/* Description: 解析read的name中的信息，比如tile, x, y等 Copyright : All right reserved by ICT Author : Zhang Zhonghai Date : 2023/11/6 */ #ifndef READ_NAME_PARSER_H_ #define READ_NAME_PARSER_H_ #include "read_ends.h" #include #include #include // #include #include // using std::regex; using boost::cmatch; using boost::regex; using std::string; /** * Provides access to the physical location information about a cluster. * All values should be defaulted to -1 if unavailable. ReadGroup and Tile should only allow * non-zero positive integers, x and y coordinates may be negative. * 非线程安全 */ struct ReadNameParser { /** * The read name regular expression (regex) is used to extract three pieces of information from the read name: tile, x location, * and y location. Any read name regex should parse the read name to produce these and only these values. An example regex is: * (?:.*:)?([0-9]+)[^:]*:([0-9]+)[^:]*:([0-9]+)[^:]*$ * which assumes that fields in the read name are delimited by ':' and the last three fields correspond to the tile, x and y locations, * ignoring any trailing non-digit characters. * * The default regex is optimized for fast parsing (see {@link #getLastThreeFields(String, char, int[])}) by searching for the last * three fields, ignoring any trailing non-digit characters, assuming the delimiter ':'. This should consider correctly read names * where we have 5 or 7 field with the last three fields being tile/x/y, as is the case for the majority of read names produced by * Illumina technology. */ const string DEFAULT_READ_NAME_REGEX = "(?:.*:)?([0-9]+)[^:]*:([0-9]+)[^:]*:([0-9]+)[^:]*$"; string readNameStored = ""; PhysicalLocation physicalLocationStored; int tmpLocationFields[3]; // for optimization of addLocationInformation bool useOptimizedDefaultParsing = true; // was the regex default? string readNameRegex = DEFAULT_READ_NAME_REGEX; regex readNamePattern; bool warnedAboutRegexNotMatching = true; ReadNameParser() : ReadNameParser(DEFAULT_READ_NAME_REGEX) {} ReadNameParser(const string &strReadNameRegex) : ReadNameParser(strReadNameRegex, true) {} ReadNameParser(const string &strReadNameRegex, bool isWarn) { readNameRegex = strReadNameRegex; if (strReadNameRegex == DEFAULT_READ_NAME_REGEX) useOptimizedDefaultParsing = true; else useOptimizedDefaultParsing = false; readNamePattern = boost::regex(strReadNameRegex, boost::regex_constants::optimize); warnedAboutRegexNotMatching = isWarn; } /* 重新设置readNameRegex */ void SetReadNameRegex(const string &strReadNameRegex) { readNameRegex = strReadNameRegex; if (strReadNameRegex == DEFAULT_READ_NAME_REGEX) useOptimizedDefaultParsing = true; else useOptimizedDefaultParsing = false; readNamePattern = boost::regex(strReadNameRegex, boost::regex_constants::optimize); // readNamePattern = strReadNameRegex; } /* 添加测序时候的tile x y 信息 */ bool AddLocationInformation(const string &readName, PhysicalLocation *loc) { if (!(readName == readNameStored)) { if (ReadLocationInformation(readName, loc)) { readNameStored = readName; physicalLocationStored = *loc; return true; } // return false if read name cannot be parsed return false; } else { *loc = physicalLocationStored; return true; } } /** * Method used to extract tile/x/y from the read name and add it to the PhysicalLocationShort so that it * can be used later to determine optical duplication * * @param readName the name of the read/cluster * @param loc the object to add tile/x/y to * @return true if the read name contained the information in parsable form, false otherwise */ bool ReadLocationInformation(const string &readName, PhysicalLocation *loc) { try { // Optimized version if using the default read name regex (== used on purpose): if (useOptimizedDefaultParsing) { const int fields = getLastThreeFields(readName, ':'); if (!(fields == 5 || fields == 7)) { if (warnedAboutRegexNotMatching) { Warn( "Default READ_NAME_REGEX '%s' did not match read name '%s'." "You may need to specify a READ_NAME_REGEX in order to correctly identify optical duplicates. " "Note that this message will not be emitted again even if other read names do not match the regex.", readNameRegex.c_str(), readName.c_str()); warnedAboutRegexNotMatching = false; } return false; } loc->tile = (int16_t)tmpLocationFields[0]; loc->x = tmpLocationFields[1]; loc->y = tmpLocationFields[2]; return true; } else if (readNameRegex.empty()) { return false; } else { // Standard version that will use the regex cmatch m; if (boost::regex_match(readName.c_str(), m, readNamePattern)) { loc->tile = std::stoi(m[1].str()); loc->x = std::stoi(m[2].str()); loc->y = std::stoi(m[3].str()); return true; } else { if (warnedAboutRegexNotMatching) { Warn( "READ_NAME_REGEX '%s' did not match read name '%s'." "Your regex may not be correct. " "Note that this message will not be emitted again even if other read names do not match the regex.", readNameRegex.c_str(), readName.c_str()); warnedAboutRegexNotMatching = false; } return false; } } } catch (const std::runtime_error &e) { if (warnedAboutRegexNotMatching) { Warn( "A field parsed out of a read name was expected to contain an integer and did not. READ_NAME_REGEX: %s; Read name: %s; Error Msg: %s", readNameRegex.c_str(), readName.c_str(), e.what()); warnedAboutRegexNotMatching = false; } } return true; } /** * Given a string, splits the string by the delimiter, and returns the the last three fields parsed as integers. Parsing a field * considers only a sequence of digits up until the first non-digit character. The three values are stored in the passed-in array. * * @throws NumberFormatException if any of the tokens that should contain numbers do not start with parsable numbers */ int getLastThreeFields(const string &readName, char delim) { int tokensIdx = 2; // start at the last token int numFields = 0; int i, endIdx; endIdx = readName.size(); // find the last three tokens only for (i = readName.size() - 1; 0 <= i && 0 <= tokensIdx; i--) { if (readName.at(i) == delim || 0 == i) { numFields++; const int startIdx = (0 == i) ? 0 : (i + 1); tmpLocationFields[tokensIdx] = std::stoi(readName.substr(startIdx, endIdx - startIdx)); tokensIdx--; endIdx = i; } } // continue to find the # of fields while (0 <= i) { if (readName.at(i) == delim || 0 == i) numFields++; i--; } if (numFields < 3) { tmpLocationFields[0] = tmpLocationFields[1] = tmpLocationFields[2] = -1; numFields = -1; } return numFields; } }; #endif