// Run the cluster process. If the number of total nodes
// exceeds max, abort the search.
void ReadCluster::run(size_t max)
{
while(!m_queue.empty())
{
if(m_queue.size() + m_outCluster.size() > max)
{
while(!m_queue.empty())
m_queue.pop();
m_outCluster.clear();
return;
}
ClusterNode node = m_queue.front();
m_queue.pop();
// Add this node to the output
m_outCluster.push_back(node);
// Find overlaps for the current node
SeqRecord tempRecord;
tempRecord.id = "cluster";
tempRecord.seq = node.sequence;
OverlapBlockList blockList;
m_pOverlapper->overlapRead(tempRecord, m_minOverlap, &blockList);
// Parse each member of the block list and potentially expand the cluster
for(OverlapBlockList::const_iterator iter = blockList.begin(); iter != blockList.end(); ++iter)
{
// Check if the reads in this block are part of the cluster already
BWTInterval canonicalInterval = iter->getCanonicalInterval();
int64_t canonicalIndex = canonicalInterval.lower;
if(m_usedIndex.count(canonicalIndex) == 0)
{
// This is a new node that isn't in the cluster. Add it.
m_usedIndex.insert(canonicalIndex);
ClusterNode newNode;
newNode.sequence = iter->getFullString(node.sequence);
newNode.interval = canonicalInterval;
newNode.isReverseInterval = iter->flags.isTargetRev();
m_queue.push(newNode);
}
}
}
}
ClusterResult ClusterProcess::process(const SequenceWorkItem& item)
{
// Calculate the intervals in the forward FM-index for this read
const BWT* pBWT = m_pOverlapper->getBWT();
// Check if this read is a substring
OverlapBlockList tempBlockList;
OverlapResult overlapResult = m_pOverlapper->alignReadDuplicate(item.read, &tempBlockList);
if(overlapResult.isSubstring)
{
std::cerr << "Error: substring reads found in sga-cluster. Please run rmdup before cluster\n";
exit(1);
}
// Find the interval in the fm-index containing the read
std::string readString = item.read.seq.toString();
BWTInterval readInterval = BWTAlgorithms::findInterval(pBWT, readString);
BWTAlgorithms::updateInterval(readInterval, '$', pBWT);
// The read must be present in the index
assert(readInterval.isValid());
// Check if this read has been used yet
bool used = false;
for(int64_t i = readInterval.lower; i <= readInterval.upper; ++i)
{
if(m_pMarkedReads->test(i))
{
used = true;
break;
}
}
ClusterResult result;
if(used)
return result; // already part of a cluster, return nothing
// Compute a new cluster around this read
std::set<int64_t> usedIndex;
ClusterNodeQueue queue;
ClusterNode node;
node.sequence = item.read.seq.toString();
node.interval = readInterval;
node.isReverseInterval = false;
usedIndex.insert(readInterval.lower);
queue.push(node);
while(!queue.empty())
{
ClusterNode node = queue.front();
queue.pop();
// Update the used index and the result structure with this node's data
result.clusterNodes.push_back(node);
SeqRecord tempRecord;
tempRecord.id = "cluster";
tempRecord.seq = node.sequence;
OverlapBlockList blockList;
OverlapResult result = m_pOverlapper->overlapRead(tempRecord, m_minOverlap, &blockList);
//m_pOverlapper->buildForwardHistory(&blockList);
// Parse each member of the block list and potentially expand the cluster
for(OverlapBlockList::const_iterator iter = blockList.begin(); iter != blockList.end(); ++iter)
{
// Check if the reads in this block are part of the cluster already
BWTInterval canonicalInterval = iter->getCanonicalInterval();
int64_t canonicalIndex = canonicalInterval.lower;
if(usedIndex.count(canonicalIndex) == 0)
{
usedIndex.insert(canonicalIndex);
ClusterNode newNode;
newNode.sequence = iter->getFullString(node.sequence);
newNode.interval = canonicalInterval;
newNode.isReverseInterval = iter->flags.isTargetRev();
queue.push(newNode);
}
}
}
// If some work was performed, update the bitvector so other threads do not try to merge the same set of reads.
// This uses compare-and-swap instructions to ensure the uppdate is atomic.
// If some other thread has merged this set (and updated
// the bitvector), we discard all the merged data.
// As a given set of reads should all be merged together, we only need to make sure we atomically update
// the bit for the read with the lowest index in the set.
// Sort the intervals into ascending order and remove any duplicate intervals (which can occur
// if the subgraph has a simple cycle)
std::sort(result.clusterNodes.begin(), result.clusterNodes.end(), ClusterNode::compare);
std::vector<ClusterNode>::iterator newEnd = std::unique(result.clusterNodes.begin(),
result.clusterNodes.end(),
ClusterNode::equal);
size_t oldSize = result.clusterNodes.size();
result.clusterNodes.erase(newEnd, result.clusterNodes.end());
size_t newSize = result.clusterNodes.size();
if(oldSize != newSize)
std::cout << "Warning: duplicate cluster nodes were found\n";
// Check if the bit in the vector has already been set for the lowest read index
// If it has some other thread has already output this set so we do nothing
int64_t lowestIndex = result.clusterNodes.front().interval.lower;
bool currentValue = m_pMarkedReads->test(lowestIndex);
bool updateSuccess = false;
if(currentValue == false)
{
// Attempt to update the bit vector with an atomic CAS. If this returns false
// the bit was set by some other thread
updateSuccess = m_pMarkedReads->updateCAS(lowestIndex, currentValue, true);
}
if(updateSuccess)
{
// We successfully atomically set the bit for the first read in this set
// to true. We can safely update the rest of the bits and keep the merged sequences
// for output.
std::vector<ClusterNode>::const_iterator iter = result.clusterNodes.begin();
for(; iter != result.clusterNodes.end(); ++iter)
{
for(int64_t i = iter->interval.lower; i <= iter->interval.upper; ++i)
{
if(i == lowestIndex) //already set
continue;
currentValue = m_pMarkedReads->test(i);
if(currentValue)
{
// This value should not be true, emit a warning
std::cout << "Warning: Bit " << i << " was set outside of critical section\n";
std::cout << "Read: " << readString << "\n";
}
else
{
m_pMarkedReads->updateCAS(i, currentValue, true);
}
}
}
}
else
{
// Some other thread merged these reads already, discard the intermediate
// data and set the result to false
result.clusterNodes.clear();
}
return result;
}