@gmod/bam 1.1.10 → 1.1.13

package/esm/record.js

@@ -1,23 +1,20 @@
 /* eslint-disable @typescript-eslint/no-empty-function */
 import Constants from './constants';
-const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('').map(s => s.charCodeAt(0));
+const SEQRET_DECODER = '=ACMGRSVTWYHKDBN'.split('');
 const CIGAR_DECODER = 'MIDNSHP=X???????'.split('');
 /**
  * Class of each BAM record returned by this API.
  */
 export default class BamRecord {
     constructor(args) {
-        this._tagOffset = undefined;
+        this.data = {};
         this._tagList = [];
         this._allTagsParsed = false;
+        const { bytes, fileOffset } = args;
+        const { byteArray, start } = bytes;
         this.data = {};
-        this.bytes = {
-            start: args.bytes.start,
-            end: args.bytes.end,
-            byteArray: args.bytes.byteArray,
-        };
-        this._id = args.fileOffset;
-        const { start, byteArray } = this.bytes;
+        this.bytes = bytes;
+        this._id = fileOffset;
         this._refID = byteArray.readInt32LE(start + 4);
         this.data.start = byteArray.readInt32LE(start + 8);
         this.flags = (byteArray.readInt32LE(start + 16) & 0xffff0000) >> 16;
@@ -67,7 +64,7 @@ export default class BamRecord {
             }
         });
         const seen = {};
-        tags = tags.filter(t => {
+        return tags.filter(t => {
             if ((t in this.data && this.data[t] === undefined) ||
                 t === 'CG' ||
                 t === 'cg') {
@@ -78,7 +75,6 @@ export default class BamRecord {
             seen[lt] = true;
             return !s;
         });
-        return tags;
     }
     parent() {
         return undefined;
@@ -108,18 +104,14 @@ export default class BamRecord {
         if (this.isSegmentUnmapped()) {
             return undefined;
         }
-        const { byteArray } = this.bytes;
-        const p = this.bytes.start +
+        const { start, byteArray } = this.bytes;
+        const p = start +
             36 +
             this.get('_l_read_name') +
             this.get('_n_cigar_op') * 4 +
             this.get('_seq_bytes');
         const lseq = this.get('seq_length');
-        const qseq = Buffer.allocUnsafe(lseq);
-        for (let j = 0; j < lseq; ++j) {
-            qseq[j] = byteArray[p + j];
-        }
-        return qseq;
+        return byteArray.subarray(p, p + lseq);
     }
     strand() {
         return this.isReverseComplemented() ? -1 : 1;
@@ -135,7 +127,8 @@ export default class BamRecord {
     }
     _read_name() {
         const nl = this.get('_l_read_name');
-        return this.bytes.byteArray.toString('ascii', this.bytes.start + 36, this.bytes.start + 36 + nl - 1);
+        const { byteArray, start } = this.bytes;
+        return byteArray.toString('ascii', start + 36, start + 36 + nl - 1);
     }
     /**
      * Get the value of a tag, parsing the tags as far as necessary.
@@ -148,9 +141,9 @@ export default class BamRecord {
         if (this._allTagsParsed) {
             return undefined;
         }
-        const { byteArray } = this.bytes;
+        const { byteArray, start } = this.bytes;
         let p = this._tagOffset ||
-            this.bytes.start +
+            start +
                 36 +
                 this.get('_l_read_name') +
                 this.get('_n_cigar_op') * 4 +
@@ -446,25 +439,24 @@ export default class BamRecord {
         return this.seq();
     }
     seq() {
-        const { byteArray } = this.bytes;
-        const p = this.bytes.start +
-            36 +
-            this.get('_l_read_name') +
-            this.get('_n_cigar_op') * 4;
+        const { start, byteArray } = this.bytes;
+        const p = start + 36 + this.get('_l_read_name') + this.get('_n_cigar_op') * 4;
         const seqBytes = this.get('_seq_bytes');
         const len = this.get('seq_length');
-        let buf = '';
-        let i = 0;
-        for (let j = 0; j < seqBytes; ++j) {
+        const buf = [];
+        for (let j = 0; j < seqBytes - 1; ++j) {
             const sb = byteArray[p + j];
-            buf += String.fromCharCode(SEQRET_DECODER[(sb & 0xf0) >> 4]);
-            i++;
-            if (i < len) {
-                buf += String.fromCharCode(SEQRET_DECODER[sb & 0x0f]);
-                i++;
-            }
+            buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
+            buf.push(SEQRET_DECODER[sb & 0x0f]);
+        }
+        // there are two bases per byte, so this handles the case where it is odd
+        // length
+        const sb = byteArray[p + seqBytes - 1];
+        buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
+        if (len % 2 === 0) {
+            buf.push(SEQRET_DECODER[sb & 0x0f]);
         }
-        return buf;
+        return buf.join('');
     }
     // adapted from igv.js
     getPairOrientation() {

package/esm/record.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@gmod/bam",
-  "version": "1.1.10",
+  "version": "1.1.13",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",
@@ -39,34 +39,29 @@
   ],
   "dependencies": {
     "@gmod/bgzf-filehandle": "^1.3.3",
-    "abortable-promise-cache": "^1.4.0",
     "buffer-crc32": "^0.2.13",
     "cross-fetch": "^3.0.2",
-    "es6-promisify": "^6.0.1",
     "generic-filehandle": "^2.0.0",
     "long": "^4.0.0",
-    "object.entries-ponyfill": "^1.0.1",
-    "quick-lru": "^2.0.0",
-    "range-parser": "^1.2.1"
+    "object.entries-ponyfill": "^1.0.1"
   },
   "devDependencies": {
     "@types/buffer-crc32": "^0.2.0",
-    "@types/jest": "^27.0.2",
+    "@types/jest": "^27.4.1",
     "@types/long": "^4.0.0",
-    "@types/node": "^12.7.8",
-    "@types/range-parser": "^1.2.3",
-    "@typescript-eslint/eslint-plugin": "^5.7.0",
-    "@typescript-eslint/parser": "^5.7.0",
-    "eslint": "^7.0.0",
-    "eslint-config-prettier": "^8.3.0",
-    "eslint-plugin-import": "^2.25.3",
+    "@types/node": "^17.0.21",
+    "@typescript-eslint/eslint-plugin": "^5.12.1",
+    "@typescript-eslint/parser": "^5.12.1",
+    "eslint": "^8.9.0",
+    "eslint-config-prettier": "^8.4.0",
+    "eslint-plugin-import": "^2.25.4",
     "eslint-plugin-prettier": "^4.0.0",
-    "jest": "^27.3.1",
+    "jest": "^27.5.1",
     "prettier": "^2.4.1",
     "rimraf": "^3.0.2",
-    "standard-changelog": "^1.0.0",
-    "ts-jest": "^27.0.7",
-    "typescript": "^4.4.4"
+    "standard-changelog": "^2.0.27",
+    "ts-jest": "^27.1.3",
+    "typescript": "^4.5.5"
   },
   "publishConfig": {
     "access": "public"