Fix speed issue by switching to BufferList

lib/fasta-parser.js

@@ -37,14 +37,14 @@
 var through = require('through2')
 var split = require('split')
 var pumpify = require('pumpify')
+var BufferList = require('bl')
 
 module.exports = function() {
   return pumpify(split(), parser())
 }
 
 function parser() {
   var cacheBuf
-  var cacheBufLen = 8
   var openID = new Buffer('{"id":"')
   var closeIDOpenSeq = new Buffer('","seq":"')
   var closeSeq = new Buffer('"}\n')
@@ -55,23 +55,24 @@ function parser() {
   function transform(buf, enc, next) {
     if (buf[0] === 62) { // If line starts with '>', this is an ID
       if (cacheBuf) { // If a previous object is in cache, push it
-        cacheBuf = Buffer.concat([cacheBuf, closeSeq], cacheBufLen+3)
-        this.push(cacheBuf)
+        cacheBuf.append(closeSeq)
+        this.push(cacheBuf.slice())
       }
       var id = buf.toString().slice(1).trim().replace(/"/g, '\\"')
-      cacheBufLen = id.length + 16
-      cacheBuf = Buffer.concat([openID, new Buffer(id), closeIDOpenSeq], cacheBufLen)
+      cacheBuf = new BufferList()
+      cacheBuf.append(openID)
+      cacheBuf.append(id)
+      cacheBuf.append(closeIDOpenSeq)
     }
     else {
-      cacheBufLen += buf.length
-      cacheBuf = Buffer.concat([cacheBuf, buf], cacheBufLen)
+      cacheBuf.append(buf)
     }
     next()
   }
 
   function flush() {
-    cacheBuf = Buffer.concat([cacheBuf, closeSeq], cacheBufLen+3)
-    this.push(cacheBuf)
+    cacheBuf.append(closeSeq)
+    this.push(cacheBuf.slice())
     this.push(null)
   }
 }

package.json

@@ -13,6 +13,7 @@
   },
   "license": "MIT",
   "dependencies": {
+    "bl": "^0.9.0",
     "pumpify": "^1.3.0",
     "split": "^0.3.0",
     "through2": "~0.6.0"