count_positive_kmers.cuh File Reference

#include <cuda/__cmath/ceil_div.h>
#include <cuda_runtime.h>
#include <thrust/count.h>
#include <thrust/device_ptr.h>
#include <thrust/execution_policy.h>
#include <cstdint>
#include <cusbf/config.cuh>
#include <cusbf/detail/query_layout.cuh>
#include <cusbf/device_span.cuh>
#include <cusbf/error.hpp>
#include <cusbf/helpers.cuh>

Go to the source code of this file.

Namespaces
namespace	cusbf
namespace	cusbf::detail

Functions
template<typename Config >
__global__ void	cusbf::detail::count_positive_kmers_per_record_kernel (const uint8_t *hits, const QueryLayoutRecord *records, uint64_t *positive_kmers_out, uint64_t record_count)
	Per-record kernel: sums hits[hit_offset ..] for each QueryLayoutRecord.
template<typename Config >
uint64_t	cusbf::detail::count_positive_kmers_total (device_span< const uint8_t > hits, cuda::stream_ref stream)
	Device-wide count of set bits in a per-k-mer hit buffer.
template<typename Config >
Result< void >	cusbf::detail::count_positive_kmers_per_record (device_span< const uint8_t > hits, device_span< const QueryLayoutRecord > records, device_span< uint64_t > positive_kmers_out, cuda::stream_ref stream)
	Fills positive_kmers_out with per-record positive k-mer counts.