@gmod/bam 1.1.13 → 1.1.14

package/CHANGELOG.md

@@ -1,6 +1,10 @@
-## [1.1.13](https://github.com/GMOD/bam-js/compare/v1.1.12...v1.1.13) (2022-02-25)
+## [1.1.14](https://github.com/GMOD/bam-js/compare/v1.1.13...v1.1.14) (2022-03-14)
+
 
 
+- Fix seq function for corner case
+
+## [1.1.13](https://github.com/GMOD/bam-js/compare/v1.1.12...v1.1.13) (2022-02-25)
 
 - Optimize qual and sequence string record functions for less GC pressure
 

package/dist/csi.js

@@ -16,7 +16,11 @@ var __extends = (this && this.__extends) || (function () {
 })();
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
-    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[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];

package/dist/csi.js.map

@@ -1 +1 @@
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package/dist/htsget.js

@@ -27,7 +27,11 @@ var __assign = (this && this.__assign) || function () {
 };
 var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
     if (k2 === undefined) k2 = k;
-    Object.defineProperty(o, k2, { enumerable: true, get: function() { return m[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];

package/dist/htsget.js.map

@@ -1 +1 @@
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package/dist/record.js

@@ -445,24 +445,22 @@ var BamRecord = /** @class */ (function () {
         return this.seq();
     };
     BamRecord.prototype.seq = function () {
-        var _a = this.bytes, start = _a.start, byteArray = _a.byteArray;
+        var _a = this.bytes, byteArray = _a.byteArray, start = _a.start;
         var p = start + 36 + this.get('_l_read_name') + this.get('_n_cigar_op') * 4;
         var seqBytes = this.get('_seq_bytes');
         var len = this.get('seq_length');
-        var buf = [];
-        for (var j = 0; j < seqBytes - 1; ++j) {
-            var sb_1 = byteArray[p + j];
-            buf.push(SEQRET_DECODER[(sb_1 & 0xf0) >> 4]);
-            buf.push(SEQRET_DECODER[sb_1 & 0x0f]);
-        }
-        // there are two bases per byte, so this handles the case where it is odd
-        // length
-        var sb = byteArray[p + seqBytes - 1];
-        buf.push(SEQRET_DECODER[(sb & 0xf0) >> 4]);
-        if (len % 2 === 0) {
-            buf.push(SEQRET_DECODER[sb & 0x0f]);
+        var buf = '';
+        var i = 0;
+        for (var j = 0; j < seqBytes; ++j) {
+            var sb = byteArray[p + j];
+            buf += SEQRET_DECODER[(sb & 0xf0) >> 4];
+            i++;
+            if (i < len) {
+                buf += SEQRET_DECODER[sb & 0x0f];
+                i++;
+            }
         }
-        return buf.join('');
+        return buf;
     };
     // adapted from igv.js
     BamRecord.prototype.getPairOrientation = function () {

package/dist/record.js.map

@@ -1 +1 @@
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package/esm/record.js

@@ -439,24 +439,22 @@ export default class BamRecord {
         return this.seq();
     }
     seq() {
-        const { start, byteArray } = this.bytes;
+        const { byteArray, start } = 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');
-        const buf = [];
-        for (let j = 0; j < seqBytes - 1; ++j) {
+        let buf = '';
+        let i = 0;
+        for (let j = 0; j < seqBytes; ++j) {
             const sb = byteArray[p + j];
-            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]);
+            buf += SEQRET_DECODER[(sb & 0xf0) >> 4];
+            i++;
+            if (i < len) {
+                buf += SEQRET_DECODER[sb & 0x0f];
+                i++;
+            }
         }
-        return buf.join('');
+        return buf;
     }
     // 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": "1.1.13",
+  "version": "1.1.14",
   "description": "Parser for BAM and BAM index (bai) files",
   "license": "MIT",
   "repository": "GMOD/bam-js",