aligner_inst.h

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 * nvbio
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#include <nvBowtie/bowtie2/cuda/aligner.h>
#include <nvBowtie/bowtie2/cuda/fmindex_def.h>
#include <nvBowtie/bowtie2/cuda/scoring.h>

namespace nvbio {
namespace bowtie2 {
namespace cuda {

void all_ed(
          Aligner&                          aligner,
    const Params&                           params,
    const FMIndexDef::type                  fmi,
    const FMIndexDef::type                  rfmi,
    const UberScoringScheme&                scoring_scheme,
    const io::SequenceDataDevice&           reference_data,
    const io::FMIndexDataDevice&            driver_data,
    io::SequenceDataDevice&                 read_data,
    io::HostOutputBatchSE&                  cpu_batch,
    Stats&                                  stats);

void all_sw(
          Aligner&                          aligner,
    const Params&                           params,
    const FMIndexDef::type                  fmi,
    const FMIndexDef::type                  rfmi,
    const UberScoringScheme&                scoring_scheme,
    const io::SequenceDataDevice&           reference_data,
    const io::FMIndexDataDevice&            driver_data,
    io::SequenceDataDevice&                 read_data,
    io::HostOutputBatchSE&                  cpu_batch,
    Stats&                                  stats);

void best_approx_ed(
          Aligner&                          aligner,
    const Params&                           params,
    const FMIndexDef::type                  fmi,
    const FMIndexDef::type                  rfmi,
    const UberScoringScheme&                scoring_scheme,
    const io::SequenceDataDevice&           reference_data,
    const io::FMIndexDataDevice&            driver_data,
    io::SequenceDataDevice&                 read_data,
    io::HostOutputBatchSE&                  cpu_batch,
    Stats&                                  stats);

void best_approx_sw(
          Aligner&                          aligner,
    const Params&                           params,
    const FMIndexDef::type                  fmi,
    const FMIndexDef::type                  rfmi,
    const UberScoringScheme&                scoring_scheme,
    const io::SequenceDataDevice&           reference_data,
    const io::FMIndexDataDevice&            driver_data,
    io::SequenceDataDevice&                 read_data,
    io::HostOutputBatchSE&                  cpu_batch,
    Stats&                                  stats);

void best_approx_ed(
          Aligner&                          aligner,
    const Params&                           params,
    const FMIndexDef::type                  fmi,
    const FMIndexDef::type                  rfmi,
    const UberScoringScheme&                scoring_scheme,
    const io::SequenceDataDevice&           reference_data,
    const io::FMIndexDataDevice&            driver_data,
    io::SequenceDataDevice&                 read_data1,
    io::SequenceDataDevice&                 read_data2,
    io::HostOutputBatchPE&                  cpu_batch,
    Stats&                                  stats);

void best_approx_sw(
          Aligner&                          aligner,
    const Params&                           params,
    const FMIndexDef::type                  fmi,
    const FMIndexDef::type                  rfmi,
    const UberScoringScheme&                scoring_scheme,
    const io::SequenceDataDevice&           reference_data,
    const io::FMIndexDataDevice&            driver_data,
    io::SequenceDataDevice&                 read_data1,
    io::SequenceDataDevice&                 read_data2,
    io::HostOutputBatchPE&                  cpu_batch,
    Stats&                                  stats);

} // namespace cuda
} // namespace bowtie2
} // namespace nvbio