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CMakeLists.txt
View file @ f119fd6e
cmake_minimum_required(VERSION 3.2)
project(racon)
set(racon_version 1.4.7)
set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)
......@@ -42,6 +43,9 @@ else()
add_executable(racon ${racon_sources})
endif()
# Add version information to bibary.
target_compile_definitions(racon PRIVATE RACON_VERSION="v${racon_version}")
if (NOT TARGET bioparser)
add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL)
endif()
......@@ -139,3 +143,9 @@ if (racon_build_wrapper)
add_subdirectory(vendor/rampler)
endif()
endif()
# Add Debian packaging
SET(CPACK_GENERATOR "DEB")
SET(CPACK_DEBIAN_PACKAGE_MAINTAINER "Robert Vaser")
set(CPACK_PACKAGE_VERSION "${racon_version}")
include(CPack)
README.md
View file @ f119fd6e
# Racon
[![Latest GitHub release](https://img.shields.io/github/release/isovic/racon.svg)](https://github.com/isovic/racon/releases/latest)
[![Build status for gcc/clang](https://travis-ci.org/isovic/racon.svg?branch=master)](https://travis-ci.org/isovic/racon)
[![Latest GitHub release](https://img.shields.io/github/release/lbcb-sci/racon.svg)](https://github.com/lbcb-sci/racon/releases/latest)
[![Build status for gcc/clang](https://travis-ci.org/lbcb-sci/racon.svg?branch=master)](https://travis-ci.org/lbcb-sci/racon)
[![Published in Genome Research](https://img.shields.io/badge/published%20in-Genome%20Research-blue.svg)](https://doi.org/10.1101/gr.214270.116)
Consensus module for raw de novo DNA assembly of long uncorrected reads.
......@@ -24,13 +24,13 @@ A **wrapper script** is also available to enable easier usage to the end-user fo
### CUDA Support
1. gcc 5.0+
2. cmake 3.10+
4. CUDA 10.0+
4. CUDA 9.0+
## Installation
To install Racon run the following commands:
```bash
git clone --recursive https://github.com/isovic/racon.git racon
git clone --recursive https://github.com/lbcb-sci/racon.git racon
cd racon
mkdir build
cd build
......@@ -62,6 +62,13 @@ make
***Note***: Short read polishing with CUDA is still in development!
### Packaging
To generate a Debian package for `racon`, run the following command from the build folder -
```bash
make package
```
## Usage
Usage of `racon` is as following:
......@@ -92,14 +99,16 @@ Usage of `racon` is as following:
-e, --error-threshold <float>
default: 0.3
maximum allowed error rate used for filtering overlaps
--no-trimming
disables consensus trimming at window ends
-m, --match <int>
default: 5
default: 3
score for matching bases
-x, --mismatch <int>
default: -4
default: -5
score for mismatching bases
-g, --gap <int>
default: -8
default: -4
gap penalty (must be negative)
-t, --threads <int>
default: 1
......@@ -115,7 +124,7 @@ Usage of `racon` is as following:
number of batches for CUDA accelerated polishing
-b, --cuda-banded-alignment
use banding approximation for polishing on GPU. Only applicable when -c is used.
--cudaaligner-batches (experimental)
--cudaaligner-batches
Number of batches for CUDA accelerated alignment
`racon_test` is run without any parameters.
......
debian/changelog
View file @ f119fd6e
racon (1.4.3-1) UNRELEASED; urgency=medium
racon (1.4.7-1) UNRELEASED; urgency=medium
* New upstream version
* debhelper-compat 12
* Standards-Version: 4.4.0
TODO: https://salsa.debian.org/med-team/liblogger
* Build-Depends: liblogger-dev
Closes: #940564
* Point watch file to new location
* New homepage
* Versioned Build-Depends: libthread-pool-dev (>= 2)
* New upstream version
* New upstream version
-- Andreas Tille <tille@debian.org> Fri, 02 Aug 2019 22:44:04 +0200
-- Andreas Tille <tille@debian.org> Wed, 18 Sep 2019 11:43:24 +0200
racon (1.3.2-1) unstable; urgency=medium
......
debian/control
View file @ f119fd6e
......@@ -10,12 +10,13 @@ Build-Depends: debhelper-compat (= 12),
libbioparser-dev,
libedlib-dev,
libspoa-dev,
libthread-pool-dev,
libthread-pool-dev (>= 2),
liblogger-dev,
rampler
Standards-Version: 4.4.0
Vcs-Browser: https://salsa.debian.org/med-team/racon
Vcs-Git: https://salsa.debian.org/med-team/racon.git
Homepage: https://github.com/isovic/racon
Homepage: https://github.com/lbcb-sci/racon
Package: racon
Architecture: any
......
debian/copyright
View file @ f119fd6e
......@@ -2,7 +2,7 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: racon
Upstream-Contact: Ivan Sovic <ivan.sovic@irb.hr>
Mile Sikic <mile.sikic@fer.hr>
Source: https://github.com/isovic/racon/releases
Source: https://github.com/lbcb-sci/racon/releases
Files: *
Copyright: 2016-2018 Ivan Sovic <ivan.sovic@irb.hr>, Robert Vaser, Mile Šiki
......
debian/patches/use_debian_packaged_libs.patch
View file @ f119fd6e
......@@ -4,9 +4,9 @@ Description: Use Debian packaged libraries
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -42,18 +42,6 @@ else()
add_executable(racon ${racon_sources})
endif()
@@ -46,21 +46,6 @@ endif()
