@gmod/cram 3.0.7 → 4.0.1

package/dist/craiIndex.js

@@ -1,18 +1,9 @@
 "use strict";
-var __awaiter = (this && this.__awaiter) || function (thisArg, _arguments, P, generator) {
-    function adopt(value) { return value instanceof P ? value : new P(function (resolve) { resolve(value); }); }
-    return new (P || (P = Promise))(function (resolve, reject) {
-        function fulfilled(value) { try { step(generator.next(value)); } catch (e) { reject(e); } }
-        function rejected(value) { try { step(generator["throw"](value)); } catch (e) { reject(e); } }
-        function step(result) { result.done ? resolve(result.value) : adopt(result.value).then(fulfilled, rejected); }
-        step((generator = generator.apply(thisArg, _arguments || [])).next());
-    });
-};
 Object.defineProperty(exports, "__esModule", { value: true });
-const unzip_1 = require("./unzip");
-const io_1 = require("./io");
 const errors_1 = require("./errors");
-const BAI_MAGIC = 21578050; // BAI\1
+const io_1 = require("./io");
+const unzip_1 = require("./unzip");
+const BAI_MAGIC = 21_578_050; // BAI\1
 function addRecordToIndex(index, record) {
     const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record;
     const s = seqId;
@@ -28,10 +19,7 @@ function addRecordToIndex(index, record) {
     });
 }
 function maybeUnzip(data) {
-    if (data[0] === 31 && data[1] === 139) {
-        return (0, unzip_1.unzip)(data);
-    }
-    return data;
+    return data[0] === 31 && data[1] === 139 ? (0, unzip_1.unzip)(data) : data;
 }
 class CraiIndex {
     /**
@@ -44,55 +32,54 @@ class CraiIndex {
     constructor(args) {
         this.filehandle = (0, io_1.open)(args.url, args.path, args.filehandle);
     }
-    parseIndex() {
-        return __awaiter(this, void 0, void 0, function* () {
-            const index = {};
-            const uncompressedBuffer = maybeUnzip(yield this.filehandle.readFile());
-            if (uncompressedBuffer.length > 4 &&
-                uncompressedBuffer.readUInt32LE(0) === BAI_MAGIC) {
-                throw new errors_1.CramMalformedError('invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support');
-            }
-            // interpret the text as regular ascii, since it is
-            // supposed to be only digits and whitespace characters
-            // this is written in a deliberately low-level fashion for performance,
-            // because some .crai files can be pretty large.
-            let currentRecord = [];
-            let currentString = '';
-            for (const charCode of uncompressedBuffer) {
-                if ((charCode >= 48 && charCode <= 57) /* 0-9 */ ||
-                    (!currentString && charCode === 45) /* leading - */) {
-                    currentString += String.fromCharCode(charCode);
-                }
-                else if (charCode === 9 /* \t */) {
-                    currentRecord.push(Number.parseInt(currentString, 10));
-                    currentString = '';
-                }
-                else if (charCode === 10 /* \n */) {
-                    currentRecord.push(Number.parseInt(currentString, 10));
-                    currentString = '';
-                    addRecordToIndex(index, currentRecord);
-                    currentRecord = [];
-                }
-                else if (charCode !== 13 /* \r */ && charCode !== 32 /* space */) {
-                    // if there are other characters in the file besides
-                    // space and \r, something is wrong.
-                    throw new errors_1.CramMalformedError('invalid .crai index file');
-                }
+    async parseIndex() {
+        const index = {};
+        const uncompressedBuffer = maybeUnzip(await this.filehandle.readFile());
+        const dataView = new DataView(uncompressedBuffer.buffer);
+        if (uncompressedBuffer.length > 4 &&
+            dataView.getUint32(0, true) === BAI_MAGIC) {
+            throw new errors_1.CramMalformedError('invalid .crai index file. note: file appears to be a .bai index. this is technically legal but please open a github issue if you need support');
+        }
+        // interpret the text as regular ascii, since it is supposed to be only
+        // digits and whitespace characters this is written in a deliberately
+        // low-level fashion for performance, because some .crai files can be
+        // pretty large.
+        let currentRecord = [];
+        let currentString = '';
+        for (const charCode of uncompressedBuffer) {
