int bam_writer(void *data) {
struct timeval start, end;
double time;
//if (time_on) { start_timer(start); }
batch_t *batch = (batch_t *) data;
fastq_read_t *fq_read;
array_list_t *array_list;
size_t num_items;
//bam1_t *bam1;
//alignment_t *alig;
mapping_batch_t *mapping_batch = (mapping_batch_t *) batch->mapping_batch;
batch_writer_input_t *writer_input = batch->writer_input;
bam_file_t *bam_file = writer_input->bam_file;
linked_list_t *linked_list = writer_input->list_p;
size_t num_reads_b = array_list_size(mapping_batch->fq_batch);
size_t num_mapped_reads = 0;
size_t total_mappings = 0;
unsigned char found_p1 = 0;
unsigned char found_p2 = 0;
int i = 0;
extern size_t bwt_correct;
extern size_t bwt_error;
extern pthread_mutex_t bwt_mutex, mutex_sp;
writer_input->total_batches++;
extern size_t *histogram_sw;
extern size_t num_reads_map;
extern size_t num_reads;
extern size_t tot_reads;
extern st_bwt_t st_bwt;
st_bwt.total_reads += num_reads_b;
free(mapping_batch->histogram_sw);
//
// DNA/RNA mode
//
for (size_t i = 0; i < num_reads_b; i++) {
num_items = array_list_size(mapping_batch->mapping_lists[i]);
total_mappings += num_items;
fq_read = (fastq_read_t *) array_list_get(i, mapping_batch->fq_batch);
// mapped or not mapped ?
if (num_items == 0) {
total_mappings++;
write_unmapped_read(fq_read, bam_file);
if (mapping_batch->mapping_lists[i]) {
array_list_free(mapping_batch->mapping_lists[i], NULL);
}
} else {
num_mapped_reads++;
if (array_list_size(mapping_batch->mapping_lists[i]) == 1) {
st_bwt.single_alig++;
} else {
st_bwt.multi_alig++;
}
write_mapped_read(mapping_batch->mapping_lists[i], bam_file);
}
}
if (mapping_batch) {
mapping_batch_free(mapping_batch);
}
if (batch) batch_free(batch);
basic_statistics_add(num_reads_b, num_mapped_reads, total_mappings, 0, basic_st);
}
void ydb_batch_free(struct ydb_batch *ybatch)
{
struct batch *batch = (struct batch *)ybatch;
batch_free(batch);
}
int sam_writer(void *data) {
batch_t *batch = (batch_t *) data;
batch_writer_input_t *writer_input = batch->writer_input;
//bam_file_t *bam_file = writer_input->bam_file;
FILE *out_file = (FILE *) writer_input->bam_file;
genome_t *genome = writer_input->genome;
fastq_read_t *read;
mapping_batch_t *mapping_batch = (mapping_batch_t *) batch->mapping_batch;
size_t num_reads = array_list_size(mapping_batch->fq_batch);
//linked_list_t *linked_list = writer_input->list_p;
array_list_t *read_list = mapping_batch->fq_batch;
array_list_t *mapping_list;
size_t num_mappings;
size_t num_mapped_reads = 0;
size_t total_mappings = 0;
alignment_t *alig;
int flag, pnext = 0, tlen = 0;
char rnext[4] = "*\0";
extern st_bwt_t st_bwt;
st_bwt.total_reads += num_reads;
for (size_t i = 0; i < num_reads; i++) {
read = (fastq_read_t *) array_list_get(i, read_list);
mapping_list = mapping_batch->mapping_lists[i];
num_mappings = array_list_size(mapping_list);
total_mappings += num_mappings;
//printf("%i.Read %s (num_mappings %i)\n", i, read->id, num_mappings);
if (num_mappings > 0) {
if (num_mappings == 1) {
st_bwt.single_alig++;
} else {
st_bwt.multi_alig++;
}
num_mapped_reads++;
for (size_t j = 0; j < num_mappings; j++) {
alig = (alignment_t *) array_list_get(j, mapping_list);
flag = (alig->seq_strand ? 16 : 0);
fprintf(out_file, "%s\t%i\t%s\t%i\t%i\t%s\t%s\t%i\t%i\t%s\t%s\n",
alig->query_name,
flag,
genome->chr_name[alig->chromosome],
alig->position + 1,
alig->map_quality,
alig->cigar,
rnext,
pnext,
tlen,
alig->sequence,
alig->quality);
//alig->optional_fields);
alignment_free(alig);
}
array_list_free(mapping_list, NULL);
} else {
total_mappings++;
if (mapping_list) {
array_list_free(mapping_list, NULL);
}
fprintf(out_file, "%s\t4\t*\t0\t0\t*\t*\t0\t0\t%s\t%s\n",
read->id,
read->sequence,
read->quality);
}
}
if (mapping_batch) {
mapping_batch_free(mapping_batch);
}
if (batch) batch_free(batch);
basic_statistics_add(num_reads, num_mapped_reads, total_mappings, 0, basic_st);
}
