void Dedup_LowMem::handleMissingMate(int32_t refID, int32_t mateRefID)
{
static bool firstDifferChrom = true;
static bool firstSameChrom = true;
++myNumMissingMate;
// Passed the mate, but it was not found.
if(refID != mateRefID)
{
if(firstDifferChrom)
{
std::cerr << "Mate on different chromosome was not found.\n"
<< "If you are running single chromosome, consider "
<< "using --oneChrom to treat reads with mates on "
<< "different chromosomes as single-ended.\n";
firstDifferChrom = false;
}
}
else if(firstSameChrom)
{
std::cerr << "ERROR: Records with missing mate can't be checked for "
<< "duplicates.\n";
firstSameChrom = false;
}
// Don't consider this record to be a duplicate.
handleNonDuplicate();
}
void Dedup::handleMissingMate(SamRecord* recordPtr)
{
static bool firstDifferChrom = true;
static bool firstSameChrom = true;
if(recordPtr == NULL)
{
return;
}
// Passed the mate, but it was not found.
if(recordPtr->getMateReferenceID() != recordPtr->getReferenceID())
{
if(firstDifferChrom)
{
std::cerr << "Mate on different chromosome was not found.\n"
<< "If you are running single chromosome, consider "
<< "using --oneChrom to treat reads with mates on "
<< "different chromosomes as single-ended.\n";
firstDifferChrom = false;
}
}
else if(firstSameChrom)
{
std::cerr << "ERROR: Records with missing mate can't be checked for "
<< "duplicates.\n";
firstSameChrom = false;
}
// Don't consider this record to be a duplicate.
// Release this record since there is nothing more to do with it.
++myNumMissingMate;
handleNonDuplicate(recordPtr);
}
// Now that we've reached coordinate on chromosome reference, look back and
// clean up any previous positions from being tracked.
void Dedup_LowMem::cleanupPriorReads(SamRecord* record)
{
static DupKey emptyKey;
static DupKey tempKey2;
// Set where to stop cleaning out the structures.
// Initialize to the end of the structures.
FragmentMap::iterator fragmentFinish = myFragmentMap.end();
PairedMap::iterator pairedFinish = myPairedMap.end();
uint64_t mateStopPos = 0;
// If a record was specified, stop before this record.
if(record != NULL)
{
int32_t reference = record->getReferenceID();
int32_t coordinate = record->get0BasedPosition();
tempKey2.cleanupKey(reference, coordinate);
fragmentFinish = myFragmentMap.lower_bound(tempKey2);
// Now do the same thing with the paired reads
PairedKey pairedKey(emptyKey, tempKey2);
pairedFinish = myPairedMap.lower_bound(pairedKey);
mateStopPos =
SamHelper::combineChromPos(reference,
coordinate);
}
// For each key k < fragmentFinish, release the record since we are
// done with that position and it is not a duplicate.
for(FragmentMap::iterator iter = myFragmentMap.begin();
iter != fragmentFinish; iter++)
{
// If it is not paired, we are done with this record.
// If it is paired, it will be handled separately.
if(!iter->second.paired)
{
// Unpaired, non-duplicate, so perform any additional handling.
handleNonDuplicate();
}
}
// Erase the entries from the map.
if(fragmentFinish != myFragmentMap.begin())
{
myFragmentMap.erase(myFragmentMap.begin(), fragmentFinish);
}
// Now do the same thing with the paired reads
for(PairedMap::iterator iter = myPairedMap.begin();
iter != pairedFinish; iter++)
{
// These are not duplicates, but we are done with them,
// so perform any additional handling.
handleNonDuplicatePair();
}
// Erase the entries.
if (pairedFinish != myPairedMap.begin())
{
myPairedMap.erase(myPairedMap.begin(), pairedFinish);
}
// Clean up the Mate map from any reads whose mates were not found.
// Loop through the mate map and release records prior to this position.
MateMap::iterator mateIter;
for(mateIter = myMateMap.begin(); mateIter != myMateMap.end(); mateIter++)
{
// stop if a record was specified and we have gone past the mate
// stop position. If no record was specified, we want to clean
// it all out.
if((record != NULL) && (mateIter->first >= mateStopPos))
{
break;
}
// Passed the mate, but it was not found.
handleMissingMate(mateIter->second.key.reference,
mateIter->first >> 32);
}
// Erase the entries.
if(mateIter != myMateMap.begin())
{
myMateMap.erase(myMateMap.begin(), mateIter);
}
return;
}
