DebugOutput::DebugOutput(const char *file_name, AlignmentType alignment_type, BNT bnt)
: OutputFile(file_name, alignment_type, bnt)
{
if (alignment_type == PAIRED_END)
{
char fname[256];
char *mate_number;
NVBIO_CUDA_ASSERT(strlen(file_name) < sizeof(fname));
strncpy(fname, file_name, sizeof(fname));
mate_number = strstr(fname, "#");
if (mate_number)
{
*mate_number = '1';
}
fp = gzopen(fname, "wb");
if (mate_number)
{
*mate_number = '2';
fp_opposite_mate = gzopen(fname, "wb");
} else {
fp_opposite_mate = fp;
}
} else {
fp = gzopen(file_name, "wb");
fp_opposite_mate = NULL;
}
}
void OutputFile::readback(struct CPUOutputBatch& cpu_batch,
const struct GPUOutputBatch& gpu_batch,
const AlignmentMate mate,
const AlignmentScore score)
{
Timer timer;
timer.start();
// read back the scores
// readback_scores will do the "right thing" based on the pass and score that we're getting
// (i.e., it'll update either the first or second score for either the anchor or opposite mate)
gpu_batch.readback_scores(cpu_batch.best_alignments, mate, score);
if (score == BEST_SCORE)
{
// if this is the best alignment, read back CIGARs and MD strings as well
gpu_batch.readback_cigars(cpu_batch.cigar[mate]);
gpu_batch.readback_mds(cpu_batch.mds[mate]);
if (mate == MATE_1)
{
// mate 1 best score comes first; stash the count
cpu_batch.count = gpu_batch.count;
// set up the read data pointers
// this is not strictly related to which mate or scoring pass we're processing,
// but must be done once per batch, so we do it here
cpu_batch.read_data[MATE_1] = read_data_1;
cpu_batch.read_data[MATE_2] = read_data_2;
}
}
// sanity check to make sure the number of reads matches what we got previously
// (for mate 1 best score this will always pass due to the assignment above)
NVBIO_CUDA_ASSERT(cpu_batch.count == gpu_batch.count);
timer.stop();
iostats.output_process_timings.add(gpu_batch.count, timer.seconds());
iostats.alignments_DtoH_time += timer.seconds();
iostats.alignments_DtoH_count += gpu_batch.count;
}
void BamOutput::close()
{
// protect this section
ScopedLock lock( &mutex );
// flush all non-emtpy blocks
if (data_buffers[ buffer_id ].get_pos())
write_block();
flush_blocks();
NVBIO_CUDA_ASSERT(fp);
// write out the BAM EOF marker
static const unsigned char magic[28] = { 0037, 0213, 0010, 0004, 0000, 0000, 0000, 0000, 0000,
0377, 0006, 0000, 0102, 0103, 0002, 0000, 0033, 0000,
0003, 0000, 0000, 0000, 0000, 0000, 0000, 0000, 0000, 0000 };
fwrite(magic, sizeof(magic), 1, fp);
fclose(fp);
fp = NULL;
}