# Add version information to bibary.
target_compile_definitions(racon PRIVATE RACON_VERSION="v${racon_version}")
-if (NOT TARGET bioparser)
- add_subdirectory(vendor/bioparser EXCLUDE_FROM_ALL)
......@@ -20,19 +20,24 @@ Description: Use Debian packaged libraries
-if (NOT TARGET edlib)
- add_subdirectory(vendor/edlib EXCLUDE_FROM_ALL)
-endif()
if (NOT TARGET logger)
add_subdirectory(vendor/logger EXCLUDE_FROM_ALL)
endif()
@@ -86,7 +74,7 @@ if (racon_enable_cuda)
-if (NOT TARGET logger)
- add_subdirectory(vendor/logger EXCLUDE_FROM_ALL)
-endif()
if (racon_enable_cuda)
if (DEFINED CLARAGENOMICSANALYSIS_SDK_PATH)
list(APPEND CMAKE_PREFIX_PATH "${CLARAGENOMICSANALYSIS_SDK_PATH}/cmake")
@@ -90,7 +75,9 @@ if (racon_enable_cuda)
endif()
endif()
-target_link_libraries(racon bioparser spoa thread_pool edlib_static logger)
+target_link_libraries(racon spoa thread_pool pthread edlib logger z)
+#set_target_properties(racon PROPERTIES COMPILE_FLAGS -pthread LINK_FLAGS -pthread) # does not work
+target_link_libraries(racon spoa thread_pool edlib logger z)
+set_target_properties(racon PROPERTIES COMPILE_FLAGS -pthread LINK_FLAGS -pthread)
if (racon_enable_cuda)
target_link_libraries(racon cudapoa cudaaligner)
endif()
@@ -115,11 +103,7 @@ if (racon_build_tests)
@@ -119,11 +106,7 @@ if (racon_build_tests)
add_executable(racon_test ${racon_test_sources})
endif()
......
debian/rules
View file @ f119fd6e
......@@ -9,3 +9,6 @@ DEB_CMAKE_EXTRA_FLAGS = -Dracon_build_tests=ON
override_dh_auto_configure:
dh_auto_configure -- $(DEB_CMAKE_EXTRA_FLAGS)
# Somehow the means in the patch for CMakeLists.txt to replace -lpthread by -pthread to not work
# Just hack it here
sed -i 's/-lpthread/-pthread/' obj-*/CMakeFiles/racon_test.dir/link.txt
debian/watch
View file @ f119fd6e
version=4
https://github.com/isovic/racon/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@
https://github.com/lbcb-sci/racon/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@
src/cuda/cudaaligner.cpp
View file @ f119fd6e
......@@ -4,7 +4,7 @@
* @brief CUDABatchAligner class source file
*/
#include <cudautils/cudautils.hpp>
#include <claragenomics/utils/cudautils.hpp>
#include "cudaaligner.hpp"
......@@ -27,19 +27,21 @@ CUDABatchAligner::CUDABatchAligner(uint32_t max_query_size,
uint32_t max_target_size,
uint32_t max_alignments,
uint32_t device_id)
: aligner_(claragenomics::cudaaligner::create_aligner(max_query_size,
max_target_size,
max_alignments,
claragenomics::cudaaligner::AlignmentType::global,
device_id))
, overlaps_()
: overlaps_()
, stream_(0)
{
bid_ = CUDABatchAligner::batches++;
CGA_CU_CHECK_ERR(cudaSetDevice(device_id));
CGA_CU_CHECK_ERR(cudaStreamCreate(&stream_));
aligner_->set_cuda_stream(stream_);
aligner_ = claragenomics::cudaaligner::create_aligner(max_query_size,
max_target_size,
max_alignments,
claragenomics::cudaaligner::AlignmentType::global,
stream_,
device_id);
}
CUDABatchAligner::~CUDABatchAligner()
......@@ -51,11 +53,14 @@ bool CUDABatchAligner::addOverlap(Overlap* overlap, std::vector<std::unique_ptr<
{
const char* q = !overlap->strand_ ? &(sequences[overlap->q_id_]->data()[overlap->q_begin_]) :
&(sequences[overlap->q_id_]->reverse_complement()[overlap->q_length_ - overlap->q_end_]);
int32_t q_len = overlap->q_end_ - overlap->q_begin_;
const char* t = &(sequences[overlap->t_id_]->data()[overlap->t_begin_]);
int32_t t_len = overlap->t_end_ - overlap->t_begin_;
claragenomics::cudaaligner::StatusType s =
aligner_->add_alignment(q, overlap->q_end_ - overlap->q_begin_,
t, overlap->t_end_ - overlap->t_begin_);
// NOTE: The cudaaligner API for adding alignments is the opposite of edlib. Hence, what is
// treated as target in edlib is query in cudaaligner and vice versa.
claragenomics::cudaaligner::StatusType s = aligner_->add_alignment(t, t_len,
q, q_len);
if (s == claragenomics::cudaaligner::StatusType::exceeded_max_alignments)
{
return false;
......@@ -63,8 +68,8 @@ bool CUDABatchAligner::addOverlap(Overlap* overlap, std::vector<std::unique_ptr<
else if (s == claragenomics::cudaaligner::StatusType::exceeded_max_alignment_difference
|| s == claragenomics::cudaaligner::StatusType::exceeded_max_length)
{
cpu_overlap_data_.emplace_back(std::make_pair<std::string, std::string>(std::string(q, q + overlap->q_end_ - overlap->q_begin_),
std::string(t, t + overlap->t_end_ - overlap->t_begin_)));
cpu_overlap_data_.emplace_back(std::make_pair<std::string, std::string>(std::string(q, q + q_len),
std::string(t, t + t_len)));
cpu_overlaps_.push_back(overlap);
}
else if (s != claragenomics::cudaaligner::StatusType::success)
......
src/cuda/cudaaligner.hpp
View file @ f119fd6e
......@@ -3,9 +3,9 @@
*
* @brief CUDA aligner class header file
*/
#include "cudaaligner/cudaaligner.hpp"
#include "cudaaligner/aligner.hpp"
#include "cudaaligner/alignment.hpp"
#include <claragenomics/cudaaligner/cudaaligner.hpp>
#include <claragenomics/cudaaligner/aligner.hpp>
#include <claragenomics/cudaaligner/alignment.hpp>
#include "overlap.hpp"
#include "sequence.hpp"
......
