@gmod/bbi 7.0.5 → 8.0.0

package/esm/wasm/inflate-wasm-inlined.js.map

@@ -0,0 +1 @@
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package/esm/wasm/inflate_wasm.d.ts

@@ -0,0 +1 @@
+export * from "./inflate_wasm_bg.js";

package/esm/wasm/inflate_wasm.js

@@ -0,0 +1,5 @@
+import * as wasm from "./inflate_wasm_bg.wasm";
+export * from "./inflate_wasm_bg.js";
+import { __wbg_set_wasm } from "./inflate_wasm_bg.js";
+__wbg_set_wasm(wasm);
+//# sourceMappingURL=inflate_wasm.js.map

package/esm/wasm/inflate_wasm.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"inflate_wasm.js","sourceRoot":"","sources":["../../src/wasm/inflate_wasm.js"],"names":[],"mappings":"AAAA,OAAO,KAAK,IAAI,MAAM,wBAAwB,CAAC;AAC/C,cAAc,sBAAsB,CAAC;AACrC,OAAO,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AACtD,cAAc,CAAC,IAAI,CAAC,CAAC"}

package/esm/wasm/inflate_wasm_bg.d.ts

@@ -0,0 +1,68 @@
+export function __wbg_set_wasm(val: any): void;
+/**
+ * Combined decompress + parse for BigWig blocks
+ * Returns same format as parse_bigwig_block but handles multiple compressed blocks
+ * @param {Uint8Array} inputs
+ * @param {Uint32Array} input_offsets
+ * @param {Uint32Array} input_lengths
+ * @param {number} max_block_size
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function decompress_and_parse_bigwig(inputs: Uint8Array, input_offsets: Uint32Array, input_lengths: Uint32Array, max_block_size: number, req_start: number, req_end: number): Uint8Array;
+/**
+ * Combined decompress + parse for summary blocks
+ * @param {Uint8Array} inputs
+ * @param {Uint32Array} input_offsets
+ * @param {Uint32Array} input_lengths
+ * @param {number} max_block_size
+ * @param {number} req_chr_id
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function decompress_and_parse_summary(inputs: Uint8Array, input_offsets: Uint32Array, input_lengths: Uint32Array, max_block_size: number, req_chr_id: number, req_start: number, req_end: number): Uint8Array;
+/**
+ * @param {Uint8Array} input
+ * @param {number} output_size
+ * @returns {Uint8Array}
+ */
+export function inflate_raw(input: Uint8Array, output_size: number): Uint8Array;
+/**
+ * @param {Uint8Array} inputs
+ * @param {Uint32Array} input_offsets
+ * @param {Uint32Array} input_lengths
+ * @param {number} max_block_size
+ * @returns {Uint8Array}
+ */
+export function inflate_raw_batch(inputs: Uint8Array, input_offsets: Uint32Array, input_lengths: Uint32Array, max_block_size: number): Uint8Array;
+/**
+ * @param {Uint8Array} input
+ * @returns {Uint8Array}
+ */
+export function inflate_raw_unknown_size(input: Uint8Array): Uint8Array;
+/**
+ * Parse a BigWig data block and return packed typed arrays
+ * Block types: 1 = bedGraph, 2 = varstep, 3 = fixedstep
+ *
+ * Returns packed binary: [count: u32][starts: i32*count][ends: i32*count][scores: f32*count]
+ * @param {Uint8Array} data
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function parse_bigwig_block(data: Uint8Array, req_start: number, req_end: number): Uint8Array;
+/**
+ * Parse a BigWig summary block and return packed typed arrays
+ * Summary blocks contain: chromId, start, end, validCnt, minScore, maxScore, sumData, sumSqData
+ *
+ * Returns: [count: u32][starts: i32*n][ends: i32*n][scores: f32*n][minScores: f32*n][maxScores: f32*n]
+ * @param {Uint8Array} data
+ * @param {number} req_chr_id
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function parse_summary_block(data: Uint8Array, req_chr_id: number, req_start: number, req_end: number): Uint8Array;
+export function __wbg_Error_52673b7de5a0ca89(arg0: any, arg1: any): number;

