// Soft clip the record from the front and/or the back.
SamFilter::FilterStatus SamFilter::softClip(SamRecord& record,
int32_t numFrontClips,
int32_t numBackClips)
{
//////////////////////////////////////////////////////////
Cigar* cigar = record.getCigarInfo();
FilterStatus status = NONE;
int32_t startPos = record.get0BasedPosition();
CigarRoller updatedCigar;
status = softClip(*cigar, numFrontClips, numBackClips,
startPos, updatedCigar);
if(status == FILTERED)
{
/////////////////////////////
// The entire read is clipped, so rather than clipping it,
// filter it out.
filterRead(record);
return(FILTERED);
}
else if(status == CLIPPED)
{
// Part of the read was clipped, and now that we have
// an updated cigar, update the read.
record.setCigar(updatedCigar);
// Update the starting position.
record.set0BasedPosition(startPos);
}
return(status);
}
float MultiDistortion::processSample(float input, int type)
{
// process input sample based on type
switch (type) {
case distTypeTube:
return tubeClip(input);
break;
case distTypeSoftClip:
return softClip(input);
break;
case distTypeExpClip:
return expClip(input);
default:
return input;
break;
}
}
// Process a single read by quality trimming, filtering
// returns true if the read should be kept
bool processRead(SeqRecord& record)
{
// let's remove the adapter if the user has requested so
// before doing any filtering
if(!opt::adapterF.empty())
{
std::string _tmp(record.seq.toString());
size_t found = _tmp.find(opt::adapterF);
int _length;
if(found != std::string::npos)
{
_length = opt::adapterF.length();
}
else
{
// Couldn't find the fwd adapter; Try the reverse version
found = _tmp.find(opt::adapterR);
_length = opt::adapterR.length();
}
if(found != std::string::npos) // found the adapter
{
_tmp.erase(found, _length);
record.seq = _tmp;
// We have to remove the qualities of the adapter
if(!record.qual.empty())
{
_tmp = record.qual;
_tmp.erase(found, _length);
record.qual = _tmp;
}
}
}
// Check if the sequence has uncalled bases
std::string seqStr = record.seq.toString();
std::string qualStr = record.qual;
++s_numReadsRead;
s_numBasesRead += seqStr.size();
// If ambiguity codes are present in the sequence
// and the user wants to keep them, we randomly
// select one of the DNA symbols from the set of
// possible bases
if(!opt::bDiscardAmbiguous)
{
for(size_t i = 0; i < seqStr.size(); ++i)
{
// Convert '.' to 'N'
if(seqStr[i] == '.')
seqStr[i] = 'N';
if(!IUPAC::isAmbiguous(seqStr[i]))
continue;
// Get the string of possible bases for this ambiguity code
std::string possibles = IUPAC::getPossibleSymbols(seqStr[i]);
// select one of the bases at random
int j = rand() % possibles.size();
seqStr[i] = possibles[j];
}
}
// Ensure sequence is entirely ACGT
size_t pos = seqStr.find_first_not_of("ACGT");
if(pos != std::string::npos)
return false;
// Validate the quality string (if present) and
// perform any necessary transformations
if(!qualStr.empty())
{
// Calculate the range of phred scores for validation
bool allValid = true;
for(size_t i = 0; i < qualStr.size(); ++i)
{
if(opt::qualityScale == QS_PHRED64)
qualStr[i] = Quality::phred64toPhred33(qualStr[i]);
allValid = Quality::isValidPhred33(qualStr[i]) && allValid;
}
if(!allValid)
{
std::cerr << "Error: read " << record.id << " has out of range quality values.\n";
std::cerr << "Expected phred" << (opt::qualityScale == QS_SANGER ? "33" : "64") << ".\n";
std::cerr << "Quality string: " << qualStr << "\n";
std::cerr << "Check your data and re-run preprocess with the correct quality scaling flag.\n";
exit(EXIT_FAILURE);
}
}
// Hard clip
if(opt::hardClip > 0)
{
seqStr = seqStr.substr(0, opt::hardClip);
if(!qualStr.empty())
qualStr = qualStr.substr(0, opt::hardClip);
}
// Quality trim
if(opt::qualityTrim > 0 && !qualStr.empty())
softClip(opt::qualityTrim, seqStr, qualStr);
// Quality filter
if(opt::qualityFilter >= 0 && !qualStr.empty())
{
int numLowQuality = countLowQuality(seqStr, qualStr);
if(numLowQuality > opt::qualityFilter)
return false;
}
// Dust filter
if(opt::bDustFilter)
{
double dustScore = calculateDustScore(seqStr);
bool bAcceptDust = dustScore < opt::dustThreshold;
if(!bAcceptDust)
{
s_numFailedDust += 1;
if(opt::verbose >= 1)
{
printf("Failed dust: %s %s %lf\n", record.id.c_str(),
seqStr.c_str(),
dustScore);
}
return false;
}
}
// Filter by GC content
if(opt::bFilterGC)
{
double gc = calcGC(seqStr);
if(gc < opt::minGC || gc > opt::maxGC)
return false;
}
// Primer screen
if(!opt::bDisablePrimerCheck)
{
bool containsPrimer = PrimerScreen::containsPrimer(seqStr);
if(containsPrimer)
{
++s_numReadsPrimer;
return false;
}
}
record.seq = seqStr;
record.qual = qualStr;
if(record.seq.length() == 0 || record.seq.length() < opt::minLength)
return false;
return true;
}
SamFilter::FilterStatus SamFilter::clipOnMismatchThreshold(SamRecord& record,
GenomeSequence& refSequence,
double mismatchThreshold)
{
// Read & clip from the left & right.
