// converts a space separated quality string into a compressed quality string
// NOTE: this function has horrible amounts of overhead, but lean and mean code that I had before
// failed some of the unit tests.
void CRegexUtilities::ConvertQualities(string& qualities, CMosaikString& compQualities) {
string::iterator strIte = qualities.end() - 1;
while ( *strIte == ' ' ) {
qualities.erase( strIte );
strIte--;
}
vector<string> columns;
vector<string>::const_iterator sIter;
char* pQualities = (char*)qualities.c_str();
Chomp(pQualities);
back_insert_iterator<vector<string> > backiter(columns);
SplitString(backiter, " ", pQualities);
const unsigned int numQualities = (unsigned int)columns.size();
compQualities.Reserve(numQualities);
compQualities.SetLength(numQualities);
unsigned char* pCompQualities = (unsigned char*)compQualities.Data();
for(sIter = columns.begin(); sIter != columns.end(); ++sIter, ++pCompQualities) {
if(sIter->empty()) continue;
*pCompQualities = GetUnsignedChar((char*)sIter->c_str());
}
}
// converts the supplied read from colorspace to pseudo-colorspace
void CColorspaceUtilities::ConvertReadColorspaceToPseudoColorspace(CMosaikString& s) {
char* pBases = s.Data();
for(unsigned int i = 0; i < s.Length(); ++i, ++pBases) {
switch(*pBases) {
case '0':
*pBases = 'A';
break;
case '1':
*pBases = 'C';
break;
case '2':
*pBases = 'G';
break;
case '3':
*pBases = 'T';
break;
case 'X':
break;
case '-':
*pBases = 'N';
break;
case '.':
// here we pick an arbitrary colorspace transition, this will have at
// least 25 % of being correct as opposed to specifying an 'N'.
*pBases = 'A';
break;
default:
printf("ERROR: Unrecognized nucleotide (%c) when converting read to pseudo-colorspace.\n", pBases[i]);
exit(1);
break;
}
}
}
// converts the supplied read from pseudo-colorspace to colorspace
// The function is used by the unaligned-read writer.
void CColorspaceUtilities::ConvertReadPseudoColorspaceToColorspace(CMosaikString& s) {
char* pBases = s.Data();
for(unsigned int i = 0; i < s.Length(); ++i, ++pBases) {
switch(*pBases) {
case 'A':
*pBases = '0';
break;
case 'C':
*pBases = '1';
break;
case 'G':
*pBases = '2';
break;
case 'T':
*pBases = '3';
break;
case 'X':
case 'N':
break;
default:
printf("ERROR: Unrecognized nucleotide (%c) when converting read to colorspace.\n", pBases[i]);
exit(1);
break;
}
}
}
// converts the supplied read from basespace to pseudo-colorspace
void CColorspaceUtilities::ConvertReadBasespaceToPseudoColorspace(CMosaikString& s) {
char* pPrev = s.Data();
char* pString = pPrev + 1;
// simplify various ambiguity codes
*pPrev = GetSimplifiedBase(*pPrev);
CS_MAP_t::const_iterator csIter;
for(unsigned int i = 1; i < s.Length(); ++i, ++pString, ++pPrev) {
// simplify various ambiguity codes
*pString = GetSimplifiedBase(*pString);
csIter = mCSMap.find(PACK_SHORT(*pPrev, *pString));
if(csIter == mCSMap.end()) {
printf("ERROR: Unknown combination found when converting to colorspace: [%c] & [%c]\n", *pPrev, *pString);
exit(1);
}
*pPrev = csIter->second;
}
// adjust the read
s.TrimEnd(1);
}