Allow gizpped barcode translate file. Bump up version number. Update a comment. (d72e3595) · Commits · github_fork / Chromap

src/barcode_translator.h

+22 −4

Original line number	Diff line number	Diff line
		@@ -9,6 +9,8 @@
		#include <string>
		#include <vector>

		#include <zlib.h>

		#include "khash.h"
		#include "utils.h"

		@@ -39,11 +41,27 @@ class BarcodeTranslator {

		void SetTranslateTable(const std::string &file) {
		barcode_translate_table_ = kh_init(k64_str);

		if (1) {
		gzFile barcode_translate_file = gzopen(file.c_str(), "r");
		const uint32_t line_buffer_size = 512;
		char file_line[line_buffer_size];
		while (gzgets(barcode_translate_file, file_line, line_buffer_size) != NULL) {
		int line_len = strlen(file_line);
		if (file_line[line_len - 1] == '\n') {
		file_line[line_len - 1] = '\0';
		}
		std::string tmp_string(file_line);
		ProcessTranslateFileLine(tmp_string);
		}
		} else {
		// Old implementation, which does not support gzipped input.
		std::ifstream file_stream(file);
		std::string file_line;
		while (getline(file_stream, file_line)) {
		ProcessTranslateFileLine(file_line);
		}
		}

		mask_ = (1ull << (2 * from_bc_length_)) - 1;
		/*for (int i = 0; i < from_bc_length_; ++i)

+1 −1

+1 −1

Original line number	Diff line number	Diff line
		@@ -48,7 +48,7 @@ void MappingGenerator<SAMMapping>::EmplaceBackSingleEndMappingRecord(
		mapping_in_memory.read_id, std::string(mapping_in_memory.read_name),
		mapping_in_memory.barcode_key, /num_dups=/1,
		mapping_in_memory.GetFragmentStartPosition(), mapping_in_memory.rid,
		/mpos=/0, /mrid=/-1, 0,
		/mpos=/0, /mrid=/-1, /tlen=/0,
		mapping_in_memory.SAM_flag, mapping_in_memory.GetStrand(),
		/is_alt=/0, mapping_in_memory.is_unique, mapping_in_memory.mapq,
		mapping_in_memory.NM, mapping_in_memory.n_cigar, mapping_in_memory.cigar,