max_num_mappings_in_mem when using too many temp files (2af1986f) · Commits · github_fork / Chromap

src/chromap.h

+7 −0

Original line number	Diff line number	Diff line
		@@ -457,6 +457,10 @@ void Chromap::MapSingleEndReads() {
		mapping_writer.OutputTempMappings(num_reference_sequences,
		mappings_on_diff_ref_seqs,
		temp_mapping_file_handles);

		if (temp_mapping_file_handles.size() > 900
		&& temp_mapping_file_handles.size() % 10 == 1) // every 10 temp files, double the temp file size
		max_num_mappings_in_mem <<= 1;
		num_mappings_in_mem = 0;
		}
		}
		@@ -1016,6 +1020,9 @@ void Chromap::MapPairedEndReads() {
		mapping_writer.OutputTempMappings(num_reference_sequences,
		mappings_on_diff_ref_seqs,
		temp_mapping_file_handles);
		if (temp_mapping_file_handles.size() > 900
		&& temp_mapping_file_handles.size() % 10 == 1) // every 10 temp files, double the temp file size
		max_num_mappings_in_mem <<= 1;
		num_mappings_in_mem = 0;
		}
		} // end of omp task to handle output

+1 −1

Original line number	Diff line number	Diff line
		@@ -40,7 +40,7 @@ struct TempMappingFileHandle {
		inline void InitializeTempMappingLoading(uint32_t temp_mapping_block_size) {
		file = fopen(file_path.c_str(), "rb");
		if (file == NULL) {
		std::cerr << "Temporary file " << file_path << " is missing.\n" ;
		std::cerr << "Cannot open temporary file " << file_path << ". This may be caused by creating too many temporary files, please consider using command like \"ulimit -n 32768 -u 32768\" to increase the limit.\n" ;
		}
		assert(file != NULL);
		num_mappings = 0;