@gmod/cram 7.0.3 → 8.0.1

package/dist/indexedCramFile.js

@@ -45,9 +45,12 @@ class IndexedCramFile {
      * @param end end of the range of interest. 1-based closed coordinates.
      */
     async getRecordsForRange(seq, start, end, opts = {}) {
-        opts.viewAsPairs = opts.viewAsPairs || false;
-        opts.pairAcrossChr = opts.pairAcrossChr || false;
-        opts.maxInsertSize = opts.maxInsertSize || 200000;
+        const viewAsPairs = opts.viewAsPairs || false;
+        const pairAcrossChr = opts.pairAcrossChr || false;
+        const maxInsertSize = opts.maxInsertSize || 200000;
+        const decodeOptions = {
+            decodeTags: opts.decodeTags,
+        };
         if (typeof seq === 'string') {
             // TODO: support string reference sequence names somehow
             throw new errors_ts_1.CramUnimplementedError('string sequence names not yet supported');
@@ -69,9 +72,9 @@ class IndexedCramFile {
             // Use > instead of >= for start boundary to match samtools behavior
             return (feature.alignmentStart <= end &&
                 feature.alignmentStart + feature.lengthOnRef - 1 > start);
-        })));
+        }, decodeOptions)));
         let ret = Array.prototype.concat(...sliceResults);
-        if (opts.viewAsPairs) {
+        if (viewAsPairs) {
             const readNames = {};
             const readIds = {};
             for (const read of ret) {
@@ -100,9 +103,9 @@ class IndexedCramFile {
                 }
                 if (unmatedPairs[name] &&
                     cramRecord.mate &&
-                    (cramRecord.mate.sequenceId === seqId || opts.pairAcrossChr) &&
+                    (cramRecord.mate.sequenceId === seqId || pairAcrossChr) &&
                     Math.abs(cramRecord.alignmentStart - cramRecord.mate.alignmentStart) <
-                        opts.maxInsertSize) {
+                        maxInsertSize) {
                     const mateSlices = this.index.getEntriesForRange(cramRecord.mate.sequenceId, cramRecord.mate.alignmentStart, cramRecord.mate.alignmentStart + 1);
                     matePromises.push(mateSlices);
                 }
@@ -147,10 +150,10 @@ class IndexedCramFile {
         }
         return ret;
     }
-    getRecordsInSlice({ containerStart, sliceStart, sliceBytes, }, filterFunction) {
+    getRecordsInSlice({ containerStart, sliceStart, sliceBytes, }, filterFunction, decodeOptions) {
         const container = this.cram.getContainerAtPosition(containerStart);
         const slice = container.getSlice(sliceStart, sliceBytes);
-        return slice.getRecords(filterFunction);
+        return slice.getRecords(filterFunction, decodeOptions);
     }
     /**
      *

package/dist/indexedCramFile.js.map

@@ -1 +1 @@
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package/dist/wasm/htscodecs.js.map

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package/dist/wasm/noodles-cram/noodles_cram_wasm.d.ts

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

package/dist/wasm/noodles-cram/noodles_cram_wasm.js

@@ -0,0 +1,44 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+const wasm = __importStar(require("./noodles_cram_wasm_bg.wasm"));
+__exportStar(require("./noodles_cram_wasm_bg.js"), exports);
+const noodles_cram_wasm_bg_js_1 = require("./noodles_cram_wasm_bg.js");
+(0, noodles_cram_wasm_bg_js_1.__wbg_set_wasm)(wasm);
+wasm.__wbindgen_start();
+//# sourceMappingURL=noodles_cram_wasm.js.map

package/dist/wasm/noodles-cram/noodles_cram_wasm.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"noodles_cram_wasm.js","sourceRoot":"","sources":["../../../src/wasm/noodles-cram/noodles_cram_wasm.js"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,kEAAoD;AACpD,4DAA0C;AAC1C,uEAA2D;AAC3D,IAAA,wCAAc,EAAC,IAAI,CAAC,CAAC;AACrB,IAAI,CAAC,gBAAgB,EAAE,CAAC"}