src/cuda/cudabatch.cpp
View file @ f119fd6e
......@@ -13,28 +13,53 @@
#include "cudautils.hpp"
#include "spoa/spoa.hpp"
#include <cudautils/cudautils.hpp>
#include <claragenomics/utils/cudautils.hpp>
namespace racon {
std::atomic<uint32_t> CUDABatchProcessor::batches;
std::unique_ptr<CUDABatchProcessor> createCUDABatch(uint32_t max_windows, uint32_t max_window_depth, uint32_t device, int8_t gap, int8_t mismatch, int8_t match, bool cuda_banded_alignment)
{
return std::unique_ptr<CUDABatchProcessor>(new CUDABatchProcessor(max_windows, max_window_depth, device, gap, mismatch, match, cuda_banded_alignment));
std::unique_ptr<CUDABatchProcessor> createCUDABatch(uint32_t max_window_depth,
uint32_t device,
size_t avail_mem,
int8_t gap,
int8_t mismatch,
int8_t match,
bool cuda_banded_alignment)
{
return std::unique_ptr<CUDABatchProcessor>(new CUDABatchProcessor(max_window_depth,
device,
avail_mem,
gap,
mismatch,
match,
cuda_banded_alignment));
}
CUDABatchProcessor::CUDABatchProcessor(uint32_t max_windows, uint32_t max_window_depth, uint32_t device, int8_t gap, int8_t mismatch, int8_t match, bool cuda_banded_alignment)
: max_windows_(max_windows)
, cudapoa_batch_(claragenomics::cudapoa::create_batch(max_windows, max_window_depth, device, claragenomics::cudapoa::OutputType::consensus, gap, mismatch, match, cuda_banded_alignment))
, windows_()
CUDABatchProcessor::CUDABatchProcessor(uint32_t max_window_depth,
uint32_t device,
size_t avail_mem,
int8_t gap,
int8_t mismatch,
int8_t match,
bool cuda_banded_alignment)
: windows_()
, seqs_added_per_window_()
{
bid_ = CUDABatchProcessor::batches++;
// Create new CUDA stream.
CGA_CU_CHECK_ERR(cudaStreamCreate(&stream_));
cudapoa_batch_->set_cuda_stream(stream_);
cudapoa_batch_ = claragenomics::cudapoa::create_batch(max_window_depth,
device,
stream_,
avail_mem,
claragenomics::cudapoa::OutputType::consensus,
gap,
mismatch,
match,
cuda_banded_alignment);
}
CUDABatchProcessor::~CUDABatchProcessor()
......@@ -45,79 +70,21 @@ CUDABatchProcessor::~CUDABatchProcessor()
bool CUDABatchProcessor::addWindow(std::shared_ptr<Window> window)
{
if (windows_.size() < max_windows_)
{
windows_.push_back(window);
seqs_added_per_window_.push_back(0);
return true;
}
else
{
return false;
}
}
bool CUDABatchProcessor::hasWindows() const
{
return (windows_.size() != 0);
}
void CUDABatchProcessor::convertPhredQualityToWeights(const char* qual,
uint32_t qual_length,
std::vector<int8_t>& weights)
{
weights.clear();
for(uint32_t i = 0; i < qual_length; i++)
{
weights.push_back(static_cast<uint8_t>(qual[i]) - 33); // PHRED quality
}
}
claragenomics::cudapoa::StatusType CUDABatchProcessor::addSequenceToPoa(std::pair<const char*, uint32_t>& seq,
std::pair<const char*, uint32_t>& qualities)
{
// Add sequences to latest poa in batch.
std::vector<int8_t> weights;
claragenomics::cudapoa::StatusType status = claragenomics::cudapoa::StatusType::success;
if (qualities.first == nullptr)
{
status = cudapoa_batch_->add_seq_to_poa(seq.first, nullptr, seq.second);
}
else
{
convertPhredQualityToWeights(qualities.first, qualities.second, weights);
status = cudapoa_batch_->add_seq_to_poa(seq.first, weights.data(), seq.second);
}
return status;
}
void CUDABatchProcessor::generateMemoryMap()
{
auto num_windows = windows_.size();
for(uint32_t w = 0; w < num_windows; w++)
{
// Add new poa
claragenomics::cudapoa::StatusType status = cudapoa_batch_->add_poa();
if (status != claragenomics::cudapoa::StatusType::success)
{
fprintf(stderr, "Failed to add new POA to batch %d.\n",
cudapoa_batch_->batch_id());
exit(1);
}
std::shared_ptr<Window> window = windows_.at(w);
claragenomics::cudapoa::Group poa_group;
uint32_t num_seqs = window->sequences_.size();
std::vector<uint8_t> weights;
std::vector<std::vector<int8_t>> all_read_weights(num_seqs, std::vector<int8_t>());
// Add first sequence as backbone to graph.
std::pair<const char*, uint32_t> seq = window->sequences_.front();
std::pair<const char*, uint32_t> qualities = window->qualities_.front();
status = addSequenceToPoa(seq, qualities);
if (status != claragenomics::cudapoa::StatusType::success)
{
fprintf(stderr, "Could not add backbone to window. Fatal error.\n");
exit(1);
}
std::vector<int8_t> backbone_weights;
convertPhredQualityToWeights(qualities.first, qualities.second, all_read_weights[0]);
claragenomics::cudapoa::Entry e = {
seq.first,
all_read_weights[0].data(),
static_cast<int32_t>(seq.second)
};
poa_group.push_back(e);
// Add the rest of the sequences in sorted order of starting positions.
std::vector<uint32_t> rank;
......@@ -138,27 +105,56 @@ void CUDABatchProcessor::generateMemoryMap()
uint32_t i = rank.at(j);
seq = window->sequences_.at(i);
qualities = window->qualities_.at(i);
// Add sequences to latest poa in batch.
status = addSequenceToPoa(seq, qualities);
if (status == claragenomics::cudapoa::StatusType::exceeded_maximum_sequence_size)
convertPhredQualityToWeights(qualities.first, qualities.second, all_read_weights[i]);
claragenomics::cudapoa::Entry p = {
seq.first,
all_read_weights[i].data(),
static_cast<int32_t>(seq.second)
};
poa_group.push_back(p);
}
// Add group to CUDAPOA batch object.
std::vector<claragenomics::cudapoa::StatusType> entry_status;
claragenomics::cudapoa::StatusType status = cudapoa_batch_->add_poa_group(entry_status,
poa_group);
// If group was added, then push window in accepted windows list.
if (status != claragenomics::cudapoa::StatusType::success)
{
return false;
}
else
{
windows_.push_back(window);
}
// Keep track of how many sequences were actually processed for this
// group. This acts as the effective coverage for that window.
