void remove_pcr_duplicates(BaseQuality& base_quality, bool use_bam_rgs,
std::map<std::string, std::string>& rg_to_library,
std::vector< std::vector<BamTools::BamAlignment> >& paired_strs_by_rg,
std::vector< std::vector<BamTools::BamAlignment> >& mate_pairs_by_rg,
std::vector< std::vector<BamTools::BamAlignment> >& unpaired_strs_by_rg, std::ostream& logger){
int32_t dup_count = 0;
assert(paired_strs_by_rg.size() == mate_pairs_by_rg.size() && paired_strs_by_rg.size() == unpaired_strs_by_rg.size());
for (unsigned int i = 0; i < paired_strs_by_rg.size(); i++){
assert(paired_strs_by_rg[i].size() == mate_pairs_by_rg[i].size());
std::vector<ReadPair> read_pairs;
for (unsigned int j = 0; j < paired_strs_by_rg[i].size(); j++){
std::string library = use_bam_rgs ? get_library(paired_strs_by_rg[i][j], rg_to_library): rg_to_library[paired_strs_by_rg[i][j].Filename];
read_pairs.push_back(ReadPair(paired_strs_by_rg[i][j], mate_pairs_by_rg[i][j], library));
}
for (unsigned int j = 0; j < unpaired_strs_by_rg[i].size(); j++){
std::string library = use_bam_rgs ? get_library(unpaired_strs_by_rg[i][j], rg_to_library): rg_to_library[unpaired_strs_by_rg[i][j].Filename];
read_pairs.push_back(ReadPair(unpaired_strs_by_rg[i][j], library));
}
std::sort(read_pairs.begin(), read_pairs.end());
paired_strs_by_rg[i].clear();
mate_pairs_by_rg[i].clear();
unpaired_strs_by_rg[i].clear();
if (read_pairs.size() == 0)
continue;
int best_index = 0;
for (unsigned int j = 1; j < read_pairs.size(); j++){
if (read_pairs[j].duplicate(read_pairs[best_index])){
dup_count++;
// Update index if new pair's STR read has a higher total base quality
if (base_quality.sum_log_prob_correct(read_pairs[j].aln_one().Qualities) >
base_quality.sum_log_prob_correct(read_pairs[best_index].aln_one().Qualities))
best_index = j;
}
else {
// Keep best pair from prior set of duplicates
if (read_pairs[best_index].single_ended())
unpaired_strs_by_rg[i].push_back(read_pairs[best_index].aln_one());
else {
paired_strs_by_rg[i].push_back(read_pairs[best_index].aln_one());
mate_pairs_by_rg[i].push_back(read_pairs[best_index].aln_two());
}
best_index = j; // Update index for new set of duplicates
}
}
// Keep best pair for last set of duplicates
if (read_pairs[best_index].single_ended())
unpaired_strs_by_rg[i].push_back(read_pairs[best_index].aln_one());
else {
paired_strs_by_rg[i].push_back(read_pairs[best_index].aln_one());
mate_pairs_by_rg[i].push_back(read_pairs[best_index].aln_two());
}
}
logger << "Removed " << dup_count << " sets of PCR duplicate reads" << std::endl;
}
int NASAKeywordHandler::ReadGroup( const char *pszPathPrefix )
{
CPLString osName, osValue;
for( ; TRUE; )
{
if( !ReadPair( osName, osValue ) )
return FALSE;
if( EQUAL(osName,"OBJECT") || EQUAL(osName,"GROUP") )
{
if( !ReadGroup( (CPLString(pszPathPrefix) + osValue + ".").c_str() ) )
return FALSE;
}
else if( EQUALN(osName,"END",3) )
{
return TRUE;
}
else
{
osName = pszPathPrefix + osName;
papszKeywordList = CSLSetNameValue( papszKeywordList,
osName, osValue );
}
}
}
bool plConfigSource::ReadString(const std::string & in)
{
std::string work = in;
xtl::trim(work);
// comment
if (work[0] == '#')
return true;
// comment
if (work[0] == ';')
return true;
// section
if (work[0] == '[')
{
int close = work.find_first_of("]");
if(close == std::string::npos)
return false;
fCurrSection = work.substr(1,close-1);
fEffectiveSection = fCurrSection;
return true;
}
// key=value
std::string key, value;
SplitAt(key, value, '=', work);
// dot notation makes section change for this key=value only.
int t = key.find('.');
if (t>0 && t<key.size()-1)
{
fEffectiveSection.assign(key.substr(0,t));
key.assign(key.substr(t+1));
}
bool ret=ReadPair(key, value);
fEffectiveSection = fCurrSection;
if(ret && strcmp("LoadIni",key.c_str()) == 0)
{
ret = ReadSubSource( value.c_str() );
}
return ret;
}
bool plIniNoSectionsConfigSource::ReadString(const std::string & in)
{
std::string work = in;
xtl::trim(work);
// ignore comments
if (work[0]=='#' || work[0]==';')
return true;
// ignore sections
if (work[0] == '[')
return true;
// parse key value
std::string key, value;
SplitAt(key, value, '=', work);
return ReadPair(key, value);
}
int VICARKeywordHandler::ReadGroup( CPL_UNUSED const char *pszPathPrefix ) {
CPLString osName, osValue, osProperty;
for( ; true; ) {
if( !ReadPair( osName, osValue ) )
return FALSE;
if( EQUAL(osName,"END") )
return TRUE;
if( EQUAL(osName,"PROPERTY") || EQUAL(osName,"HISTORY") || EQUAL(osName,"TASK"))
osProperty = osValue;
else {
if ( !EQUAL(osProperty,"") )
osName = osProperty + "." + osName;
papszKeywordList = CSLSetNameValue( papszKeywordList, osName, osValue );
}
}
}
