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Sparsify barcode edge coverage
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@Itolstoganov
Itolstoganov committed Jun 27, 2023
1 parent f3c221a commit ec4371c
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Showing 3 changed files with 55 additions and 83 deletions.
124 changes: 55 additions & 69 deletions assembler/src/common/barcode_index/barcode_index.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@

#include <boost/dynamic_bitset.hpp>
#include <cuckoo/cuckoohash_map.hh>
#include <unordered_set>

using std::string;
using std::istringstream;
Expand Down Expand Up @@ -307,21 +308,17 @@ inline std::istream& operator >>(std::istream& os, SimpleBarcodeInfo& info)
*/
class FrameBarcodeInfo {
public:
typedef boost::dynamic_bitset<> IsOnFrameT;

/**
*
* @param frames Number of bin in the edge
* @return empty info
*/
FrameBarcodeInfo(size_t frames = 0): count_(0), is_on_frame_(), leftmost_index_(frames), rightmost_index_(0) {
is_on_frame_.resize(frames, false);
}
FrameBarcodeInfo(size_t frames = 0): count_(0), covered_bins_(), leftmost_index_(frames), rightmost_index_(0) {}

void Update(size_t count, size_t left_frame, size_t right_frame) {
count_ += count;
for (size_t i = left_frame; i <= right_frame; ++i) {
is_on_frame_.set(i);
covered_bins_.insert(i);
}
leftmost_index_ = std::min(left_frame, leftmost_index_);
rightmost_index_ = std::max(right_frame, rightmost_index_);
Expand All @@ -330,9 +327,11 @@ class FrameBarcodeInfo {
void Update(const FrameBarcodeInfo& other) {
TRACE(count_);
TRACE(other.count_);
TRACE(is_on_frame_.size());
TRACE(other.is_on_frame_.size());
is_on_frame_ |= other.is_on_frame_;
TRACE(covered_bins_.size());
TRACE(other.covered_bins_.size());
for (const auto &frame: other.covered_bins_) {
covered_bins_.insert(frame);
}
leftmost_index_ = std::min(leftmost_index_, other.leftmost_index_);
rightmost_index_ = std::max(rightmost_index_, other.rightmost_index_);
count_ += other.count_;
Expand All @@ -359,32 +358,12 @@ class FrameBarcodeInfo {
return rightmost_index_;
}

const IsOnFrameT& GetBitSet() const {
return is_on_frame_;
}

/**
* @param frame index of bin
* @return true if bin is barcoded, false otherwise
*/
bool GetFrame(size_t frame) const {
return is_on_frame_[frame];
}

/**
*
* @return number of frames
*/
size_t GetSize() const {
return is_on_frame_.size();
}

/**
*
* @return number of barcoded bins
*/
size_t GetCovered() const {
return is_on_frame_.count();
return covered_bins_.size();
}

void SetCount(size_t count) {
Expand All @@ -399,50 +378,40 @@ class FrameBarcodeInfo {
rightmost_index_ = index;
}

void SetBitSet(const IsOnFrameT &bitset) {
is_on_frame_ = bitset;
}

void BinRead(std::istream &str) {
using io::binary::BinRead;
auto count = BinRead<size_t>(str);
SetCount(count);

auto set_positions = BinRead<std::vector<size_t>>(str);
VERIFY_DEV(set_positions.back() < is_on_frame_.size());
TRACE("Last position: " << set_positions.back());
TRACE("Bitset size: " << is_on_frame_.size());
for (const auto &pos: set_positions) {
auto num_positions = BinRead<size_t>(str);
size_t min_pos = std::numeric_limits<size_t>::max();
size_t max_pos = 0;
for (size_t i = 0; i < num_positions; ++i) {
auto pos = BinRead<size_t>(str);
TRACE("Position: " << pos);
is_on_frame_.set(pos, true);
}

SetLeftMost(is_on_frame_.find_first());
size_t rightmost = 0;
for (size_t i = is_on_frame_.size() - 1; i > 0; --i) {
if (is_on_frame_.test(i)) {
rightmost = i;
break;
covered_bins_.insert(pos);
if (pos < min_pos) {
min_pos = pos;
}
if (pos > max_pos) {
max_pos = pos;
}
}
SetRightMost(rightmost);