package/esm/wasm/inflate_wasm_bg.js

@@ -0,0 +1,296 @@
+let wasm;
+export function __wbg_set_wasm(val) {
+    wasm = val;
+}
+function addHeapObject(obj) {
+    if (heap_next === heap.length)
+        heap.push(heap.length + 1);
+    const idx = heap_next;
+    heap_next = heap[idx];
+    heap[idx] = obj;
+    return idx;
+}
+function dropObject(idx) {
+    if (idx < 132)
+        return;
+    heap[idx] = heap_next;
+    heap_next = idx;
+}
+function getArrayU8FromWasm0(ptr, len) {
+    ptr = ptr >>> 0;
+    return getUint8ArrayMemory0().subarray(ptr / 1, ptr / 1 + len);
+}
+let cachedDataViewMemory0 = null;
+function getDataViewMemory0() {
+    if (cachedDataViewMemory0 === null || cachedDataViewMemory0.buffer.detached === true || (cachedDataViewMemory0.buffer.detached === undefined && cachedDataViewMemory0.buffer !== wasm.memory.buffer)) {
+        cachedDataViewMemory0 = new DataView(wasm.memory.buffer);
+    }
+    return cachedDataViewMemory0;
+}
+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) {
+        cachedUint8ArrayMemory0 = new Uint8Array(wasm.memory.buffer);
+    }
+    return cachedUint8ArrayMemory0;
+}
+function getObject(idx) { return heap[idx]; }
+let heap = new Array(128).fill(undefined);
+heap.push(undefined, null, true, false);
+let heap_next = heap.length;
+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);
+    WASM_VECTOR_LEN = arg.length;
+    return ptr;
+}
+function takeObject(idx) {
+    const ret = getObject(idx);
+    dropObject(idx);
+    return ret;
+}
+let cachedTextDecoder = new TextDecoder('utf-8', { ignoreBOM: true, fatal: true });
+cachedTextDecoder.decode();
+const MAX_SAFARI_DECODE_BYTES = 2146435072;
+let numBytesDecoded = 0;
+function decodeText(ptr, len) {
+    numBytesDecoded += len;
+    if (numBytesDecoded >= MAX_SAFARI_DECODE_BYTES) {
+        cachedTextDecoder = new TextDecoder('utf-8', { ignoreBOM: true, fatal: true });
+        cachedTextDecoder.decode();
+        numBytesDecoded = len;
+    }
+    return cachedTextDecoder.decode(getUint8ArrayMemory0().subarray(ptr, ptr + len));
+}
+let WASM_VECTOR_LEN = 0;
+/**
+ * Combined decompress + parse for BigWig blocks
+ * Returns same format as parse_bigwig_block but handles multiple compressed blocks
+ * @param {Uint8Array} inputs
+ * @param {Uint32Array} input_offsets
+ * @param {Uint32Array} input_lengths
+ * @param {number} max_block_size
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function decompress_and_parse_bigwig(inputs, input_offsets, input_lengths, max_block_size, req_start, req_end) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(inputs, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passArray32ToWasm0(input_offsets, wasm.__wbindgen_export);
+        const len1 = WASM_VECTOR_LEN;
+        const ptr2 = passArray32ToWasm0(input_lengths, wasm.__wbindgen_export);
+        const len2 = WASM_VECTOR_LEN;
+        wasm.decompress_and_parse_bigwig(retptr, ptr0, len0, ptr1, len1, ptr2, len2, max_block_size, req_start, req_end);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var r2 = getDataViewMemory0().getInt32(retptr + 4 * 2, true);
+        var r3 = getDataViewMemory0().getInt32(retptr + 4 * 3, true);
+        if (r3) {
+            throw takeObject(r2);
+        }
+        var v4 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v4;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+/**
+ * Combined decompress + parse for summary blocks
+ * @param {Uint8Array} inputs
+ * @param {Uint32Array} input_offsets
+ * @param {Uint32Array} input_lengths
+ * @param {number} max_block_size
+ * @param {number} req_chr_id
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function decompress_and_parse_summary(inputs, input_offsets, input_lengths, max_block_size, req_chr_id, req_start, req_end) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(inputs, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passArray32ToWasm0(input_offsets, wasm.__wbindgen_export);
+        const len1 = WASM_VECTOR_LEN;
+        const ptr2 = passArray32ToWasm0(input_lengths, wasm.__wbindgen_export);
+        const len2 = WASM_VECTOR_LEN;
+        wasm.decompress_and_parse_summary(retptr, ptr0, len0, ptr1, len1, ptr2, len2, max_block_size, req_chr_id, req_start, req_end);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var r2 = getDataViewMemory0().getInt32(retptr + 4 * 2, true);
+        var r3 = getDataViewMemory0().getInt32(retptr + 4 * 3, true);
+        if (r3) {
+            throw takeObject(r2);
+        }
