int main(int argc, char** argv)
{
struct function_queue fq;
struct qtpool_startup_info tqsi;
struct qtpool tq;
size_t threads = 4;
int i = 0;
int tqse[4];
puts("fq_init");
fq_init(&fq, FQTYPE_IA, 25);
tqsi.fq = &fq;
tqsi.max_threads = threads;
puts("qtinit");
qtinit(&tq, &tqsi);
puts("start");
qtstart(&tq, tqse);
puts("pushing");
for(i = 0; i < 100; ++i) {
fq_push(&fq, i %3 ? my_puts2 : my_puts, (void*) i, 1);
printf("pushed %p with %p\n", i %3 ? my_puts2 : my_puts, (void*) i);
}
sleep(2);
qtstop(&tq, 1);
puts("stopped");
qtdestroy(&tq);
fq_destroy(&fq);
return 0;
}
/**
* Initialize context pointers
*/
void context_init(struct csv_context *ctx) {
// Init our passthrough buffer
ctx->csv_buf = cbuf_init(BUFFER_SIZE);
// Initialize our blocking queue
fq_init(&ctx->io_queue, BG_QUEUE_MAX);
// Initialize our CSV parser
if(csv_init(&ctx->parser, 0) != 0) {
fprintf(stderr, "Couldn't initialize CSV parser!\n");
exit(EXIT_FAILURE);
}
// Set our csv block realloc size
csv_set_blk_size(&ctx->parser, CSV_BLK_SIZE);
// Initialize our thread count
ctx->thread_count = IO_THREADS_DEFAULT;
// Default to no group column
ctx->gcol = -1;
// Default to not gzipping our output files
ctx->gzip = 0;
// Header injection flags
ctx->use_header = 0;
ctx->count_header = 0;
ctx->header_len = 0;
}
fq_t *sff2fq (sff_t *sff)
{
fq_t *fq = NULL;
if (NULL == (fq = fq_init())) {
return fq;
}
int clip_left_index = 0;
int clip_right_index = 0;
clip_left_index = max (1, max (sff_clip_qual_left (sff), sff_clip_adapter_left (sff)));
clip_right_index = min ((sff_clip_qual_right (sff) == 0 ? sff_n_bases(sff):sff_clip_qual_right(sff)),
(sff_clip_adapter_right(sff) == 0 ? sff_n_bases(sff):sff_clip_adapter_right(sff)));
// NB: clip_right_index and clip_left_offset now form a 0-based, half-open range
const int clip_left_offset = clip_left_index - 1;
assert(clip_left_offset >= 0);
// If right clip precedes left, clip is invalid and truncated to 0-length read
const int clip_seqlen = (clip_right_index >= clip_left_offset) ? clip_right_index - clip_left_offset : 0;
assert(clip_seqlen >= 0);
assert(clip_seqlen <= strlen(sff_bases(sff)));
//copy name
fq->name = strdup (sff_name(sff));
//copy sequence
fq->seq = (char *) malloc (strlen (sff_bases(sff))+1);
strncpy (fq->seq, sff_bases(sff)+clip_left_offset, clip_seqlen);
fq->seq[clip_seqlen] = '\0';
//copy quality
char *qual = qual_to_fastq (sff_quality(sff));
fq->qual = (char *) malloc (strlen (sff_quality(sff))+1);
strncpy (fq->qual, qual+clip_left_offset, clip_seqlen);
fq->qual[clip_seqlen] = '\0';
free (qual);
//set length
fq->l = strlen (fq->seq);
return fq;
}
