External control over output

io/TomahawkOutput/TomahawkOutputReader.cpp

@@ -15,6 +15,7 @@ TomahawkOutputReader::TomahawkOutputReader() :
 		filesize(0),
 		position(0),
 		size(0),
+		output_header(true),
 		writer_output_type(WRITER_TYPE::binary),
 		writer(nullptr),
 		contigs(nullptr),
@@ -45,14 +46,19 @@ bool TomahawkOutputReader::view(const std::string& input){
 		return(this->__viewFilter()); // Otherwise normal filter function
 }
 
-bool TomahawkOutputReader::__viewRegion(void){
+void TomahawkOutputReader::__openWriter(void){
 	if(this->writer_output_type == WRITER_TYPE::natural){
 		this->writer = new TomahawkOutputWriterNatural(this->contigs, &this->header);
 	}
 	else this->writer = new TomahawkOutputWriter(this->contigs, &this->header);
 
 	this->writer->open();
-	this->writer->writeHeader();
+	if(this->output_header)
+		this->writer->writeHeader();
+}
+
+bool TomahawkOutputReader::__viewRegion(void){
+	this->__openWriter();
 
 	if(this->interval_tree != nullptr){
 		const entry_type*  entry;
@@ -133,11 +139,11 @@ bool TomahawkOutputReader::__viewOnly(void){
 }
 
 bool TomahawkOutputReader::__viewFilter(void){
+	this->__openWriter();
 	const entry_type*  entry;
 	while(this->nextVariant(entry)){
 		if(this->filter.filter(*entry))
-//			std::cout << this->contigs[entry->AcontigID].name << '\t' << this->contigs[entry->BcontigID].name << '\t' << *entry << '\n';
-			entry->write(std::cout, this->contigs);
+			*this->writer << entry;
 	}
 
 	return true;

io/TomahawkOutput/TomahawkOutputReader.h

@@ -60,6 +60,20 @@ class TomahawkOutputReader {
 	bool index(const std::string& filename);
 	bool summary(const std::string& input);
 
+	//
+	bool setWriterType(const int type){
+		if(type == 0)
+			this->writer_output_type = WRITER_TYPE::binary;
+		else if(type == 1)
+			this->writer_output_type = WRITER_TYPE::natural;
+		else {
+			std::cerr << "unknown writer type: " << type << std::endl;
+			return false;
+		}
+		return true;
+	}
+	void setWriteHeader(const bool write){ this->output_header = write; }
+
 	// Read entire file into memory
 	filter_type& getFilter(void){ return this->filter; }
 
@@ -70,6 +84,7 @@ class TomahawkOutputReader {
 	bool __viewFilter(void);
 	bool __viewRegion(void);
 	bool __checkRegion(const entry_type* const entry);
+	void __openWriter(void);
 
 public:
 	U64 filesize;	// input file size
@@ -79,6 +94,7 @@ class TomahawkOutputReader {
 	std::ifstream stream; // reader stream
 	reader_type reader; // reader
 	header_type header; // header
+	bool output_header;
 
 	IO::BasicBuffer buffer; // internal buffer
 	IO::BasicBuffer output_buffer; // internal buffer

view.h

@@ -12,15 +12,17 @@ void view_usage(void){
 	"\n"
 	"Options:\n"
 	"  -i FILE  input Tomahawk (required)\n"
-	"  -o FILE  output file (- for stdout)\n\n"
-
-	"Twk parameters\n"
-	"  -G       (twk) drop genotypes in output [null]\n"
+	"  -o FILE  output file (- for stdout)\n"
 	"  -h/H     (twk/two) header only / no header [null]\n"
-	"  -N       output in tab-delimited text format [null]\n"
-	"  -B       output in binary TWO/TWK format (default)[null]\n"
+	"  -O char  output type: b for TWO format, n for tab-delimited format (default: b)\n"
+	"  -N       output in tab-delimited text format (see -O) [null]\n"
+	"  -B       output in binary TWO/TWK format (see -O, default)[null]\n"
 	"  -t INT   number of CPU threads (default: maximum available)\n\n"
 
+	// Twk parameters
+	"Twk parameters\n"
+	"  -G       drop genotypes in output [null]\n\n"
+
 	// Two parameters
 	"Two parameters\n"
 	"  -p float number of parts to split problem into (default: 1)\n"
@@ -74,11 +76,13 @@ int view(int argc, char** argv){
 	float minDprime = -1, maxDprime = 1;
 	int64_t minAlleles = 0, maxAlleles = std::numeric_limits<int64_t>::max();
 	U16 flagInclude = 0, flagExclude = 0;
+	bool outputHeader = true;
+	int outputType = 0;
 
 	int c = 0;
 	int long_index = 0;
 	int hits = 0;
-	while ((c = getopt_long(argc, argv, "i:o:P:p:a:A:R:r:f:F:d:D:w:W:hHGs", long_options, &long_index)) != -1){
+	while ((c = getopt_long(argc, argv, "i:o:P:p:a:A:R:r:f:F:d:D:w:W:O:hHGsNB", long_options, &long_index)) != -1){
 		//std::cerr << c << ":" << (char)c << '\t' << long_index << std::endl;
 		hits += 2;
 		switch (c){
@@ -190,6 +194,21 @@ int view(int argc, char** argv){
 			SILENT = 1;
 			--hits;
 			break;
+		case 'h':
+			outputHeader = true;
+			break;
+		case 'H':
+			outputHeader = false;
+			break;
+		case 'N':
+			outputType = 1;
+			break;
+		case 'B':
+			outputType = 0;
+			break;
+		case 'O':
+			outputType = atoi(optarg);
+			break;
 		}
 	}
 
@@ -245,6 +264,11 @@ int view(int argc, char** argv){
 		if(!filter.setFilterJointHF(minAlleles, maxAlleles)) return false;
 		if(!filter.setFilterP(minP, maxP)) return false;
 		if(!filter.setFilterDprime(minDprime, maxDprime)) return false;
+		reader.setWriteHeader(outputHeader);
+		if(!reader.setWriterType(outputType)){
+			std::cerr << "failed set output type" << std::endl;
+			return false;
+		}
 
 		if(!reader.Open(input))
 			return false;