const std::vector<std::vector<unsigned > > SeedMemoryManager<KmerT>::getNotFoundMatchesCount(
const flowcell::TileMetadataList &unprocessedTiles,
const flowcell::BarcodeMetadataList &barcodeMetadataList,
const ReadMetadataList &readMetadataList,
const matchFinder::TileClusterInfo &foundMatches) const
{
ISAAC_ASSERT_MSG(unprocessedTiles.front().getIndex() <= unprocessedTiles.back().getIndex(),
"Expected tiles ordered by index");
std::vector<std::vector<unsigned > > ret(readMetadataList.size(), std::vector<unsigned>(
unprocessedTiles.back().getIndex() + 1));
BOOST_FOREACH(const flowcell::ReadMetadata &readMetadata, readMetadataList_)
{
const unsigned readIndex = readMetadata.getIndex();
BOOST_FOREACH(const flowcell::TileMetadata &tileMetadata, unprocessedTiles)
{
const unsigned tileIndex = tileMetadata.getIndex();
const std::vector<matchFinder::ClusterInfo> &oneTileInfo = foundMatches.at(tileIndex);
// match only clusters where no matches were found so far
ISAAC_ASSERT_MSG(oneTileInfo.size() == tileMetadata.getClusterCount(), "allTiles and foundMatches geometries must match");
ret.at(readIndex).at(tileIndex) =
std::count_if(oneTileInfo.begin(), oneTileInfo.end(),
boost::bind(&willLoadSeeds,
boost::ref(barcodeMetadataList), _1, readIndex));
}
}
return ret;
}
void ParallelSeedLoader<ReaderT, KmerT>::loadTileCycle(
const matchFinder::TileClusterInfo &tileClusterBarcode,
rta::SingleCycleBclMapper<ReaderT> &threadBclMapper,
std::vector<typename std::vector<Seed<KmerT> >::iterator> &destinationBegins,
const flowcell::TileMetadata &tile,
const unsigned cycle,
std::vector<SeedMetadata>::const_iterator cycleSeedsBegin,
const std::vector<SeedMetadata>::const_iterator cycleSeedsEnd)
{
ISAAC_ASSERT_MSG(cycleSeedsEnd > cycleSeedsBegin, "Seed list cannot be empty");
ISAAC_ASSERT_MSG((cycleSeedsEnd -1)->getReadIndex() == cycleSeedsBegin->getReadIndex(), "All seeds must belong to the same read");
const unsigned readIndex = cycleSeedsBegin->getReadIndex();
const std::vector<matchFinder::ClusterInfo> &clustersToDiscard = tileClusterBarcode.at(tile.getIndex());
ISAAC_ASSERT_MSG(tile.getClusterCount() == clustersToDiscard.size(), "Found matches from a wrong tile/read");
threadBclMapper.mapTileCycle(BaseT::flowcellLayout_, tile, cycle);
while (cycleSeedsEnd != cycleSeedsBegin)
{
for (unsigned int clusterId = 0; tile.getClusterCount() > clusterId; ++clusterId)
{
const unsigned barcodeIndex = clustersToDiscard.at(clusterId).getBarcodeIndex();
const unsigned referenceIndex = BaseT::barcodeMetadataList_.at(barcodeIndex).getReferenceIndex();
char base = 0;
threadBclMapper.get(clusterId, &base);
if (flowcell::BarcodeMetadata::UNMAPPED_REFERENCE_INDEX != referenceIndex)
{
if (!clustersToDiscard.at(clusterId).isReadComplete(readIndex))
{
Seed<KmerT> & forwardSeed = *destinationBegins[referenceIndex]++;
// skip those previously found to contain Ns
if (!forwardSeed.isNSeed())
{
if (oligo::getQuality(base) >= seedBaseQualityMin_)
{
KmerT forward = forwardSeed.getKmer();
const KmerT forwardBaseValue(base & oligo::BITS_PER_BASE_MASK);
forward <<= oligo::BITS_PER_BASE;
forward |= forwardBaseValue;
forwardSeed = Seed<KmerT>(forward, SeedId(tile.getIndex(), barcodeIndex, clusterId, cycleSeedsBegin->getIndex(), 0));
}
else
{
// we can't have holes. The Ns must be stored in such a way that
// they will be easy to remove later (after sorting)
forwardSeed = makeNSeed<KmerT>(tile.getIndex(), barcodeIndex, clusterId, 0 == cycleSeedsBegin->getIndex());
}
}
}
}
}
++cycleSeedsBegin;
}
}