int32_t seq_added = 0;
for(uint32_t i = 1; i < entry_status.size(); i++)
{
if (entry_status[i] == claragenomics::cudapoa::StatusType::exceeded_maximum_sequence_size)
{
long_seq++;
continue;
}
else if (status == claragenomics::cudapoa::StatusType::exceeded_maximum_sequences_per_poa)
else if (entry_status[i] == claragenomics::cudapoa::StatusType::exceeded_maximum_sequences_per_poa)
{
skipped_seq++;
continue;
}
else if (status != claragenomics::cudapoa::StatusType::success)
else if (entry_status[i] != claragenomics::cudapoa::StatusType::success)
{
fprintf(stderr, "Could not add sequence to POA in batch %d.\n",
cudapoa_batch_->batch_id());
exit(1);
}
seqs_added_per_window_[w] = seqs_added_per_window_[w] + 1;
seq_added++;
}
seqs_added_per_window_.push_back(seq_added);
#ifndef NDEBUG
if (long_seq > 0)
{
......@@ -169,6 +165,23 @@ void CUDABatchProcessor::generateMemoryMap()
fprintf(stderr, "Skipped (%d / %d)\n", skipped_seq, num_seqs);
}
#endif
return true;
}
bool CUDABatchProcessor::hasWindows() const
{
return (cudapoa_batch_->get_total_poas() > 0);
}
void CUDABatchProcessor::convertPhredQualityToWeights(const char* qual,
uint32_t qual_length,
std::vector<int8_t>& weights)
{
weights.clear();
for(uint32_t i = 0; i < qual_length; i++)
{
weights.push_back(static_cast<uint8_t>(qual[i]) - 33); // PHRED quality
}
}
......@@ -197,6 +210,7 @@ void CUDABatchProcessor::getConsensus()
{
// This is a special case borrowed from the CPU version.
// TODO: We still run this case through the GPU, but could take it out.
bool consensus_status = false;
if (window->sequences_.size() < 3)
{
window->consensus_ = std::string(window->sequences_.front().first,
......@@ -204,11 +218,11 @@ void CUDABatchProcessor::getConsensus()
// This status is borrowed from the CPU version which considers this
// a failed consensus. All other cases are true.
window_consensus_status_.emplace_back(false);
consensus_status = false;
}
else
{
window->consensus_ = consensuses.at(i);
window->consensus_ = consensuses[i];
if (window->type_ == WindowType::kTGS)
{
uint32_t num_seqs_in_window = seqs_added_per_window_[i];
......@@ -216,12 +230,12 @@ void CUDABatchProcessor::getConsensus()
int32_t begin = 0, end = window->consensus_.size() - 1;
for (; begin < static_cast<int32_t>( window->consensus_.size()); ++begin) {
if (coverages.at(i).at(begin) >= average_coverage) {
if (coverages[i][begin] >= average_coverage) {
break;
}
}
for (; end >= 0; --end) {
if (coverages.at(i).at(end) >= average_coverage) {
if (coverages[i][end] >= average_coverage) {
break;
}
}
......@@ -229,12 +243,14 @@ void CUDABatchProcessor::getConsensus()
if (begin >= end) {
fprintf(stderr, "[CUDABatchProcessor] warning: "
"contig might be chimeric in window %lu!\n", window->id_);
consensus_status = false;
} else {
window->consensus_ = window->consensus_.substr(begin, end - begin + 1);
consensus_status = true;
}
}
window_consensus_status_.emplace_back(true);
}
window_consensus_status_.emplace_back(consensus_status);
}
}
}
......@@ -242,7 +258,6 @@ void CUDABatchProcessor::getConsensus()
const std::vector<bool>& CUDABatchProcessor::generateConsensus()
{
// Generate consensus for all windows in the batch
generateMemoryMap();
generatePOA();
getConsensus();
......
src/cuda/cudabatch.hpp
View file @ f119fd6e
......@@ -11,7 +11,7 @@
#include <atomic>
#include "window.hpp"
#include "cudapoa/batch.hpp"
#include <claragenomics/cudapoa/batch.hpp>
namespace spoa {
class AlignmentEngine;
......@@ -22,7 +22,7 @@ namespace racon {
class Window;
class CUDABatchProcessor;
std::unique_ptr<CUDABatchProcessor> createCUDABatch(uint32_t max_windows, uint32_t max_window_depth, uint32_t device, int8_t gap, int8_t mismatch, int8_t match, bool cuda_banded_alignment);
std::unique_ptr<CUDABatchProcessor> createCUDABatch(uint32_t max_window_depth, uint32_t device, size_t avail_mem, int8_t gap, int8_t mismatch, int8_t match, bool cuda_banded_alignment);
class CUDABatchProcessor
{
......@@ -65,27 +65,19 @@ public:
// Builder function to create a new CUDABatchProcessor object.
friend std::unique_ptr<CUDABatchProcessor>
createCUDABatch(uint32_t max_windows, uint32_t max_window_depth, uint32_t device, int8_t gap, int8_t mismatch, int8_t match, bool cuda_banded_alignment);
createCUDABatch(uint32_t max_window_depth, uint32_t device, size_t avail_mem, int8_t gap, int8_t mismatch, int8_t match, bool cuda_banded_alignment);
protected:
/**
* @brief Constructor for CUDABatch class.
*
* @param[in] max_windows : Maximum number windows in batch
* @param[in] max_window_depth : Maximum number of sequences per window
* @param[in] cuda_banded_alignment : Use banded POA alignment
*/
CUDABatchProcessor(uint32_t max_windows, uint32_t max_window_depth, uint32_t device, int8_t gap, int8_t mismatch, int8_t match, bool cuda_banded_alignment);
CUDABatchProcessor(uint32_t max_window_depth, uint32_t device, size_t avail_mem, int8_t gap, int8_t mismatch, int8_t match, bool cuda_banded_alignment);
CUDABatchProcessor(const CUDABatchProcessor&) = delete;
const CUDABatchProcessor& operator=(const CUDABatchProcessor&) = delete;
/*
* @brief Process all the windows and re-map them into
* memory for more efficient processing in the CUDA
* kernels.
*/
void generateMemoryMap();
/*
* @brief Run the CUDA kernel for generating POA on the batch.
* This call is asynchronous.
......@@ -106,13 +98,6 @@ protected:
uint32_t qual_length,
std::vector<int8_t>& weights);
/*
* @brief Add sequence and qualities to cudapoa.
