Add more space and brackets. (de5470ae) · Commits · github_fork / Chromap

src/chromap.cc

+7 −2

Original line number	Diff line number	Diff line
		@@ -714,13 +714,15 @@ void Chromap::OutputMappingStatistics() {
		}

		void Chromap::ParseReadFormat(const std::string &read_format) {
		uint32_t i, j;
		read1_effective_range_.Init();
		read2_effective_range_.Init();
		barcode_effective_range_.Init();

		uint32_t i, j;
		for (i = 0; i < read_format.size();) {
		for (j = i + 1; j < read_format.size() && j != ','; ++j)
		;

		bool parse_success = true;
		if (read_format[i] == 'r' && read_format[i + 1] == '1') {
		parse_success = read1_effective_range_.ParseEffectiveRange(
		@@ -734,8 +736,11 @@ void Chromap::ParseReadFormat(const std::string &read_format) {
		} else {
		parse_success = false;
		}
		if (!parse_success)

		if (!parse_success) {
		ExitWithMessage("Unknown read format: " + read_format + "\n");
		}

		i = j;
		}
		}

src/sequence_effective_range.h

+34 −13

Original line number	Diff line number	Diff line
		@@ -10,8 +10,8 @@

		namespace chromap {

		// The class handles the custom read format indicating
		// the effective range on a sequence.
		// The class handles the custom read format indicating the effective range on a
		// sequence.
		class SequenceEffectiveRange {
		public:
		SequenceEffectiveRange() {}
		@@ -24,7 +24,7 @@ class SequenceEffectiveRange {
		range_num = 1;
		}

		// Return: false - fail to parse
		// Return false if it fails to parse the format string.
		bool ParseEffectiveRange(const char *s, int len) {
		int i;
		int j = 0; // start, end, strand section
		@@ -33,15 +33,19 @@ class SequenceEffectiveRange {
		starts.clear();
		ends.clear();
		strand = 1;

		for (i = 3; i <= len; ++i) {
		if (i == len \|\| s[i] == '/' \|\| s[i] == ':') {
		buffer[blen] = '\0';
		if (j == 0)

		if (j == 0) {
		starts.push_back(atoi(buffer));
		else if (j == 1)
		} else if (j == 1) {
		ends.push_back(atoi(buffer));
		else
		} else {
		strand = buffer[0] == '+' ? 1 : -1;
		}

		blen = 0;
		if (i < len && s[i] == ':') ++j;
		} else {
		@@ -49,27 +53,41 @@ class SequenceEffectiveRange {
		++blen;
		}
		}
		if (j >= 3 \|\| starts.size() != ends.size()) return false;

		if (j >= 3 \|\| starts.size() != ends.size()) {
		return false;
		}

		std::sort(starts.begin(), starts.end());
		std::sort(ends.begin(), ends.end());

		range_num = starts.size();
		if (ends[0] == -1) {
		for (i = 0; i < range_num - 1; ++i) ends[i] = ends[i + 1];
		for (i = 0; i < range_num - 1; ++i) {
		ends[i] = ends[i + 1];
		}
		ends[i] = -1;
		}

		return true;
		}

		// Check whether the effective range is the full range
		bool IsFullRange() {
		if (strand == 1 && starts[0] == 0 && ends[0] == -1) return true;
		if (strand == 1 && starts[0] == 0 && ends[0] == -1) {
		return true;
		}

		return false;
		}

		// Replace by the range specified in the starts, ends section, but does not
		// apply the strand operation. return new length
		// apply the strand operation. Return new length.
		int Replace(char *s, int len, bool need_complement) {
		if (IsFullRange()) return len;
		if (IsFullRange()) {
		return len;
		}

		int i, j, k;
		i = 0;
		for (k = 0; k < range_num; ++k) {
		@@ -78,13 +96,16 @@ class SequenceEffectiveRange {
		if (end == -1) end = len - 1;
		for (j = start; j <= end; ++i, ++j) s[i] = s[j];
		}

		s[i] = '\0';
		len = i;

		if (strand == -1) {
		if (need_complement) {
		for (i = 0; i < len; ++i)
		for (i = 0; i < len; ++i) {
		s[i] = Uint8ToChar(((uint8_t)3) ^ (CharToUint8(s[i])));
		}
		}

		for (i = 0, j = len - 1; i < j; ++i, --j) {
		char tmp = s[i];

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