@gmod/bam - npm Package Compare versions

Comparing version 1.0.5 to 1.0.6

CHANGELOG.md

@@ -0,1 +1,8 @@
+<a name="1.0.6"></a>
+## [1.0.6](https://github.com/GMOD/bam-js/compare/v1.0.5...v1.0.6) (2018-10-19)
+
+
+
+- Add bugfix for where bytes for an invalid request returns 0 resulting in pako unzip errors
+
 <a name="1.0.5"></a>
@@ -2,0 +9,0 @@ ## [1.0.5](https://github.com/GMOD/bam-js/compare/v1.0.4...v1.0.5) (2018-10-16)

dist/bamFile.js

@@ -130,3 +130,3 @@ 'use strict';
                 if (!ret) {
-                  _context.next = 13;
+                  _context.next = 15;
                   break;
@@ -142,2 +142,10 @@ }
 
+                if (bytesRead) {
+                  _context.next = 12;
+                  break;
+                }
+
+                throw new Error('Error reading header');
+
+              case 12:
                 if (bytesRead < ret) {
@@ -148,21 +156,21 @@ buf = buf.slice(0, bytesRead);
                 }
-                _context.next = 16;
+                _context.next = 18;
                 break;
 
-              case 13:
-                _context.next = 15;
+              case 15:
+                _context.next = 17;
                 return this.bam.readFile();
 
-              case 15:
+              case 17:
                 buf = _context.sent;
 
-              case 16:
-                _context.next = 18;
+              case 18:
+                _context.next = 20;
                 return unzip(buf);
 
-              case 18:
+              case 20:
                 uncba = _context.sent;
 
                 if (!(uncba.readInt32LE(0) !== BAM_MAGIC)) {
-                  _context.next = 21;
+                  _context.next = 23;
                   break;
@@ -173,3 +181,3 @@ }
 
-              case 21:
+              case 23:
                 headLen = uncba.readInt32LE(4);
@@ -179,6 +187,6 @@
                 this.header = uncba.toString('utf8', 8, 8 + headLen);
-                _context.next = 25;
+                _context.next = 27;
                 return this._readRefSeqs(headLen + 8, 65535);
 
-              case 25:
+              case 27:
                 _ref3 = _context.sent;
@@ -193,3 +201,3 @@ chrToIndex = _ref3.chrToIndex;
 
-              case 31:
+              case 33:
               case 'end':
@@ -228,2 +236,10 @@ return _context.stop();
 
+                if (bytesRead) {
+                  _context2.next = 6;
+                  break;
+                }
+
+                return _context2.abrupt('return', new Error('Error reading refseqs from header'));
+
+              case 6:
                 if (bytesRead < refSeqBytes) {
@@ -234,6 +250,6 @@ buf = buf.slice(0, bytesRead);
                 }
-                _context2.next = 7;
+                _context2.next = 9;
                 return unzip(buf);
 
-              case 7:
+              case 9:
                 uncba = _context2.sent;
@@ -246,5 +262,5 @@ nRef = uncba.readInt32LE(start);
 
-              case 13:
+              case 15:
                 if (!(i < nRef)) {
-                  _context2.next = 27;
+                  _context2.next = 29;
                   break;
@@ -266,3 +282,3 @@ }
                 if (!(p > uncba.length)) {
-                  _context2.next = 24;
+                  _context2.next = 26;
                   break;
@@ -274,11 +290,11 @@ }
 
-              case 24:
+              case 26:
                 i += 1;
-                _context2.next = 13;
+                _context2.next = 15;
                 break;
 
-              case 27:
+              case 29:
                 return _context2.abrupt('return', { chrToIndex: chrToIndex, indexToChr: indexToChr });
 
-              case 28:
+              case 30:
               case 'end':
@@ -560,2 +576,10 @@ return _context2.stop();
 
+                if (bytesRead) {
+                  _context5.next = 7;
+                  break;
+                }
+
+                return _context5.abrupt('return', []);
+
+              case 7:
                 if (bytesRead < bufsize) {
@@ -567,10 +591,10 @@ buf = buf.slice(0, bytesRead);
 
-                _context5.next = 8;
+                _context5.next = 10;
                 return unzip(buf);
 
-              case 8:
+              case 10:
                 data = _context5.sent;
                 return _context5.abrupt('return', this.readBamFeatures(data, chunk.minv.dataPosition));
 
-              case 10:
+              case 12:
               case 'end':
@@ -577,0 +601,0 @@ return _context5.stop();

package.json

 {
   "name": "@gmod/bam",
-  "version": "1.0.5",
+  "version": "1.0.6",
   "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

126423

increased by0.83%

Lines of code

2047

increased by0.89%

No dependency changes