support stdin for FastqReader

OpenGene · Aug 1, 2018 · e230b4f · e230b4f
1 parent fc84cbd
commit e230b4f
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Showing 2 changed files with 11 additions and 5 deletions.
diff --git a/src/fastqreader.cpp b/src/fastqreader.cpp
@@ -9,6 +9,7 @@ FastqReader::FastqReader(string filename, bool hasQuality, bool phred64){
 	mZipFile = NULL;
 	mZipped = false;
 	mFile = NULL;
+	mStdinMode = false;
 	mPhred64 = phred64;
 	mHasQuality = hasQuality;
 	mBuf = new char[FQ_BUF_SIZE];
@@ -29,8 +30,6 @@ void FastqReader::readToBuf() {
 			cerr << "Error to read gzip file" << endl;
 		}
 	} else {
-		//mFile.read(mBuf, FQ_BUF_SIZE);
-		//mBufDataLen = mFile.gcount();
 		mBufDataLen = fread(mBuf, 1, FQ_BUF_SIZE, mFile);
 	}
 	mBufUsedLen = 0;
@@ -42,9 +41,15 @@ void FastqReader::init(){
 		mZipped = true;
 		gzrewind(mZipFile);
 	}
-	else if (isFastq(mFilename)){
-		//mFile.open(mFilename.c_str(), ifstream::in);
-		mFile = fopen(mFilename.c_str(), "r");
+	else {
+		if(mFilename == "/dev/stdin") {
+			mFile = stdin;
+		}
+		else
+			mFile = fopen(mFilename.c_str(), "rb");
+		if(mFile == NULL) {
+			error_exit("Failed to open file: " + mFilename);
+		}
 		mZipped = false;
 	}
 	readToBuf();

diff --git a/src/fastqreader.h b/src/fastqreader.h
@@ -44,6 +44,7 @@ class FastqReader{
 	char* mBuf;
 	int mBufDataLen;
 	int mBufUsedLen;
+	bool mStdinMode;
 
 };