Increased VCF line buffer size to support VCFs with many samples.

Author: marc-sturm

src/VcfAnnotateFromVcf/ChunkProcessor.cpp

@@ -164,11 +164,12 @@ QByteArrayList getVcfHeaderLines(const QByteArray &vcf_file_path, QByteArrayList
 			return QByteArrayList();
         }
 
-        char* buffer = new char[1048576]; //1MB buffer
+		const int buffer_size = 10485760; //10MB buffer (necessary for large multi-sample VCFs)
+		char* buffer = new char[buffer_size];
         while(!gzeof(vcfgz_file))
         {
 
-            char* char_array = gzgets(vcfgz_file, buffer, 1048576);
+			char* char_array = gzgets(vcfgz_file, buffer, buffer_size);
 
             //handle errors like truncated GZ file
             if (char_array==nullptr)

src/VcfAnnotateFromVcf/main.cpp

@@ -238,7 +238,7 @@ class ConcreteTool
 			THROW(FileAccessException, "Could not open file '" + input_path + "' for reading!");
 		}
 
-		const int buffer_size = 1048576; //1MB buffer
+		const int buffer_size = 10485760; //10MB buffer (necessary for large multi-sample VCFs)
 		char* buffer = new char[buffer_size];
 		int current_chunk = 0;
 		int vcf_line_idx = 0;

src/VcfToBedpe/VcfToBedpe.cpp

@@ -185,7 +185,7 @@ VcfToBedpe::VcfToBedpe(const QByteArray& filename)
 {
 	//set buffer size for gz file line
 	filename_ = filename;
-	buffer_size_ = 1048576; //1MB buffer
+	buffer_size_ = 10485760; //10MB buffer (necessary for large multi-sample VCFs)
 	buffer_ = new char[buffer_size_];
 
 	file_ = gzopen(filename.data(),"rb");

src/cppNGS/VcfFile.cpp

@@ -393,7 +393,7 @@ void VcfFile::loadFromVCFGZ(const QString& filename, bool allow_multi_sample, Ch
 
 	//parse
 	int line_number = 0;
-	const int buffer_size = 1048576; //1MB buffer
+	const int buffer_size = 10485760; //10MB buffer (necessary for large multi-sample VCFs)
 	char* buffer = new char[buffer_size]; 
 	//Sets holding all INFO and FORMAT IDs defined in the header (might be extended if a vcf line contains new ones)
 	QSet<QByteArray> info_ids_in_header;
@@ -1254,7 +1254,7 @@ bool VcfFile::isValid(QString filename, QString ref_file, QTextStream& out_strea
 	bool in_header = true;
 	int c_data = 0;
 	int l = 0;
-	const int buffer_size = 1048576; //1MB buffer
+	const int buffer_size = 10485760; //10MB buffer (necessary for large multi-sample VCFs)
 	char* buffer = new char[buffer_size];
 	while(!gzeof(file) && l<max_lines)
 	{