+        var v4 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v4;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+/**
+ * @param {Uint8Array} input
+ * @param {number} output_size
+ * @returns {Uint8Array}
+ */
+export function inflate_raw(input, output_size) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(input, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.inflate_raw(retptr, ptr0, len0, output_size);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var r2 = getDataViewMemory0().getInt32(retptr + 4 * 2, true);
+        var r3 = getDataViewMemory0().getInt32(retptr + 4 * 3, true);
+        if (r3) {
+            throw takeObject(r2);
+        }
+        var v2 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v2;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+/**
+ * @param {Uint8Array} inputs
+ * @param {Uint32Array} input_offsets
+ * @param {Uint32Array} input_lengths
+ * @param {number} max_block_size
+ * @returns {Uint8Array}
+ */
+export function inflate_raw_batch(inputs, input_offsets, input_lengths, max_block_size) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(inputs, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        const ptr1 = passArray32ToWasm0(input_offsets, wasm.__wbindgen_export);
+        const len1 = WASM_VECTOR_LEN;
+        const ptr2 = passArray32ToWasm0(input_lengths, wasm.__wbindgen_export);
+        const len2 = WASM_VECTOR_LEN;
+        wasm.inflate_raw_batch(retptr, ptr0, len0, ptr1, len1, ptr2, len2, max_block_size);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var r2 = getDataViewMemory0().getInt32(retptr + 4 * 2, true);
+        var r3 = getDataViewMemory0().getInt32(retptr + 4 * 3, true);
+        if (r3) {
+            throw takeObject(r2);
+        }
+        var v4 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v4;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+/**
+ * @param {Uint8Array} input
+ * @returns {Uint8Array}
+ */
+export function inflate_raw_unknown_size(input) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(input, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.inflate_raw_unknown_size(retptr, ptr0, len0);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var r2 = getDataViewMemory0().getInt32(retptr + 4 * 2, true);
+        var r3 = getDataViewMemory0().getInt32(retptr + 4 * 3, true);
+        if (r3) {
+            throw takeObject(r2);
+        }
+        var v2 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v2;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+/**
+ * Parse a BigWig data block and return packed typed arrays
+ * Block types: 1 = bedGraph, 2 = varstep, 3 = fixedstep
+ *
+ * Returns packed binary: [count: u32][starts: i32*count][ends: i32*count][scores: f32*count]
+ * @param {Uint8Array} data
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function parse_bigwig_block(data, req_start, req_end) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(data, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.parse_bigwig_block(retptr, ptr0, len0, req_start, req_end);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var v2 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v2;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+/**
+ * Parse a BigWig summary block and return packed typed arrays
+ * Summary blocks contain: chromId, start, end, validCnt, minScore, maxScore, sumData, sumSqData
+ *
+ * Returns: [count: u32][starts: i32*n][ends: i32*n][scores: f32*n][minScores: f32*n][maxScores: f32*n]
+ * @param {Uint8Array} data
+ * @param {number} req_chr_id
+ * @param {number} req_start
+ * @param {number} req_end
+ * @returns {Uint8Array}
+ */
+export function parse_summary_block(data, req_chr_id, req_start, req_end) {
+    try {
+        const retptr = wasm.__wbindgen_add_to_stack_pointer(-16);
+        const ptr0 = passArray8ToWasm0(data, wasm.__wbindgen_export);
+        const len0 = WASM_VECTOR_LEN;
+        wasm.parse_summary_block(retptr, ptr0, len0, req_chr_id, req_start, req_end);
+        var r0 = getDataViewMemory0().getInt32(retptr + 4 * 0, true);
+        var r1 = getDataViewMemory0().getInt32(retptr + 4 * 1, true);
+        var v2 = getArrayU8FromWasm0(r0, r1).slice();
+        wasm.__wbindgen_export2(r0, r1 * 1, 1);
+        return v2;
+    }
+    finally {
+        wasm.__wbindgen_add_to_stack_pointer(16);
+    }
+}
+export function __wbg_Error_52673b7de5a0ca89(arg0, arg1) {
+    const ret = Error(getStringFromWasm0(arg0, arg1));
+    return addHeapObject(ret);
+}
+;
+//# sourceMappingURL=inflate_wasm_bg.js.map