*
*/
claragenomics::cudapoa::StatusType addSequenceToPoa(std::pair<const char*, uint32_t>& seq,
std::pair<const char*, uint32_t>& quality);
protected:
// Static batch count used to generate batch IDs.
static std::atomic<uint32_t> batches;
......@@ -120,9 +105,6 @@ protected:
// Batch ID.
uint32_t bid_ = 0;
// Maximum windows allowed in batch.
uint32_t max_windows_;
// CUDA-POA library object that manages POA batch.
std::unique_ptr<claragenomics::cudapoa::Batch> cudapoa_batch_;
......
src/cuda/cudapolisher.cpp
View file @ f119fd6e
......@@ -11,7 +11,7 @@
#include "sequence.hpp"
#include "cudapolisher.hpp"
#include <cudautils/cudautils.hpp>
#include <claragenomics/utils/cudautils.hpp>
#include "bioparser/bioparser.hpp"
#include "logger/logger.hpp"
......@@ -27,12 +27,12 @@ CUDAPolisher::CUDAPolisher(std::unique_ptr<bioparser::Parser<Sequence>> sparser,
std::unique_ptr<bioparser::Parser<Overlap>> oparser,
std::unique_ptr<bioparser::Parser<Sequence>> tparser,
PolisherType type, uint32_t window_length, double quality_threshold,
double error_threshold, int8_t match, int8_t mismatch, int8_t gap,
double error_threshold, bool trim, int8_t match, int8_t mismatch, int8_t gap,
uint32_t num_threads, uint32_t cudapoa_batches, bool cuda_banded_alignment,
uint32_t cudaaligner_batches)
: Polisher(std::move(sparser), std::move(oparser), std::move(tparser),
type, window_length, quality_threshold,
error_threshold, match, mismatch, gap, num_threads)
type, window_length, quality_threshold, error_threshold, trim,
match, mismatch, gap, num_threads)
, cudapoa_batches_(cudapoa_batches)
, cudaaligner_batches_(cudaaligner_batches)
, gap_(gap)
......@@ -82,6 +82,7 @@ std::vector<uint32_t> CUDAPolisher::calculate_batches_per_gpu(uint32_t batches,
return batches_per_gpu;
}
void CUDAPolisher::find_overlap_breaking_points(std::vector<std::unique_ptr<Overlap>>& overlaps)
{
if (cudaaligner_batches_ < 1)
......@@ -92,7 +93,7 @@ void CUDAPolisher::find_overlap_breaking_points(std::vector<std::unique_ptr<Over
else
{
// TODO: Experimentally this is giving decent perf
const uint32_t MAX_ALIGNMENTS = 50;
const uint32_t MAX_ALIGNMENTS = 200;
logger_->log();
std::mutex mutex_overlaps;
......@@ -149,7 +150,6 @@ void CUDAPolisher::find_overlap_breaking_points(std::vector<std::unique_ptr<Over
else if (logger_step != 0 && log_bar_idx < static_cast<int32_t>(RACON_LOGGER_BIN_SIZE))
{
logger_->bar("[racon::CUDAPolisher::initialize] aligning overlaps");
std::cerr<<std::endl;
log_bar_idx_prev = log_bar_idx;
}
}
......@@ -168,10 +168,12 @@ void CUDAPolisher::find_overlap_breaking_points(std::vector<std::unique_ptr<Over
{
for(uint32_t batch = 0; batch < batches_per_gpu.at(device); batch++)
{
batch_aligners_.emplace_back(createCUDABatchAligner(10000, 10000, MAX_ALIGNMENTS, device));
batch_aligners_.emplace_back(createCUDABatchAligner(15000, 15000, MAX_ALIGNMENTS, device));
}
}
logger_->log("[racon::CUDAPolisher::initialize] allocated memory on GPUs for alignment");
// Run batched alignment.
std::vector<std::future<void>> thread_futures;
for(auto& aligner : batch_aligners_)
......@@ -203,7 +205,6 @@ void CUDAPolisher::polish(std::vector<std::unique_ptr<Sequence>>& dst,
else
{
// Creation and use of batches.
const uint32_t MAX_WINDOWS = 256;
const uint32_t MAX_DEPTH_PER_WINDOW = 200;
// Bin batches into each GPU.
......@@ -211,13 +212,19 @@ void CUDAPolisher::polish(std::vector<std::unique_ptr<Sequence>>& dst,
for(int32_t device = 0; device < num_devices_; device++)
{
size_t total = 0, free = 0;
CGA_CU_CHECK_ERR(cudaSetDevice(device));
CGA_CU_CHECK_ERR(cudaMemGetInfo(&free, &total));
// Using 90% of available memory as heuristic since not all available memory can be used
// due to fragmentation.
size_t mem_per_batch = 0.9 * free/batches_per_gpu.at(device);
for(uint32_t batch = 0; batch < batches_per_gpu.at(device); batch++)
{
batch_processors_.emplace_back(createCUDABatch(MAX_WINDOWS, MAX_DEPTH_PER_WINDOW, device, gap_, mismatch_, match_, cuda_banded_alignment_));
batch_processors_.emplace_back(createCUDABatch(MAX_DEPTH_PER_WINDOW, device, mem_per_batch, gap_, mismatch_, match_, cuda_banded_alignment_));
}
}
logger_->log("[racon::CUDAPolisher::polish] allocated memory on GPUs");
logger_->log("[racon::CUDAPolisher::polish] allocated memory on GPUs for polishing");
// Mutex for accessing the vector of windows.
std::mutex mutex_windows;
......@@ -294,10 +301,12 @@ void CUDAPolisher::polish(std::vector<std::unique_ptr<Sequence>>& dst,
continue;
}
else if (logger_step != 0 && log_bar_idx < static_cast<int32_t>(RACON_LOGGER_BIN_SIZE))
{
while(log_bar_idx_prev <= log_bar_idx)
{
logger_->bar("[racon::CUDAPolisher::polish] generating consensus");
std::cerr<<std::endl;
log_bar_idx_prev = log_bar_idx;
log_bar_idx_prev++;
}
}
}
}
......@@ -343,7 +352,7 @@ void CUDAPolisher::polish(std::vector<std::unique_ptr<Sequence>>& dst,
exit(1);
}
return window_consensus_status_.at(j) = windows_[j]->generate_consensus(
alignment_engines_[it->second]);
alignment_engines_[it->second], trim_);
}, i));
}
}
......
