void*
writer_run(void *arg)
{
writer_t *w = (writer_t*)arg;
block_t *b = NULL;
int32_t wait;
uint64_t n = 0;
//fprintf(stderr, "writer starting w->output->n=%d\n", w->output->n);
while(!w->is_done) {
#ifdef PBGZF_USE_LOCAL_POOLS
while(w->pool_local->n < w->pool_local->m) { // more to read from the output queue
wait = (0 == w->pool_local->n) ? 1 : 0;
b = queue_get(w->output, wait);
if(NULL == b) {
if(1 == wait) {
if(QUEUE_STATE_OK == w->output->state) {
fprintf(stderr, "writer queue_get: bug encountered\n");
exit(1);
}
else if(QUEUE_STATE_EOF == w->output->state || 0 == w->output->num_adders) {
break;
}
else {
queue_wait_until_not_flush(w->output);
continue;
}
}
else {
break;
}
}
if(0 == block_pool_add(w->pool_local, b)) {
fprintf(stderr, "writer block_pool_add: bug encountered\n");
exit(1);
}
b = NULL;
}
//fprintf(stderr, "writer: read from output w->pool_local->n=%d %d\n", w->pool_local->n, w->pool_local->m);
if(0 == w->pool_local->n && (QUEUE_STATE_EOF == w->output->state || 0 == w->output->num_adders)) {
break;
}
while(0 < w->pool_local->n) { // write all the blocks
b = block_pool_get(w->pool_local);
if(NULL == b) {
fprintf(stderr, "writer block_pool_get: bug encountered\n");
exit(1);
}
if(0 == w->compress) {
if(writer_write_block1(w->fp_file, b) != b->block_length) {
fprintf(stderr, "writer writer_write_block: bug encountered\n");
exit(1);
}
}
else {
if(writer_write_block2(w->fp_bgzf, b) != b->block_length) {
fprintf(stderr, "writer writer_write_block: bug encountered\n");
exit(1);
}
}
if(0 == block_pool_add(w->pool_fp, b)) {
fprintf(stderr, "writer block_pool_add: bug encountered\n");
exit(1);
}
n++;
}
#else
wait = 1;
b = queue_get(w->output, wait);
if(NULL == b) {
if(1 == wait) {
if(QUEUE_STATE_OK == w->output->state) {
fprintf(stderr, "writer queue_get: bug encountered\n");
exit(1);
}
else if(QUEUE_STATE_EOF == w->output->state || 0 == w->output->num_adders) {
break;
}
else {
queue_wait_until_not_flush(w->output);
continue;
}
}
else {
break;
}
}
if(0 == w->compress) {
if(writer_write_block1(w->fp_file, b) != b->block_length) {
fprintf(stderr, "writer writer_write_block: bug encountered\n");
exit(1);
}
}
else {
if(writer_write_block2(w->fp_bgzf, b) != b->block_length) {
fprintf(stderr, "writer writer_write_block: bug encountered\n");
exit(1);
}
}
block_destroy(b);
b = NULL;
n++;
#endif
}
w->is_done = 1;
//fprintf(stderr, "writer written %llu blocks\n", n);
// NB: will wake all
queue_remove_getter(w->output);
return arg;
}
void*
reader_run(void *arg)
{
reader_t *r = (reader_t*)arg;
block_t *b = NULL;
int32_t wait;
uint64_t n = 0;
block_pool_t *pool;
//fprintf(stderr, "reader staring\n");
pool = block_pool_init2(PBGZF_BLOCKS_POOL_NUM);
while(!r->is_done) {
#ifdef PBGZF_USE_LOCAL_POOLS
// read block
while(pool->n < pool->m) {
if(NULL == r->pool || NULL == (b = block_pool_get(r->pool))) {
b = block_init();
}
if(0 == r->compress) {
if(reader_read_block(r->fp_bgzf, b) < 0) {
fprintf(stderr, "reader reader_read_block: bug encountered\n");
exit(1);
}
}
else {
if((b->block_length = read(r->fd_file, b->buffer, WINDOW_SIZE)) < 0) {
fprintf(stderr, "reader read: bug encountered\n");
exit(1);
}
}
if(NULL == b || 0 == b->block_length) {
block_pool_add(r->pool, b);
b = NULL;
break;
}
if(0 == block_pool_add(pool, b)) {
fprintf(stderr, "reader block_pool_add: bug encountered\n");
exit(1);
}
}
//fprintf(stderr, "reader: read in pool->n=%d\n", pool->n);
if(0 == pool->n) {
break;
}
// add to the queue
while(0 < pool->n) {
b = block_pool_peek(pool);
if(NULL == b) {
fprintf(stderr, "reader block_pool_get: bug encountered\n");
exit(1);
}
wait = (pool->n == pool->m) ? 1 : 0; // NB: only wait if we cannot read in any more...
if(0 == queue_add(r->input, b, wait)) {
if(1 == wait) {
if(QUEUE_STATE_OK == r->input->state) {
fprintf(stderr, "reader queue_add: bug encountered\n");
exit(1);
}
else if(QUEUE_STATE_EOF == r->input->state) { // EOF, quit
break;
}
else {
// NB: if the reader has blocks, it does not make sense to
// flush
fprintf(stderr, "reader queue_add: bug encountered\n");
exit(1);
}
}
else {
break;
}
}
block_pool_get(pool); // ignore return
b = NULL;
n++;
}
//fprintf(stderr, "reader: add to pool->n=%d\n", pool->n);
//fprintf(stderr, "r->output->n=%d\n", r->input->n);
#else
// read block
//fprintf(stderr, "Reader #%d read block\n", 0);
b = block_init();
if(0 == r->compress) {
if(reader_read_block(r->fp_bgzf, b) < 0) {
fprintf(stderr, "reader reader_read_block: bug encountered\n");
exit(1);
}
}
else {
if((b->block_length = read(r->fd_file, b->buffer, WINDOW_SIZE)) < 0) {
fprintf(stderr, "reader read: bug encountered\n");
exit(1);
}
}
if(NULL == b || 0 == b->block_length) {
block_destroy(b);
b = NULL;
break;
}
// add to the queue
//fprintf(stderr, "Reader #%d add to queue\n", 0);
wait = 1;
if(0 == queue_add(r->input, b, wait)) {
if(1 == wait) {
if(QUEUE_STATE_OK == r->input->state) {
fprintf(stderr, "reader queue_add: bug encountered\n");
exit(1);
}
else if(QUEUE_STATE_EOF == r->input->state) { // EOF, quit
block_destroy(b);
b = NULL;
break;
}
else {
queue_wait_until_not_flush(r->input);
continue;
}
}
else {
block_destroy(b);
b = NULL;
break;
}
}
b = NULL;
n++;
//fprintf(stderr, "reader read %llu blocks\n", n);
#endif
}
block_destroy(b);
b = NULL;
r->is_done = 1;
// NB: EOF should be handled when the adder is removed
queue_remove_adder(r->input);
//fprintf(stderr, "reader read %llu blocks\n", n);
//fprintf(stderr, "reader r->input->n=%d\n", r->input->n);
//fprintf(stderr, "reader r->input->state=%d QUEUE_STATE_EOF=%d\n", r->input->state, QUEUE_STATE_EOF);
block_pool_destroy(pool);
return arg;
}
