] >>> 0;
+    }
+    /**
+     * Number of regions in the set at the given index.
+     * @param {number} index
+     * @returns {number}
+     */
+    regionCount(index) {
+        const ret = wasm.regionsetlist_regionCount(this.__wbg_ptr, index);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return ret[0] >>> 0;
+    }
+    /**
+     * Setdiff of two sets by index (set[i] minus set[j]).
+     * @param {number} i
+     * @param {number} j
+     * @returns {RegionSet}
+     */
+    setdiffAt(i, j) {
+        const ret = wasm.regionsetlist_setdiffAt(this.__wbg_ptr, i, j);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return RegionSet.__wrap(ret[0]);
+    }
+    /**
+     * Union of all sets.
+     * @returns {RegionSet}
+     */
+    unionAll() {
+        const ret = wasm.regionsetlist_unionAll(this.__wbg_ptr);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return RegionSet.__wrap(ret[0]);
+    }
+    /**
+     * Union of two sets by index.
+     * @param {number} i
+     * @param {number} j
+     * @returns {RegionSet}
+     */
+    unionAt(i, j) {
+        const ret = wasm.regionsetlist_unionAt(this.__wbg_ptr, i, j);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return RegionSet.__wrap(ret[0]);
+    }
+    /**
+     * Union of all sets except the one at the given index.
+     * @param {number} skip
+     * @returns {RegionSet}
+     */
+    unionExcept(skip) {
+        const ret = wasm.regionsetlist_unionExcept(this.__wbg_ptr, skip);
+        if (ret[2]) {
+            throw takeFromExternrefTable0(ret[1]);
+        }
+        return RegionSet.__wrap(ret[0]);
+    }
 }
 if (Symbol.dispose) RegionSetList.prototype[Symbol.dispose] = RegionSetList.prototype.free;
 
@@ -1550,15 +1696,6 @@ export function fastaHasherUpdate(handle, chunk) {
     }
 }
 
-/**
- * @param {string} name
- */
-export function greet(name) {
-    const ptr0 = passStringToWasm0(name, wasm.__wbindgen_malloc, wasm.__wbindgen_realloc);
-    const len0 = WASM_VECTOR_LEN;
-    wasm.greet(ptr0, len0);
-}
-
 /**
  * Run LOLA enrichment analysis.
  *
@@ -1735,9 +1872,6 @@ function __wbg_get_imports() {
         __wbg___wbindgen_throw_6ddd609b62940d55: function(arg0, arg1) {
             throw new Error(getStringFromWasm0(arg0, arg1));
         },
-        __wbg_alert_42dff0589bd812e0: function(arg0, arg1) {
-            alert(getStringFromWasm0(arg0, arg1));
-        },
         __wbg_call_e133b57c9155d22c: function() { return handleError(function (arg0, arg1) {
             const ret = arg0.call(arg1);
             return ret;

package/package.json

@@ -4,7 +4,7 @@
   "collaborators": [
     "Nathan LeRoy <NLeRoy917@gmail.com>"
   ],
-  "version": "0.8.0",
+  "version": "0.8.1",
   "files": [
     "gtars_js_bg.wasm",
     "gtars_js.js",