static void async_callback(struct libusb_transfer *transfer)
{
if (libusb_state != LIB_USB_TRANSFERS_ALLOCATED) return;
int r;
// log_info("begin async_callback endpoint %x, status %x, actual length %u", transfer->endpoint, transfer->status, transfer->actual_length );
if (transfer->status == LIBUSB_TRANSFER_COMPLETED) {
queue_transfer(transfer);
} else if (transfer->status == LIBUSB_TRANSFER_STALL){
log_info("-> Transfer stalled, trying again");
r = libusb_clear_halt(handle, transfer->endpoint);
if (r) {
log_error("Error rclearing halt %d", r);
}
r = libusb_submit_transfer(transfer);
if (r) {
log_error("Error re-submitting transfer %d", r);
}
} else {
log_info("async_callback. not data -> resubmit transfer, endpoint %x, status %x, length %u", transfer->endpoint, transfer->status, transfer->actual_length);
// No usable data, just resubmit packet
r = libusb_submit_transfer(transfer);
if (r) {
log_error("Error re-submitting transfer %d", r);
}
}
// log_info("end async_callback");
}
int SPI::transfer(const Buffer& tx, const Buffer& rx, const event_callback_t& callback, int event) {
if (spi_active(&_spi)) {
return queue_transfer(tx, rx, callback, event);
}
start_transfer(tx, rx, callback, event);
return 0;
}
static int
handle_input_from_worker_line(SESSION *sess, WORKER *worker)
{
char *head, *tail, *cur, *leftend, *rightend;
head = cur = worker->inbuf->data + worker->inbuf->front;
leftend = worker->inbuf->data;
rightend = worker->inbuf->data + worker->inbuf->size;
tail = worker->inbuf->data + worker->inbuf->rear;
while (cur != tail) {
if (*cur == '\n') {
qsize_t recordsize;
worker->lineno++;
recordsize = (head <= cur ? cur + 1 - head :
(rightend - head) + (cur + 1 - leftend));
if (queue_transfer(sess->outbuf, worker->inbuf, recordsize) == -1)
break; /* TODO: handle records way too big in outbuf. */
head = cur + 1;
}
if (++cur == rightend)
cur = leftend;
}
return 0;
}
int SPI::transfer(const void *tx_buffer, int tx_length, void *rx_buffer, int rx_length, unsigned char bit_width, const event_callback_t& callback, int event)
{
if (spi_active(&_spi)) {
return queue_transfer(tx_buffer, tx_length, rx_buffer, rx_length, bit_width, callback, event);
}
start_transfer(tx_buffer, tx_length, rx_buffer, rx_length, bit_width, callback, event);
return 0;
}
static int
handle_input_from_worker_fastq(SESSION *sess, WORKER *worker)
{
char *head, *tail, *cur, *leftend, *rightend;
int line_in_record;
head = cur = worker->inbuf->data + worker->inbuf->front;
leftend = worker->inbuf->data;
rightend = worker->inbuf->data + worker->inbuf->size;
tail = worker->inbuf->data + worker->inbuf->rear;
line_in_record = 0;
while (cur != tail) {
if (*cur == '\n' && ++line_in_record == 4) {
qsize_t recordsize;
recordsize = (head <= cur ? cur + 1 - head :
(rightend - head) + (cur + 1 - leftend));
if (*head != '@')
error(0, "(worker %d) Unaligned FASTQ input at"
" line no %d\n", worker->workerid, worker->lineno);
if (queue_transfer(sess->outbuf, worker->inbuf, recordsize) == -1)
break;
/* TODO: handle records way too big in outbuf. */
//errx(13, "line %ld: found a too large record. (1)\n",
// sess->lineno);
// intended duplication of code for optimized running
cur++;
if (cur == rightend)
cur = leftend;
head = cur;
worker->lineno += 4;
line_in_record = 0;
if (head != leftend + worker->inbuf->front)
error(0, "Internal programming error: head and front "
"mismatching - %p, %p, %d\n",
head, leftend, worker->inbuf->front);
}
else {
cur++;
if (cur == rightend)
cur = leftend;
}
}
return 0;
}
static int
handle_input_from_stdin_fasta(SESSION *sess)
{
char *head, *tail, *cur, *leftend, *rightend;
int i, header_read;
head = cur = sess->inbuf->data + sess->inbuf->front;
leftend = sess->inbuf->data;
rightend = sess->inbuf->data + sess->inbuf->size;
tail = sess->inbuf->data + sess->inbuf->rear;
header_read = sess->inbuf->flags;
while (cur != tail) {
if (*cur == '\n')
sess->lineno++;
if (!header_read) {
if (*cur == '\n')
header_read = 1;
}
else if (*cur == '>') {
qsize_t recordsize;
recordsize = (head <= cur ? cur - head : (rightend - head) + (cur - leftend));
for (i = 0; i < sess->num_workers; i++) {
int wselected=(sess->rr_next + i) % sess->num_workers;
if (queue_transfer(sess->workers[wselected].outbuf,
sess->inbuf, recordsize) != -1) {
sess->rr_next = (sess->rr_next+1) % sess->num_workers;
break;
}
/* TODO: handle records way too big in outbuf. */
}
if (i == sess->num_workers) /* all buffers are full */
break;
head = cur;
header_read = 0;
}
if (++cur == rightend)
cur = leftend;
}
sess->inbuf->flags = header_read;
return 0;
}
static int
handle_input_from_stdin_fastq(SESSION *sess)
{
char *head, *tail, *cur, *corner;
int i, line_in_record;
head = cur = sess->inbuf->data + sess->inbuf->front;
corner = sess->inbuf->data + sess->inbuf->size;
tail = sess->inbuf->data + sess->inbuf->rear;
line_in_record = 0;
while (cur != tail) {
if (*cur == '\n' && ++line_in_record == 4) {
qsize_t recordsize;
recordsize = (head <= cur ? cur + 1 - head :
(corner - head) + (cur + 1 - sess->inbuf->data));
for (i = 0; i < sess->num_workers; i++) {
int wselected=(sess->rr_next + i) % sess->num_workers;
if (*head != '@')
error(0, "Unaligned FASTQ input at line %d\n",
sess->lineno);
if (queue_transfer(sess->workers[wselected].outbuf,
sess->inbuf, recordsize) != -1) {
sess->rr_next = (sess->rr_next+1) % sess->num_workers;
break;
}
/* TODO: handle records way too big in outbuf. */
//errx(13, "line %ld: found a too large record. (1)\n",
// sess->lineno);
}
if (i == sess->num_workers) /* all buffers are full */
break;
// intended duplication of code for optimized running
cur++;
if (cur == corner)
cur = sess->inbuf->data;
head = cur;
sess->lineno += 4;
line_in_record = 0;
if (head != sess->inbuf->data + sess->inbuf->front)
error(0, "Internal programming error: head and front "
"mismatching - %p, %p, %d\n",
head, sess->inbuf->data, sess->inbuf->front);
}
else {
cur++;
if (cur == corner)
cur = sess->inbuf->data;
}
}
return 0;
}
