Merge pull request #26 from haowenz/custom_read_format (0e5159f8) · Commits · github_fork / Chromap

src/chromap.cc

+66 −0

Original line number	Diff line number	Diff line
		@@ -4162,6 +4162,72 @@ uint8_t Chromap<MappingRecord>::GetMAPQForPairedEndRead(int num_positive_candida
		return (uint8_t)mapq;
		}

		template <typename MappingRecord>
		void Chromap<MappingRecord>::ParseReadFormat(const std::string &read_format) {
		uint32_t i ;
		int j = 0;
		int k = 0; // for read1, read2, or barcode
		read1_format_[0] = 0; read1_format_[1] = -1 ;
		read2_format_[0] = 0; read2_format_[1] = -1 ;
		barcode_format_[0] = 0; barcode_format_[1] = -1 ;
		int fields[2] = {0, -1} ;
		char buffer[20] ;
		int blen = 0;
		for (i = 0; i < read_format.size(); ++i) {
		if (read_format[i] == ',' \|\| i == 0) {
		if (i > 0) {
		buffer[blen] = '\0';
		fields[j] = atoi(buffer);

		if (k == 0)
		memcpy(read1_format_, fields, sizeof(fields));
		else if (k == 1)
		memcpy(read2_format_, fields, sizeof(fields));
		else
		memcpy(barcode_format_, fields, sizeof(fields));

		++i;
		}
		if (read_format[i] == 'r' && read_format[i + 1] == '1')
		k = 0;
		else if (read_format[i] == 'r' && read_format[i + 1] == '2')
		k = 1;
		else if (read_format[i] == 'b' && read_format[i + 1] == 'c')
		k = 2;
		else
		ExitWithMessage("Unknown read format: " + read_format + "\n");
		j = 0;
		fields[0] = fields[1] = 0;
		i += 2;
		blen = 0;
		} else {
		if (read_format[i] != ':') {
		if (j < 2) {
		buffer[blen] = read_format[i] ;
		++blen;
		}
		else {
		ExitWithMessage("Unknown read format: " + read_format + "\n");
		}
		} else {
		buffer[blen] = '\0';
		fields[j] = atoi(buffer);
		++j ;
		blen = 0;
		}
		}
		}
		buffer[blen] = '\0';
		fields[j] = atoi(buffer);
		// By initialization, it is fine even if there is no read_format specified
		if (k == 0)
		memcpy(read1_format_, fields, sizeof(fields));
		else if (k == 1)
		memcpy(read2_format_, fields, sizeof(fields));
		else
		memcpy(barcode_format_, fields, sizeof(fields));
		}

		void ChromapDriver::ParseArgsAndRun(int argc, char *argv[]) {
		cxxopts::Options options("chromap", "Fast alignment and preprocessing of chromatin profiles");
		options.add_options("Indexing")

src/chromap.h

+3 −64

Original line number	Diff line number	Diff line
		@@ -94,69 +94,7 @@ class Chromap {
		NUM_VPU_LANES_ = 4;
		}

		// Parse read format
		uint32_t i ;
		int j = 0;
		int k = 0; // for read1, read2, or barcode
		read1_format_[0] = 0; read1_format_[1] = -1 ;
		read2_format_[0] = 0; read2_format_[1] = -1 ;
		barcode_format_[0] = 0; barcode_format_[1] = -1 ;
		int fields[2] = {0, -1} ;
		char buffer[20] ;
		int blen = 0;
		for (i = 0; i < read_format.size(); ++i) {
		if (read_format[i] == ',' \|\| i == 0) {
		if (i > 0) {
		buffer[blen] = '\0';
		fields[j] = atoi(buffer);

		if (k == 0)
		memcpy(read1_format_, fields, sizeof(fields));
		else if (k == 1)
		memcpy(read2_format_, fields, sizeof(fields));
		else
		memcpy(barcode_format_, fields, sizeof(fields));

		++i;
		}
		if (read_format[i] == 'r' && read_format[i + 1] == '1')
		k = 0;
		else if (read_format[i] == 'r' && read_format[i + 1] == '2')
		k = 1;
		else if (read_format[i] == 'b' && read_format[i + 1] == 'c')
		k = 2;
		else
		ExitWithMessage("Unknown read format: " + read_format + "\n");
		j = 0;
		fields[0] = fields[1] = 0;
		i += 2;
		blen = 0;
		} else {
		if (read_format[i] != ':') {
		if (j < 2) {
		buffer[blen] = read_format[i] ;
		++blen;
		}
		else {
		ExitWithMessage("Unknown read format: " + read_format + "\n");
		}
		} else {
		buffer[blen] = '\0';
		fields[j] = atoi(buffer);
		++j ;
		blen = 0;
		}
		}
		}
		buffer[blen] = '\0';
		fields[j] = atoi(buffer);
		// By initialization, it is fine even if there is no read_format specified
		if (k == 0)
		memcpy(read1_format_, fields, sizeof(fields));
		else if (k == 1)
		memcpy(read2_format_, fields, sizeof(fields));
		else
		memcpy(barcode_format_, fields, sizeof(fields));
		ParseReadFormat(read_format);
		}

		~Chromap(){
		@@ -251,6 +189,7 @@ class Chromap {
		void GetRefStartEndPositionForReadFromMapping(Direction mapping_direction, const std::pair<int, uint64_t> &mapping, const char read, int read_length, int in_split_site, const SequenceBatch &reference, uint32_t ref_start_position, uint32_t ref_end_position, int n_cigar, uint32_t *cigar, int NM, std::string &MD_TAG);
		void GetRidRank(const std::string rid_order_path, const SequenceBatch &reference, std::vector<int> &rid_rank);
		void RerankCandidatesRid(std::vector<Candidate> &candidates);
		void ParseReadFormat(const std::string &read_format);

		inline static double GetRealTime() {
		struct timeval tp;

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