+            if ((charCode >= 48 && charCode <= 57) /* 0-9 */ ||
+                (!currentString && charCode === 45) /* leading - */) {
+                currentString += String.fromCharCode(charCode);
             }
-            // if the file ends without a \n, we need to flush our buffers
-            if (currentString) {
+            else if (charCode === 9 /* \t */) {
                 currentRecord.push(Number.parseInt(currentString, 10));
+                currentString = '';
             }
-            if (currentRecord.length === 6) {
+            else if (charCode === 10 /* \n */) {
+                currentRecord.push(Number.parseInt(currentString, 10));
+                currentString = '';
                 addRecordToIndex(index, currentRecord);
+                currentRecord = [];
             }
-            // sort each of them by start
-            Object.entries(index).forEach(([seqId, ent]) => {
-                const e2 = ent;
-                index[seqId] = e2.sort((a, b) => a.start - b.start || a.span - b.span);
-            });
-            return index;
+            else if (charCode !== 13 /* \r */ && charCode !== 32 /* space */) {
+                // if there are other characters in the file besides
+                // space and \r, something is wrong.
+                throw new errors_1.CramMalformedError('invalid .crai index file');
+            }
+        }
+        // if the file ends without a \n, we need to flush our buffers
+        if (currentString) {
+            currentRecord.push(Number.parseInt(currentString, 10));
+        }
+        if (currentRecord.length === 6) {
+            addRecordToIndex(index, currentRecord);
+        }
+        // sort each of them by start
+        Object.entries(index).forEach(([seqId, ent]) => {
+            const e2 = ent;
+            index[seqId] = e2.sort((a, b) => a.start - b.start || a.span - b.span);
         });
+        return index;
     }
     getIndex() {
         if (!this.parseIndexP) {
@@ -108,10 +95,8 @@ class CraiIndex {
      * @returns {Promise} true if the index contains entries for
      * the given reference sequence ID, false otherwise
      */
-    hasDataForReferenceSequence(seqId) {
-        return __awaiter(this, void 0, void 0, function* () {
-            return !!(yield this.getIndex())[seqId];
-        });
+    async hasDataForReferenceSequence(seqId) {
+        return !!(await this.getIndex())[seqId];
     }
     /**
      * fetch index entries for the given range
@@ -124,31 +109,29 @@ class CraiIndex {
      * an array of objects of the form
      * `{start, span, containerStart, sliceStart, sliceBytes }`
      */
-    getEntriesForRange(seqId, queryStart, queryEnd) {
-        return __awaiter(this, void 0, void 0, function* () {
-            const seqEntries = (yield this.getIndex())[seqId];
-            if (!seqEntries) {
-                return [];
-            }
-            const compare = (entry) => {
-                const entryStart = entry.start;
-                const entryEnd = entry.start + entry.span;
-                if (entryStart > queryEnd) {
-                    return -1;
-                } // entry is ahead of query
-                if (entryEnd <= queryStart) {
-                    return 1;
-                } // entry is behind query
-                return 0; // entry overlaps query
-            };
-            const bins = [];
-            for (const entry of seqEntries) {
-                if (compare(entry) === 0) {
-                    bins.push(entry);
-                }
+    async getEntriesForRange(seqId, queryStart, queryEnd) {
+        const seqEntries = (await this.getIndex())[seqId];
+        if (!seqEntries) {
+            return [];
+        }
+        const compare = (entry) => {
+            const entryStart = entry.start;
+            const entryEnd = entry.start + entry.span;
+            if (entryStart > queryEnd) {
+                return -1;
+            } // entry is ahead of query
+            if (entryEnd <= queryStart) {
+                return 1;
+            } // entry is behind query
+            return 0; // entry overlaps query
+        };
+        const bins = [];
+        for (const entry of seqEntries) {
+            if (compare(entry) === 0) {
+                bins.push(entry);
             }
-            return bins;
-        });
+        }
+        return bins;
     }
 }
 exports.default = CraiIndex;

package/dist/craiIndex.js.map

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