@gmod/cram 2.0.1 → 2.0.3

package/CHANGELOG.md

@@ -1,3 +1,16 @@
+# v2.0.3
+
+- Update sam header parsing to avoid breaking 'type contract'
+
+# v2.0.2
+
+- Update buffer-crc32
+- Update typescript-eslint config and related fixes
+
+# v2.0.1
+
+- Fix issue parsing header tags with : character
+
 # v2.0.0
 
 - Add lzma support via xz-decompress. This uses webassembly, so it is a major

package/dist/craiIndex.d.ts

@@ -1,11 +1,11 @@
 import { CramFileSource } from './cramFile/file';
-export type Slice = {
+export interface Slice {
     start: number;
     span: number;
     containerStart: number;
     sliceStart: number;
     sliceBytes: number;
-};
+}
 type ParsedIndex = Record<string, Slice[]>;
 export default class CraiIndex {
     private _parseCache;

package/dist/craiIndex.js

@@ -19,9 +19,6 @@ const io_1 = require("./io");
 const errors_1 = require("./errors");
 const BAI_MAGIC = 21578050; // BAI\1
 function addRecordToIndex(index, record) {
-    if (record.some(el => el === undefined)) {
-        throw new errors_1.CramMalformedError('invalid .crai index file');
-    }
     const [seqId, start, span, containerStart, sliceStart, sliceBytes] = record;
     if (!index[seqId]) {
         index[seqId] = [];
@@ -46,7 +43,7 @@ class CraiIndex {
         this.filehandle = (0, io_1.open)(args.url, args.path, args.filehandle);
         this._parseCache = new abortable_promise_cache_1.default({
             cache: new quick_lru_1.default({ maxSize: 1 }),
-            fill: (data, signal) => this.parseIndex(),
+            fill: (_data, _signal) => this.parseIndex(),
         });
     }
     parseIndex() {
@@ -70,8 +67,7 @@ class CraiIndex {
             // because some .crai files can be pretty large.
             let currentRecord = [];
             let currentString = '';
-            for (let i = 0; i < uncompressedBuffer.length; i += 1) {
-                const charCode = uncompressedBuffer[i];
+            for (const charCode of uncompressedBuffer) {
                 if ((charCode >= 48 && charCode <= 57) /* 0-9 */ ||
                     (!currentString && charCode === 45) /* leading - */) {
                     currentString += String.fromCharCode(charCode);
@@ -148,9 +144,9 @@ class CraiIndex {
                 return 0; // entry overlaps query
             };
             const bins = [];
-            for (let i = 0; i < seqEntries.length; i += 1) {
-                if (compare(seqEntries[i]) === 0) {
-                    bins.push(seqEntries[i]);
+            for (const entry of seqEntries) {
+                if (compare(entry) === 0) {
+                    bins.push(entry);
                 }
             }
             return bins;

package/dist/craiIndex.js.map

@@ -1 +1 @@
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