Merge pull request #7 from mklarqvist/dev2

Bug fix if not expanding before linear index
mklarqvist · Sep 25, 2017 · 7f08de7 · 7f08de7
2 parents 6696eca + 8ffd535
commit 7f08de7
Showing 2 changed files with 7 additions and 4 deletions.
diff --git a/src/algorithm/sort/TomahawkOutputSort.cpp b/src/algorithm/sort/TomahawkOutputSort.cpp
@@ -291,6 +291,7 @@ bool TomahawkOutputSorter::sortMerge(const std::string& inputFile, const std::st
 		return false;
 	}
 
+	toi_header.controller.partial_sort = false;
 	toi_header.controller.sorted = true;
 	writer_type writer(this->reader.contigs, &this->reader.header, toi_header);
 
@@ -358,15 +359,16 @@ bool TomahawkOutputSorter::sortMerge(const std::string& inputFile, const std::st
 	}
 
 	writer.flush();
-	if(!writer.finalize()){
+	if(!writer.finalize(toi_header.controller.expanded)){
 		std::cerr << Helpers::timestamp("ERROR","SORT") << "Failed to finalize index..." << std::endl;
 		return false;
 	}
 
 	writer.close();
 
 	// Temp
-	index_type& index = writer.getIndex();
+	//index_type& index = writer.getIndex();
+	//std::cerr << index << std::endl;
 
 	// Cleanup
 	for(U32 i = 0; i < n_toi_entries; ++i)

diff --git a/src/tomahawk/TomahawkOutput/TomahawkOutputWriter.h b/src/tomahawk/TomahawkOutput/TomahawkOutputWriter.h
@@ -318,7 +318,7 @@ class TomahawkOutputWriterIndex : public TomahawkOutputWriter{
 
 	index_type& getIndex(void){ return(this->index); }
 
-	bool finalize(void){
+	bool finalize(bool output_index){
 		// Totempole Output Index
 		// Update blocks written
 		std::fstream re(this->basePath + this->baseName + '.' + Tomahawk::Constants::OUTPUT_LD_SUFFIX + '.' + Tomahawk::Constants::OUTPUT_LD_SORT_INDEX_SUFFIX, std::ios::in | std::ios::out | std::ios::binary);
@@ -340,7 +340,8 @@ class TomahawkOutputWriterIndex : public TomahawkOutputWriter{
 		re.close();
 
 		// Write sorted index
-		this->stream_index.getNativeStream() << this->index;
+		if(output_index)
+			this->stream_index.getNativeStream() << this->index;
 
 		return true;
 	}