Merge branch 'master' into sam_pair (f7c15354) · Commits · github_fork / Chromap

src/chromap.cc

+91 −47

Original line number	Diff line number	Diff line
		@@ -321,6 +321,49 @@ uint32_t Chromap::SampleInputBarcodesAndExamineLength() {
		void Chromap::LoadBarcodeWhitelist() {
		double real_start_time = GetRealTime();
		int num_barcodes = 0;

		if (1) {
		gzFile barcode_whitelist_file =
		gzopen(mapping_parameters_.barcode_whitelist_file_path.c_str(), "r");
		const uint32_t barcode_buffer_size = 256;
		char barcode[barcode_buffer_size];
		while (gzgets(barcode_whitelist_file, barcode, barcode_buffer_size) != NULL) {
		size_t barcode_length = strlen(barcode);
		if (barcode[barcode_length - 1] == '\n') {
		barcode[barcode_length - 1] = '\0';
		--barcode_length;
		}
		if (barcode_length > 32) {
		ExitWithMessage("ERROR: barcode length is greater than 32!");
		}

		if (barcode_length != barcode_length_) {
		if (num_barcodes == 0) {
		ExitWithMessage(
		"ERROR: whitelist and input barcode lengths are not equal!");
		} else {
		ExitWithMessage(
		"ERROR: barcode lengths are not equal in the whitelist!");
		}
		}

		uint64_t barcode_key = GenerateSeedFromSequence(
		barcode, barcode_length, 0, barcode_length);

		int khash_return_code;
		khiter_t barcode_whitelist_lookup_table_iterator =
		kh_put(k64_seq, barcode_whitelist_lookup_table_, barcode_key,
		&khash_return_code);
		kh_value(barcode_whitelist_lookup_table_,
		barcode_whitelist_lookup_table_iterator) = 0;
		assert(khash_return_code != -1 && khash_return_code != 0);
		++num_barcodes;
		}
		if (!gzeof(barcode_whitelist_file)) {
		ExitWithMessage("ERROR: barcode whitelist file does not exist or is truncated!");
		}
		gzclose(barcode_whitelist_file);
		} else {
		std::ifstream barcode_whitelist_file_stream(
		mapping_parameters_.barcode_whitelist_file_path);
		std::string barcode_whitelist_file_line;
		@@ -374,6 +417,7 @@ void Chromap::LoadBarcodeWhitelist() {
		++num_barcodes;
		}
		barcode_whitelist_file_stream.close();
		}
		std::cerr << "Loaded " << num_barcodes << " barcodes in "
		<< GetRealTime() - real_start_time << "s.\n";
		}

src/chromap.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -29,7 +29,7 @@
		#include "temp_mapping.h"
		#include "utils.h"

		#define CHROMAP_VERSION "0.2.3-r458"
		#define CHROMAP_VERSION "0.2.3-r462"

		namespace chromap {

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