SamQuerySeqWithRefIter iterFromFront(record, refSequence, true);
SamQuerySeqWithRefIter iterFromBack(record, refSequence, false);
SamSingleBaseMatchInfo baseMatchInfo;
int32_t readLength = record.getReadLength();
// Init last front clip to be prior to the lastFront index (0).
const int32_t initialLastFrontClipPos = -1;
int32_t lastFrontClipPos = initialLastFrontClipPos;
// Init first back clip to be past the last index (readLength).
int32_t firstBackClipPos = readLength;
bool fromFrontComplete = false;
bool fromBackComplete = false;
int32_t numBasesFromFront = 0;
int32_t numBasesFromBack = 0;
int32_t numMismatchFromFront = 0;
int32_t numMismatchFromBack = 0;
//////////////////////////////////////////////////////////
// Determining the clip positions.
while(!fromFrontComplete || !fromBackComplete)
{
// Read from the front (left to right) of the read until
// more have been read from that direction than the opposite direction.
while(!fromFrontComplete &&
((numBasesFromFront <= numBasesFromBack) ||
(fromBackComplete)))
{
if(iterFromFront.getNextMatchMismatch(baseMatchInfo) == false)
{
// Nothing more to read in this direction.
fromFrontComplete = true;
break;
}
// Got a read. Check to see if it is to or past the last clip.
if(baseMatchInfo.getQueryIndex() >= firstBackClipPos)
{
// This base is past where we are clipping, so we
// are done reading in this direction.
fromFrontComplete = true;
break;
}
// This is an actual base read from the left to the
// right, so up the counter and determine if it was a mismatch.
++numBasesFromFront;
if(baseMatchInfo.getType() == SamSingleBaseMatchInfo::MISMATCH)
{
// Mismatch
++numMismatchFromFront;
// Check to see if it is over the threshold.
double mismatchPercent =
(double)numMismatchFromFront / numBasesFromFront;
if(mismatchPercent > mismatchThreshold)
{
// Need to clip.
lastFrontClipPos = baseMatchInfo.getQueryIndex();
// Reset the counters.
numBasesFromFront = 0;
numMismatchFromFront = 0;
}
}
}
// Now, read from right to left until more have been read
// from the back than from the front.
while(!fromBackComplete &&
((numBasesFromBack <= numBasesFromFront) ||
(fromFrontComplete)))
{
if(iterFromBack.getNextMatchMismatch(baseMatchInfo) == false)
{
// Nothing more to read in this direction.
fromBackComplete = true;
break;
}
// Got a read. Check to see if it is to or past the first clip.
if(baseMatchInfo.getQueryIndex() <= lastFrontClipPos)
{
// This base is past where we are clipping, so we
// are done reading in this direction.
fromBackComplete = true;
break;
}
// This is an actual base read from the right to the
// left, so up the counter and determine if it was a mismatch.
++numBasesFromBack;
if(baseMatchInfo.getType() == SamSingleBaseMatchInfo::MISMATCH)
{
// Mismatch
++numMismatchFromBack;
// Check to see if it is over the threshold.
double mismatchPercent =
(double)numMismatchFromBack / numBasesFromBack;
if(mismatchPercent > mismatchThreshold)
{
// Need to clip.
firstBackClipPos = baseMatchInfo.getQueryIndex();
// Reset the counters.
numBasesFromBack = 0;
numMismatchFromBack = 0;
}
}
}
}
//////////////////////////////////////////////////////////
// Done determining the clip positions, so clip.
// To determine the number of clips from the front, add 1 to the
// lastFrontClipPos since the index starts at 0.
// To determine the number of clips from the back, subtract the
// firstBackClipPos from the readLength.
// Example:
// Pos: 012345
// Read: AAAAAA
// Read Length = 6. If lastFrontClipPos = 2 and firstBackClipPos = 4, numFrontClips = 3 & numBack = 2.
return(softClip(record, lastFrontClipPos + 1, readLength - firstBackClipPos));
}
