static void *worker(void *data)
{
worker_t *w = (worker_t *)data;
for(size_t i = w->start; i < w->n; i+= w->step) {
kseq_t *s = &kv_A(w->reads, i);
aln_v result = align_read(s,
w->ref_seqs,
w->config);
kstring_t str = { 0, 0, NULL };
write_sam_records(&str,
s,
result,
w->ref_seqs,
w->read_group_id,
w->config->n_keep,
w->config->max_drop);
w->sams[i] = str;
for(size_t j = 0; j < kv_size(result); j++)
free(kv_A(result, j).cigar);
kv_destroy(result);
kseq_stack_destroy(s);
}
return 0;
}
int main(int argc, char** argv) {
char *align_file = NULL;
if (argc != 2) {
print_usage("Invalid number of arguments.");
return 2;
}
align_file = argv[1];
int *alignment = NULL;
int align_len = 0;
HMMStateMap *state_hmm_map = NULL;
int total_states = 0;
FILE *fp = fopen(align_file, "rb");
align_len = align_read(&alignment, &total_states, &state_hmm_map, fp);
fclose(fp);
printf("Frame number: %d\n", align_len);
for (int i = 0; i < align_len; i++) {
printf("%d ", alignment[i]);
}
printf("\n");
printf ("Total states: %d\n", total_states);
for (int i = 0; i < align_len; i++) {
printf("%d(%d) ", state_hmm_map[alignment[i]].hmm_id, state_hmm_map[alignment[i]].hmm_state_id);
}
printf("\n");
return 0;
}
int get_superblock(struct ext_superblock_t *sb, int fd, char *buf, uint32_t size, int fs) {
int offset = align_read(fd, buf, SUPERBLOCKOFFSET, SUPERBLOCKSIZE, size, DOM0BLOCKSIZE);
if (offset < 0) {
printf("offset:%d\n", offset);
return -1;
}
if (parse_superblock(sb, buf + offset, size - offset, fs) < 0) {
printf("parse error\n");
return -1;
}
return 0;
}
int aln_by_fingerprint(struct ALN_Options * op)
{
int tmp;
tmp = format_Options(op);
if(tmp < 0) return tmp;
fprintf(stdout, "===> Dump parameters...%d\r\n", op->verbose & 0x80);
if(op->verbose & 0x80)
{
dump_Options(op);
}
fprintf(stdout, "===> Load database...%d\r\n", op->verbose & 0x01);
if(op->verbose & 0x01)
{
tmp = load_spt(op);
if(tmp < 0) return tmp;
}
if((op->verbose & 0x07) == 0x07)
{
tmp = align_read_conflict(op);
if(tmp < 0) return tmp;
}
if((op->verbose & 0x05) == 0x05)
{
tmp = align_read_debug(op);
if(tmp < 0) return tmp;
}
fprintf(stdout, "===> Align reads...%d\r\n", (op->verbose & 0x03) == 0x03);
if((op->verbose & 0x03) == 0x03)
{
tmp = align_read(op);
if(tmp < 0) return tmp;
}
if(op->pt != NULL) free(op->pt);
if(op->index != NULL) free(op->index);
return 0;
}