src/cuda/cudapolisher.hpp
View file @ f119fd6e
......@@ -26,7 +26,7 @@ public:
friend std::unique_ptr<Polisher> createPolisher(const std::string& sequences_path,
const std::string& overlaps_path, const std::string& target_path,
PolisherType type, uint32_t window_length, double quality_threshold,
double error_threshold, int8_t match, int8_t mismatch, int8_t gap,
double error_threshold, bool trim, int8_t match, int8_t mismatch, int8_t gap,
uint32_t num_threads, uint32_t cudapoa_batches, bool cuda_banded_alignment,
uint32_t cudaaligner_batches);
......@@ -35,7 +35,7 @@ protected:
std::unique_ptr<bioparser::Parser<Overlap>> oparser,
std::unique_ptr<bioparser::Parser<Sequence>> tparser,
PolisherType type, uint32_t window_length, double quality_threshold,
double error_threshold, int8_t match, int8_t mismatch, int8_t gap,
double error_threshold, bool trim, int8_t match, int8_t mismatch, int8_t gap,
uint32_t num_threads, uint32_t cudapoa_batches, bool cuda_banded_alignment,
uint32_t cudaaligner_batches);
CUDAPolisher(const CUDAPolisher&) = delete;
......
src/main.cpp
View file @ f119fd6e
......@@ -12,7 +12,11 @@
#include "cuda/cudapolisher.hpp"
#endif
static const char* version = "v1.4.3";
#ifndef RACON_VERSION
#error "Undefined version for Racon. Please pass version using -DRACON_VERSION macro."
#endif
static const char* version = RACON_VERSION;
static const int32_t CUDAALIGNER_INPUT_CODE = 10000;
static struct option options[] = {
......@@ -21,6 +25,7 @@ static struct option options[] = {
{"window-length", required_argument, 0, 'w'},
{"quality-threshold", required_argument, 0, 'q'},
{"error-threshold", required_argument, 0, 'e'},
{"no-trimming", no_argument, 0, 'T'},
{"match", required_argument, 0, 'm'},
{"mismatch", required_argument, 0, 'x'},
{"gap", required_argument, 0, 'g'},
......@@ -44,10 +49,11 @@ int main(int argc, char** argv) {
uint32_t window_length = 500;
double quality_threshold = 10.0;
double error_threshold = 0.3;
bool trim = true;
int8_t match = 5;
int8_t mismatch = -4;
int8_t gap = -8;
int8_t match = 3;
int8_t mismatch = -5;
int8_t gap = -4;
uint32_t type = 0;
bool drop_unpolished_sequences = true;
......@@ -80,6 +86,9 @@ int main(int argc, char** argv) {
case 'e':
error_threshold = atof(optarg);
break;
case 'T':
trim = false;
break;
case 'm':
match = atoi(optarg);
break;
......@@ -137,7 +146,7 @@ int main(int argc, char** argv) {
auto polisher = racon::createPolisher(input_paths[0], input_paths[1],
input_paths[2], type == 0 ? racon::PolisherType::kC :
racon::PolisherType::kF, window_length, quality_threshold,
error_threshold, match, mismatch, gap, num_threads,
error_threshold, trim, match, mismatch, gap, num_threads,
cudapoa_batches, cuda_banded_alignment, cudaaligner_batches);
polisher->initialize();
......@@ -181,14 +190,16 @@ void help() {
" -e, --error-threshold <float>\n"
" default: 0.3\n"
" maximum allowed error rate used for filtering overlaps\n"
" --no-trimming\n"
" disables consensus trimming at window ends\n"
" -m, --match <int>\n"
" default: 5\n"
" default: 3\n"
" score for matching bases\n"
" -x, --mismatch <int>\n"
" default: -4\n"
" default: -5\n"
" score for mismatching bases\n"
" -g, --gap <int>\n"
" default: -8\n"
" default: -4\n"
" gap penalty (must be negative)\n"
" -t, --threads <int>\n"
" default: 1\n"
......@@ -203,7 +214,7 @@ void help() {
" number of batches for CUDA accelerated polishing\n"
" -b, --cuda-banded-alignment\n"
" use banding approximation for alignment on GPU\n"
" --cudaaligner-batches (experimental)\n"
" --cudaaligner-batches\n"
" Number of batches for CUDA accelerated alignment\n"
#endif
......
src/polisher.cpp
View file @ f119fd6e
......@@ -55,7 +55,7 @@ uint64_t shrinkToFit(std::vector<std::unique_ptr<T>>& src, uint64_t begin) {
std::unique_ptr<Polisher> createPolisher(const std::string& sequences_path,
const std::string& overlaps_path, const std::string& target_path,
PolisherType type, uint32_t window_length, double quality_threshold,
double error_threshold, int8_t match, int8_t mismatch, int8_t gap,
double error_threshold, bool trim, int8_t match, int8_t mismatch, int8_t gap,
uint32_t num_threads, uint32_t cudapoa_batches, bool cuda_banded_alignment,
uint32_t cudaaligner_batches) {
......@@ -80,18 +80,20 @@ std::unique_ptr<Polisher> createPolisher(const std::string& sequences_path,
return src.compare(src.size() - suffix.size(), suffix.size(), suffix) == 0;
};
if (is_suffix(sequences_path, ".fasta") || is_suffix(sequences_path, ".fa") ||
is_suffix(sequences_path, ".fasta.gz") || is_suffix(sequences_path, ".fa.gz")) {
if (is_suffix(sequences_path, ".fasta") || is_suffix(sequences_path, ".fasta.gz") ||
is_suffix(sequences_path, ".fna") || is_suffix(sequences_path, ".fna.gz") ||
is_suffix(sequences_path, ".fa") || is_suffix(sequences_path, ".fa.gz")) {
sparser = bioparser::createParser<bioparser::FastaParser, Sequence>(
sequences_path);
} else if (is_suffix(sequences_path, ".fastq") || is_suffix(sequences_path, ".fq") ||
is_suffix(sequences_path, ".fastq.gz") || is_suffix(sequences_path, ".fq.gz")) {
} else if (is_suffix(sequences_path, ".fastq") || is_suffix(sequences_path, ".fastq.gz") ||
is_suffix(sequences_path, ".fq") || is_suffix(sequences_path, ".fq.gz")) {
sparser = bioparser::createParser<bioparser::FastqParser, Sequence>(
sequences_path);
} else {
fprintf(stderr, "[racon::createPolisher] error: "