package/dist/wasm/noodles-cram/noodles_cram_wasm_bg.d.ts

@@ -0,0 +1,94 @@
+export function __wbg_set_wasm(val: any): void;
+/**
+ * Get the byte position where the header ends (first data container starts)
+ *
+ * # Arguments
+ * * `data` - The CRAM file data (only needs first ~64KB typically)
+ * @param {Uint8Array} data
+ * @returns {bigint}
+ */
+export function get_header_length(data: Uint8Array): bigint;
+export function init_panic_hook(): void;
+/**
+ * @param {Uint8Array} data
+ * @returns {any}
+ */
+export function parse_crai_index(data: Uint8Array): any;
+/**
+ * @param {Uint8Array} data
+ * @returns {any}
+ */
+export function parse_cram_file(data: Uint8Array): any;
+/**
+ * Parse a CRAM file with reference sequences provided
+ *
+ * # Arguments
+ * * `data` - The CRAM file data as bytes
+ * * `references` - Array of {name: string, sequence: string} objects
+ * @param {Uint8Array} data
+ * @param {any} references
+ * @returns {any}
+ */
+export function parse_cram_file_with_references(data: Uint8Array, references: any): any;
+/**
+ * Parse records from a specific region of a CRAM file
+ *
+ * This function is designed for indexed access. It takes:
+ * - header_data: The CRAM file from start up to the first data container
+ * - container_data: The bytes of the container(s) to parse
+ * - references: Reference sequences needed for decoding
+ *
+ * # Arguments
+ * * `header_data` - Bytes from file start through header container
+ * * `container_data` - Bytes of the data container(s) to parse
+ * * `references` - Array of {name: string, sequence: string} objects
+ * @param {Uint8Array} header_data
+ * @param {Uint8Array} container_data
+ * @param {any} references
+ * @returns {any}
+ */
+export function parse_cram_records_from_container(header_data: Uint8Array, container_data: Uint8Array, references: any): any;
+/**
+ * @param {Uint8Array} data
+ * @returns {any}
+ */
+export function parse_header(data: Uint8Array): any;
+export function __wbg_Error_52673b7de5a0ca89(arg0: any, arg1: any): Error;
+export function __wbg_String_8f0eb39a4a4c2f66(arg0: any, arg1: any): void;
+export function __wbg___wbindgen_boolean_get_dea25b33882b895b(arg0: any): 0 | 1 | 16777215;
+export function __wbg___wbindgen_debug_string_adfb662ae34724b6(arg0: any, arg1: any): void;
+export function __wbg___wbindgen_in_0d3e1e8f0c669317(arg0: any, arg1: any): boolean;
+export function __wbg___wbindgen_is_function_8d400b8b1af978cd(arg0: any): boolean;
+export function __wbg___wbindgen_is_object_ce774f3490692386(arg0: any): boolean;
+export function __wbg___wbindgen_is_undefined_f6b95eab589e0269(arg0: any): boolean;
+export function __wbg___wbindgen_jsval_loose_eq_766057600fdd1b0d(arg0: any, arg1: any): boolean;
+export function __wbg___wbindgen_number_get_9619185a74197f95(arg0: any, arg1: any): void;
+export function __wbg___wbindgen_string_get_a2a31e16edf96e42(arg0: any, arg1: any): void;
+export function __wbg___wbindgen_throw_dd24417ed36fc46e(arg0: any, arg1: any): void;
+export function __wbg_call_abb4ff46ce38be40(...args: any[]): any;
+export function __wbg_done_62ea16af4ce34b24(arg0: any): any;
+export function __wbg_error_7534b8e9a36f1ab4(arg0: any, arg1: any): void;
+export function __wbg_get_6b7bd52aca3f9671(arg0: any, arg1: any): any;
+export function __wbg_get_af9dab7e9603ea93(...args: any[]): any;
+export function __wbg_get_with_ref_key_1dc361bd10053bfe(arg0: any, arg1: any): any;
+export function __wbg_instanceof_ArrayBuffer_f3320d2419cd0355(arg0: any): boolean;
+export function __wbg_instanceof_Uint8Array_da54ccc9d3e09434(arg0: any): boolean;
+export function __wbg_isArray_51fd9e6422c0a395(arg0: any): arg0 is any[];
+export function __wbg_iterator_27b7c8b35ab3e86b(): symbol;
+export function __wbg_length_22ac23eaec9d8053(arg0: any): any;
+export function __wbg_length_d45040a40c570362(arg0: any): any;
+export function __wbg_new_1ba21ce319a06297(): Object;
+export function __wbg_new_25f239778d6112b9(): any[];
+export function __wbg_new_6421f6084cc5bc5a(arg0: any): Uint8Array<any>;
+export function __wbg_new_8a6f238a6ece86ea(): Error;
+export function __wbg_next_138a17bbf04e926c(arg0: any): any;
+export function __wbg_next_3cfe5c0fe2a4cc53(...args: any[]): any;
+export function __wbg_prototypesetcall_dfe9b766cdc1f1fd(arg0: any, arg1: any, arg2: any): void;
+export function __wbg_set_3f1d0b984ed272ed(arg0: any, arg1: any, arg2: any): void;
+export function __wbg_set_7df433eea03a5c14(arg0: any, arg1: any, arg2: any): void;
+export function __wbg_stack_0ed75d68575b0f3c(arg0: any, arg1: any): void;
+export function __wbg_value_57b7b035e117f7ee(arg0: any): any;
+export function __wbindgen_cast_2241b6af4c4b2941(arg0: any, arg1: any): string;
+export function __wbindgen_cast_4625c577ab2ec9ee(arg0: any): bigint;
+export function __wbindgen_cast_d6cd19b81560fd6e(arg0: any): any;
+export function __wbindgen_init_externref_table(): void;