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#ifndef UTILS_STRING_UTILS_H_
#define UTILS_STRING_UTILS_H_
#include <cassert>
#include <sstream>
#include <string>
#include <vector>
#include <pbdata/Types.h>
#include <pbdata/MD5Utils.hpp>
#include <pbdata/reads/ReadType.hpp>
int ExactPatternMatch(std::string orig, std::string pattern);
void MakeMD5(const char *data, unsigned int dataLength, std::string &md5Str, int nChars = 0);
void MakeMD5(std::string &data, std::string &md5Str, int nChars = 0);
int IsWhitespace(char c);
int IsSpace(char c);
size_t ToWords(std::string &orig, std::vector<std::string> &words);
int Splice(const std::string &orig, const std::string &pattern, std::vector<std::string> &tokens);
void ParseSeparatedList(const std::string &csl, std::vector<std::string> &values, char delim = ',');
int AssignUntilFirstSpace(char *orig, int origLength, std::string &result);
template <typename T_Value>
void ParseSeparatedList(const std::string &csl, std::vector<T_Value> &values, char delim,
int maxVals)
{
//Parse up to 'maxVals' lines of lists.
std::stringstream cslStrm(csl);
T_Value val;
std::string valString;
std::string next;
int valIndex = 0;
do {
if (maxVals == 0 or valIndex < maxVals - 1) {
std::getline(cslStrm, valString, delim);
} else {
// If on last value, get the rest of the line.
std::getline(cslStrm, valString);
}
if (cslStrm and valString.size() > 0) {
std::stringstream valStrm(valString);
if (!(valStrm >> val)) {
std::cout << "Error, value " << valString << " is malformatted." << std::endl;
} else {
values.push_back(val);
}
}
valIndex++;
} while (cslStrm);
}
template <typename T_Value>
void ParseSeparatedList(const std::string &csl, std::vector<T_Value> &values, char delim = ',')
{
ParseSeparatedList(csl, values, delim, 0);
}
std::string RStrip(std::string &fileName);
/// \returns Read Group Id, given movieName and readType.
std::string MakeReadGroupId(const std::string &movieName, const ReadType::ReadTypeEnum &readType);
#endif
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