"file %s has unsupported format extension (valid extensions: "
".fasta, .fasta.gz, .fa, .fa.gz, .fastq, .fastq.gz, .fq, .fq.gz)!\n",
".fasta, .fasta.gz, .fna, .fna.gz, .fa, .fa.gz, .fastq, .fastq.gz, "
".fq, .fq.gz)!\n",
sequences_path.c_str());
exit(1);
}
......@@ -112,18 +114,20 @@ std::unique_ptr<Polisher> createPolisher(const std::string& sequences_path,
exit(1);
}
if (is_suffix(target_path, ".fasta") || is_suffix(target_path, ".fa") ||
is_suffix(target_path, ".fasta.gz") || is_suffix(target_path, ".fa.gz")) {
if (is_suffix(target_path, ".fasta") || is_suffix(target_path, ".fasta.gz") ||
is_suffix(target_path, ".fna") || is_suffix(target_path, ".fna.gz") ||
is_suffix(target_path, ".fa") || is_suffix(target_path, ".fa.gz")) {
tparser = bioparser::createParser<bioparser::FastaParser, Sequence>(
target_path);
} else if (is_suffix(target_path, ".fastq") || is_suffix(target_path, ".fq") ||
is_suffix(target_path, ".fastq.gz") || is_suffix(target_path, ".fq.gz")) {
} else if (is_suffix(target_path, ".fastq") || is_suffix(target_path, ".fastq.gz") ||
is_suffix(target_path, ".fq") || is_suffix(target_path, ".fq.gz")) {
tparser = bioparser::createParser<bioparser::FastqParser, Sequence>(
target_path);
} else {
fprintf(stderr, "[racon::createPolisher] error: "
"file %s has unsupported format extension (valid extensions: "
".fasta, .fasta.gz, .fa, .fa.gz, .fastq, .fastq.gz, .fq, .fq.gz)!\n",
".fasta, .fasta.gz, .fna, .fna.gz, .fa, .fa.gz, .fastq, .fastq.gz, "
".fq, .fq.gz)!\n",
target_path.c_str());
exit(1);
}
......@@ -134,7 +138,7 @@ std::unique_ptr<Polisher> createPolisher(const std::string& sequences_path,
// If CUDA is enabled, return an instance of the CUDAPolisher object.
return std::unique_ptr<Polisher>(new CUDAPolisher(std::move(sparser),
std::move(oparser), std::move(tparser), type, window_length,
quality_threshold, error_threshold, match, mismatch, gap,
quality_threshold, error_threshold, trim, match, mismatch, gap,
num_threads, cudapoa_batches, cuda_banded_alignment, cudaaligner_batches));
#else
fprintf(stderr, "[racon::createPolisher] error: "
......@@ -149,7 +153,7 @@ std::unique_ptr<Polisher> createPolisher(const std::string& sequences_path,
(void) cuda_banded_alignment;
return std::unique_ptr<Polisher>(new Polisher(std::move(sparser),
std::move(oparser), std::move(tparser), type, window_length,
quality_threshold, error_threshold, match, mismatch, gap,
quality_threshold, error_threshold, trim, match, mismatch, gap,
num_threads));
}
}
......@@ -158,11 +162,11 @@ Polisher::Polisher(std::unique_ptr<bioparser::Parser<Sequence>> sparser,
std::unique_ptr<bioparser::Parser<Overlap>> oparser,
std::unique_ptr<bioparser::Parser<Sequence>> tparser,
PolisherType type, uint32_t window_length, double quality_threshold,
double error_threshold, int8_t match, int8_t mismatch, int8_t gap,
double error_threshold, bool trim, int8_t match, int8_t mismatch, int8_t gap,
uint32_t num_threads)
: sparser_(std::move(sparser)), oparser_(std::move(oparser)),
tparser_(std::move(tparser)), type_(type), quality_threshold_(
quality_threshold), error_threshold_(error_threshold),
quality_threshold), error_threshold_(error_threshold), trim_(trim),
alignment_engines_(), sequences_(), dummy_quality_(window_length, '!'),
window_length_(window_length), windows_(),
thread_pool_(thread_pool::createThreadPool(num_threads)),
......@@ -494,7 +498,7 @@ void Polisher::polish(std::vector<std::unique_ptr<Sequence>>& dst,
exit(1);
}
return windows_[j]->generate_consensus(
alignment_engines_[it->second]);
alignment_engines_[it->second], trim_);
}, i));
}
......
src/polisher.hpp
View file @ f119fd6e
......@@ -44,7 +44,7 @@ class Polisher;
std::unique_ptr<Polisher> createPolisher(const std::string& sequences_path,
const std::string& overlaps_path, const std::string& target_path,
PolisherType type, uint32_t window_length, double quality_threshold,
double error_threshold, int8_t match, int8_t mismatch, int8_t gap,
double error_threshold, bool trim, int8_t match, int8_t mismatch, int8_t gap,
uint32_t num_threads, uint32_t cuda_batches = 0,
bool cuda_banded_alignment = false, uint32_t cudaaligner_batches = 0);
......@@ -60,7 +60,7 @@ public:
friend std::unique_ptr<Polisher> createPolisher(const std::string& sequences_path,
const std::string& overlaps_path, const std::string& target_path,
PolisherType type, uint32_t window_length, double quality_threshold,
double error_threshold, int8_t match, int8_t mismatch, int8_t gap,
double error_threshold, bool trim, int8_t match, int8_t mismatch, int8_t gap,
uint32_t num_threads, uint32_t cuda_batches, bool cuda_banded_alignment,
uint32_t cudaaligner_batches);
......@@ -69,7 +69,7 @@ protected:
std::unique_ptr<bioparser::Parser<Overlap>> oparser,
std::unique_ptr<bioparser::Parser<Sequence>> tparser,
PolisherType type, uint32_t window_length, double quality_threshold,
double error_threshold, int8_t match, int8_t mismatch, int8_t gap,
double error_threshold, bool trim, int8_t match, int8_t mismatch, int8_t gap,
uint32_t num_threads);
Polisher(const Polisher&) = delete;
const Polisher& operator=(const Polisher&) = delete;
......@@ -82,6 +82,7 @@ protected:
PolisherType type_;
double quality_threshold_;
double error_threshold_;
bool trim_;
std::vector<std::shared_ptr<spoa::AlignmentEngine>> alignment_engines_;
std::vector<std::unique_ptr<Sequence>> sequences_;
......
