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#include <pbdata/Types.h>
#include <pbdata/MD5Utils.hpp>
#include <pbdata/StringUtils.hpp>
#include <cstdint>
#include <sstream>
#include <string>
#include <vector>
int ExactPatternMatch(std::string orig, std::string pattern)
{
std::string::size_type pos = orig.find(pattern);
if (pos == orig.npos) {
return 0;
} else {
return 1;
}
}
void MakeMD5(const char *data, unsigned int dataLength, std::string &md5Str, int nChars)
{
MD5 md5engine;
md5engine.update((unsigned char *)data, dataLength);
md5engine.finalize();
char *md5c_str = md5engine.hex_digest();
assert(md5c_str != NULL);
if (nChars == 0) {
nChars = 32;
}
md5Str.assign(md5c_str, nChars);
delete[] md5c_str;
}
void MakeMD5(std::string &data, std::string &md5Str, int nChars)
{
MakeMD5(data.c_str(), data.size(), md5Str, nChars);
}
int IsWhitespace(char c) { return (c == ' ' || c == '\t' || c == '\n' || c == '\r' || c == '\0'); }
int IsSpace(char c) { return (c == ' ' || c == '\t'); }
size_t ToWords(std::string &orig, std::vector<std::string> &words)
{
size_t curWordStart, curWordEnd;
curWordStart = 0;
while (curWordStart < orig.size()) {
while (curWordStart < orig.size() and IsSpace(orig[curWordStart])) {
curWordStart++;
}
curWordEnd = curWordStart;
while (curWordEnd < orig.size() and !IsSpace(orig[curWordEnd])) {
curWordEnd++;
}
std::string word;
if (curWordEnd != curWordStart) {
word.assign(orig, curWordStart, curWordEnd - curWordStart);
words.push_back(word);
}
curWordStart = curWordEnd;
}
return words.size();
}
// Splice a string by pattern and save to a vector of token strings.
int Splice(const std::string &orig, const std::string &pattern, std::vector<std::string> &tokens)
{
assert(pattern.size() > 0);
tokens.clear();
size_t search_start = 0;
size_t find_pos = orig.find(pattern, search_start);
while (find_pos != std::string::npos) {
std::string x = orig.substr(search_start, find_pos - search_start);
tokens.push_back(x);
search_start = find_pos + pattern.size();
find_pos = orig.find(pattern, search_start);
}
tokens.push_back(orig.substr(search_start));
return tokens.size();
}
void ParseSeparatedList(const std::string &csl, std::vector<std::string> &values, char delim)
{
std::stringstream cslStrm(csl);
std::string valString;
std::string next;
do {
if (std::getline(cslStrm, valString, delim)) {
if (valString.size() > 0) {
values.push_back(valString);
}
}
} while (cslStrm);
}
int AssignUntilFirstSpace(char *orig, int origLength, std::string &result)
{
int i;
for (i = 0; i < origLength; i++) {
if (orig[i] == ' ' || orig[i] == '\t' || orig[i] == '\n' || orig[i] == '\r' ||
orig[i] == '\0') {
break;
}
}
result.assign(orig, i);
return i;
}
std::string RStrip(std::string &fileName)
{
// Remove right-ended spaces
int i = fileName.size();
if (i == 0) {
return "";
}
while (i >= 1) {
i--;
if (not IsWhitespace(fileName[i])) {
break;
}
}
return fileName.substr(0, i + 1);
}
std::string MakeReadGroupId(const std::string &movieName, const ReadType::ReadTypeEnum &readType)
{
// PBBAM spec 3.0b5:
// Read Group Id is computed as MD5(${movieName}//${readType})[0:8], where
// movieName is PacBio platform unit id, e.g., (m140905_042...77_s1_X0),
// readtype is SUBREAD, CCS or UNKNOWN,
// CCS reads for a movie named "movie32" would have
// RGID STRING = "f5b4ffb6"
std::string seed = movieName + "//" + ReadType::ToString(readType);
std::string readGroupId;
MakeMD5(seed, readGroupId, 8);
return readGroupId;
}
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