SetLeftMost(min_pos);
SetRightMost(max_pos);
TRACE("Leftmost: " << GetLeftMost());
TRACE("Rightmost: " << GetRightMost());
}

void BinWrite(std::ostream &str) const {
using io::binary::BinWrite;
BinWrite(str, GetCount());
BinWrite(str, GetCovered());

std::vector<size_t> set_positions;
size_t current_set_pos = GetBitSet().find_first();
TRACE("Size: " << GetBitSet().size());
while (current_set_pos != IsOnFrameT::npos) {
TRACE("Current set position: " << current_set_pos);
set_positions.push_back(current_set_pos);
current_set_pos = GetBitSet().find_next(current_set_pos);
for (const size_t &pos: covered_bins_) {
BinWrite(str, pos);
}
BinWrite(str, set_positions);
}


Expand All @@ -455,9 +424,9 @@ class FrameBarcodeInfo {
*/
size_t count_;
/**
* `is_on_frame[i]` is true iff ith bin is barcoded
* Bins covered by the barcode
*/
boost::dynamic_bitset<> is_on_frame_;
std::unordered_set<size_t> covered_bins_;
/**
* Leftmost barcoded bin
*/
Expand All @@ -472,23 +441,40 @@ class FrameBarcodeInfo {

inline std::ostream& operator <<(std::ostream& os, const FrameBarcodeInfo& info)
{
os << info.count_ << " " << info.is_on_frame_;
os << info.count_ << " " << info.covered_bins_.size();
for (const auto &bin: info.covered_bins_) {
os << bin << " ";
}
return os;
}

inline std::istream& operator >>(std::istream& is, FrameBarcodeInfo& info)
{
is >> info.count_;
is >> info.is_on_frame_;
info.leftmost_index_ = info.is_on_frame_.find_first();
size_t rightmost = 0;
for (size_t i = info.is_on_frame_.size() - 1; i > 0; --i) {
if (info.is_on_frame_.test(i)) {
rightmost = i;
break;
using io::binary::BinRead;
size_t count;
is >> count;
info.SetCount(count);

size_t num_of_bins;
is >> num_of_bins;
size_t min_pos = std::numeric_limits<size_t>::max();
size_t max_pos = 0;
for (size_t i = 0; i < num_of_bins; ++i) {
size_t pos = 0;
is >> pos;
TRACE("Position: " << pos);
if (pos < min_pos) {
min_pos = pos;
}
if (pos > max_pos) {
max_pos = pos;
}
info.covered_bins_.insert(pos);
}
info.rightmost_index_ = rightmost;
info.SetLeftMost(min_pos);
info.SetRightMost(max_pos);
TRACE("Leftmost: " << info.GetLeftMost());
TRACE("Rightmost: " << info.GetRightMost());
return is;
}

Expand Down
11 changes: 0 additions & 11 deletions assembler/src/common/barcode_index/barcode_info_extractor.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -341,17 +341,6 @@ class FrameBarcodeIndexInfoExtractorTemplate : public BarcodeIndexInfoExtractor<
return this->GetInfo(edge, barcode).GetRightMost();
}


/**
*
* @param edge
* @param barcode
* @return bitset representing barcoded bins of the edge
*/
const boost::dynamic_bitset<>& GetBitSet(const EdgeId& edge, const BarcodeId& barcode) const {
return this->GetInfo(edge, barcode).GetBitSet();
}

/**
* @param edge
* @return length of the bin
Expand Down
3 changes: 0 additions & 3 deletions assembler/src/projects/online_vis/statistics_commands/print_barcodes_command.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -107,10 +107,7 @@ namespace online_visualization {
PrintElement(bitset, bitset_width, fout);
} else {
const size_t reads = barcode_extractor_.GetNumberOfReads(edge, barcode);
const auto bitset = barcode_extractor_.GetBitSet(edge, barcode);
const size_t bitset_width = bitset.size() + 5;
PrintElement(reads, number_of_reads_width_, fout);
PrintElement(bitset, bitset_width, fout);
}
}
fout << endl;
Expand Down

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