src/window.cpp
View file @ f119fd6e
......@@ -58,7 +58,8 @@ void Window::add_layer(const char* sequence, uint32_t sequence_length,
positions_.emplace_back(begin, end);
}
bool Window::generate_consensus(std::shared_ptr<spoa::AlignmentEngine> alignment_engine) {
bool Window::generate_consensus(std::shared_ptr<spoa::AlignmentEngine> alignment_engine,
bool trim) {
if (sequences_.size() < 3) {
consensus_ = std::string(sequences_.front().first, sequences_.front().second);
......@@ -86,14 +87,14 @@ bool Window::generate_consensus(std::shared_ptr<spoa::AlignmentEngine> alignment
spoa::Alignment alignment;
if (positions_[i].first < offset && positions_[i].second >
sequences_.front().second - offset) {
alignment = alignment_engine->align_sequence_with_graph(
sequences_[i].first, sequences_[i].second, graph);
alignment = alignment_engine->align(sequences_[i].first,
sequences_[i].second, graph);
} else {
std::vector<int32_t> mapping;
auto subgraph = graph->subgraph(positions_[i].first,
positions_[i].second, mapping);
alignment = alignment_engine->align_sequence_with_graph(
sequences_[i].first, sequences_[i].second, subgraph);
alignment = alignment_engine->align( sequences_[i].first,
sequences_[i].second, subgraph);
subgraph->update_alignment(alignment, mapping);
}
......@@ -110,7 +111,7 @@ bool Window::generate_consensus(std::shared_ptr<spoa::AlignmentEngine> alignment
std::vector<uint32_t> coverages;
consensus_ = graph->generate_consensus(coverages);
if (type_ == WindowType::kTGS) {
if (type_ == WindowType::kTGS && trim) {
uint32_t average_coverage = (sequences_.size() - 1) / 2;
int32_t begin = 0, end = consensus_.size() - 1;
......
src/window.hpp
View file @ f119fd6e
......@@ -44,7 +44,8 @@ public:
return consensus_;
}
bool generate_consensus(std::shared_ptr<spoa::AlignmentEngine> alignment_engine);
bool generate_consensus(std::shared_ptr<spoa::AlignmentEngine> alignment_engine,
bool trim);
void add_layer(const char* sequence, uint32_t sequence_length,
const char* quality, uint32_t quality_length, uint32_t begin,
......
test/racon_test.cpp
View file @ f119fd6e
......@@ -33,7 +33,7 @@ public:
bool cuda_banded_alignment = false, uint32_t cudaaligner_batches = 0) {
polisher = racon::createPolisher(sequences_path, overlaps_path, target_path,
type, window_length, quality_threshold, error_threshold, match,
type, window_length, quality_threshold, error_threshold, true, match,
mismatch, gap, 4, cuda_batches, cuda_banded_alignment, cudaaligner_batches);
}
......@@ -54,25 +54,25 @@ public:
TEST(RaconInitializeTest, PolisherTypeError) {
EXPECT_DEATH((racon::createPolisher("", "", "", static_cast<racon::PolisherType>(3),
0, 0, 0, 0, 0, 0, 0)), ".racon::createPolisher. error: invalid polisher"
0, 0, 0, 0, 0, 0, 0, 0)), ".racon::createPolisher. error: invalid polisher"
" type!");
}
TEST(RaconInitializeTest, WindowLengthError) {
EXPECT_DEATH((racon::createPolisher("", "", "", racon::PolisherType::kC, 0,
0, 0, 0, 0, 0, 0)), ".racon::createPolisher. error: invalid window length!");
0, 0, 0, 0, 0, 0, 0)), ".racon::createPolisher. error: invalid window length!");
}
TEST(RaconInitializeTest, SequencesPathExtensionError) {
EXPECT_DEATH((racon::createPolisher("", "", "", racon::PolisherType::kC, 500,
0, 0, 0, 0, 0, 0)), ".racon::createPolisher. error: file has unsupported "
"format extension .valid extensions: .fasta, .fasta.gz, .fa, .fa.gz, "
".fastq, .fastq.gz, .fq, .fq.gz.!");
0, 0, 0, 0, 0, 0, 0)), ".racon::createPolisher. error: file has unsupported "
"format extension .valid extensions: .fasta, .fasta.gz, .fna, .fna.gz, "
".fa, .fa.gz, .fastq, .fastq.gz, .fq, .fq.gz.!");
}
TEST(RaconInitializeTest, OverlapsPathExtensionError) {
EXPECT_DEATH((racon::createPolisher(racon_test_data_path + "sample_reads.fastq.gz",
"", "", racon::PolisherType::kC, 500, 0, 0, 0, 0, 0, 0)),
"", "", racon::PolisherType::kC, 500, 0, 0, 0, 0, 0, 0, 0)),
".racon::createPolisher. error: file has unsupported format extension "
".valid extensions: .mhap, .mhap.gz, .paf, .paf.gz, .sam, .sam.gz.!");
}
......@@ -80,9 +80,9 @@ TEST(RaconInitializeTest, OverlapsPathExtensionError) {
TEST(RaconInitializeTest, TargetPathExtensionError) {
EXPECT_DEATH((racon::createPolisher(racon_test_data_path + "sample_reads.fastq.gz",
racon_test_data_path + "sample_overlaps.paf.gz", "", racon::PolisherType::kC,
500, 0, 0, 0, 0, 0, 0)), ".racon::createPolisher. error: file has "
"unsupported format extension .valid extensions: .fasta, .fasta.gz, .fa,"
" .fa.gz, .fastq, .fastq.gz, .fq, .fq.gz.!");
500, 0, 0, 0, 0, 0, 0, 0)), ".racon::createPolisher. error: file has "
"unsupported format extension .valid extensions: .fasta, .fasta.gz, .fna, "
".fna.gz, .fa, .fa.gz, .fastq, .fastq.gz, .fq, .fq.gz.!");
}
TEST_F(RaconPolishingTest, ConsensusWithQualities) {
......