@gmod/bam - npm Package Compare versions

Comparing version 1.0.12 to 1.0.13

CHANGELOG.md

@@ -0,1 +1,9 @@
+<a name="1.0.13"></a>
+## [1.0.13](https://github.com/GMOD/bam-js/compare/v1.0.12...v1.0.13) (2018-12-25)
+
+
+
+- Use ascii decoding for read names
+- Fix error with large BAM headers with many refseqs
+
 <a name="1.0.12"></a>
@@ -2,0 +10,0 @@ ## [1.0.12](https://github.com/GMOD/bam-js/compare/v1.0.11...v1.0.12) (2018-11-25)

dist/bamFile.js

@@ -224,10 +224,19 @@ 'use strict';
                 buf = Buffer.alloc(refSeqBytes + blockLen);
-                _context2.next = 3;
+
+                if (!(start > refSeqBytes)) {
+                  _context2.next = 3;
+                  break;
+                }
+
+                return _context2.abrupt('return', this._readRefSeqs(start, refSeqBytes * 2));
+
+              case 3:
+                _context2.next = 5;
                 return this.bam.read(buf, 0, refSeqBytes + blockLen);
 
-              case 3:
+              case 5:
                 bytesRead = _context2.sent;
 
                 if (bytesRead) {
-                  _context2.next = 6;
+                  _context2.next = 8;
                   break;
@@ -238,3 +247,3 @@ }
 
-              case 6:
+              case 8:
                 if (bytesRead < refSeqBytes) {
@@ -245,6 +254,6 @@ buf = buf.slice(0, bytesRead);
                 }
-                _context2.next = 9;
+                _context2.next = 11;
                 return unzip(buf);
 
-              case 9:
+              case 11:
                 uncba = _context2.sent;
@@ -257,5 +266,5 @@ nRef = uncba.readInt32LE(start);
 
-              case 15:
+              case 17:
                 if (!(i < nRef)) {
-                  _context2.next = 29;
+                  _context2.next = 31;
                   break;
@@ -277,3 +286,3 @@ }
                 if (!(p > uncba.length)) {
-                  _context2.next = 26;
+                  _context2.next = 28;
                   break;
@@ -285,11 +294,11 @@ }
 
-              case 26:
+              case 28:
                 i += 1;
-                _context2.next = 15;
+                _context2.next = 17;
                 break;
 
-              case 29:
+              case 31:
                 return _context2.abrupt('return', { chrToIndex: chrToIndex, indexToChr: indexToChr });
 
-              case 30:
+              case 32:
               case 'end':
@@ -296,0 +305,0 @@ return _context2.stop();

dist/record.js

@@ -190,3 +190,3 @@ 'use strict';
       var nl = this._get('_l_read_name');
-      return this.bytes.byteArray.toString('utf8', this.bytes.start + 36, this.bytes.start + 36 + nl - 1);
+      return this.bytes.byteArray.toString('ascii', this.bytes.start + 36, this.bytes.start + 36 + nl - 1);
     }
@@ -193,0 +193,0 @@

package.json

 {
   "name": "@gmod/bam",
-  "version": "1.0.12",
+  "version": "1.0.13",
   "description": "Parser for BAM and BAM index (bai) files",
@@ -5,0 +5,0 @@ "license": "MIT",

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Improved metrics

Total package byte prevSize

130965

increased by0.41%

Lines of code

2100

increased by0.29%

No dependency changes