package/esm/wasm/inflate_wasm_bg.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bbi",
-  "version": "7.0.5",
+  "version": "8.0.0",
   "description": "Parser for BigWig/BigBed files",
   "license": "MIT",
   "repository": "GMOD/bbi-js",
@@ -25,15 +25,18 @@
   ],
   "scripts": {
     "test": "vitest",
+    "benchonly": "vitest bench",
+    "bench": "./scripts/build-both-branches.sh \"$BRANCH1\" \"$BRANCH2\" && vitest bench",
     "lint": "eslint --report-unused-disable-directives --max-warnings 0",
-    "format": "prettier",
+    "format": "prettier --write .",
     "clean": "rimraf dist esm",
-    "prebuild": "npm run clean",
+    "prebuild": "yarn clean",
+    "build:wasm": "./scripts/build-wasm.sh",
     "build:esm": "tsc --outDir esm",
     "build:es5": "tsc --module commonjs --outDir dist",
     "postbuild:es5": "echo '{\"type\": \"commonjs\"}' > dist/package.json",
-    "build": "npm run build:esm && npm run build:es5",
-    "preversion": "npm run lint && npm test run && npm run build",
+    "build": "yarn build:wasm && yarn build:esm && yarn build:es5",
+    "preversion": "yarn lint && yarn test --run && yarn build",
     "version": "standard-changelog && git add CHANGELOG.md",
     "postversion": "git push origin master --follow-tags"
   },
@@ -48,26 +51,27 @@
   "dependencies": {
     "@gmod/abortable-promise-cache": "^3.0.1",
     "generic-filehandle2": "^2.0.10",
-    "pako": "^2.0.0",
+    "pako-esm2": "^2.0.2",
     "quick-lru": "^4.0.0",
     "rxjs": "^7.8.0"
   },
   "devDependencies": {
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-    "@types/pako": "^2.0.0",
-    "@typescript-eslint/eslint-plugin": "^8.4.0",
-    "@typescript-eslint/parser": "^8.4.0",
-    "@vitest/coverage-v8": "^3.0.1",
+    "@types/node": "^24.10.0",
+    "@typescript-eslint/eslint-plugin": "^8.49.0",
+    "@typescript-eslint/parser": "^8.49.0",
+    "@vitest/coverage-v8": "^4.0.15",
     "eslint": "^9.9.1",
     "eslint-plugin-import": "^2.31.0",
-    "eslint-plugin-unicorn": "^59.0.0",
-    "prettier": "^3.2.5",
-    "rimraf": "^6.0.1",
-    "standard-changelog": "^6.0.0",
+    "eslint-plugin-unicorn": "^62.0.0",
+    "prettier": "^3.7.4",
+    "rimraf": "^6.1.2",
+    "standard-changelog": "^7.0.1",
     "typescript": "^5.1.6",
-    "typescript-eslint": "^8.4.0",
-    "vitest": "^3.0.1"
+    "typescript-eslint": "^8.49.0",
+    "vitest": "^4.0.15",
+    "webpack": "^5.103.0",
+    "webpack-cli": "^6.0.1"
   },
   "publishConfig": {
     "access": "public"