int gt_hcr_decoder_decode(GtHcrDecoder *hcr_dec, GtUword readnum,
char *seq, char *qual, GtStr *desc, GtError *err)
{
GtUword nearestsample = 0,
reads_to_read = 0,
idx,
current_read = hcr_dec->seq_dec->cur_read ;
size_t startofnearestsample = 0;
GtSampling *sampling;
HcrHuffDataIterator *data_iter;
GtHuffmanDecoder *huff_dec;
gt_error_check(err);
gt_assert(hcr_dec);
gt_assert(readnum < hcr_dec->seq_dec->num_of_reads);
gt_assert(seq != NULL && qual != NULL);
if (current_read == readnum) {
if (hcr_next_seq_qual(hcr_dec->seq_dec, seq, qual, err) == -1) {
gt_assert(gt_error_is_set(err));
return -1;
}
}
else {
sampling = hcr_dec->seq_dec->sampling;
data_iter = hcr_dec->seq_dec->data_iter;
huff_dec = hcr_dec->seq_dec->huff_dec;
if (sampling != NULL) {
gt_sampling_get_page(sampling,
readnum,
&nearestsample,
&startofnearestsample);
/* nearestsample <= cur_read < readnum: current sample is the right one */
if (nearestsample <= current_read && current_read <= readnum)
reads_to_read = readnum - current_read;
else { /* reset decoder to new sample */
reset_data_iterator_to_pos(data_iter, startofnearestsample);
(void) gt_huffman_decoder_get_new_mem_chunk(huff_dec, err);
if (gt_error_is_set(err))
return -1;
reads_to_read = readnum - nearestsample;
hcr_dec->seq_dec->cur_read = nearestsample;
}
gt_log_log("reads to read: "GT_WU", nearest sample: "GT_WU"",
reads_to_read,nearestsample);
gt_log_log("start of nearest: "GT_WU"", (GtUword) startofnearestsample);
}
else {
if (current_read <= readnum)
reads_to_read = readnum - current_read;
else {
reset_data_iterator_to_start(data_iter);
(void) gt_huffman_decoder_get_new_mem_chunk(huff_dec, err);
if (gt_error_is_set(err))
return -1;
reads_to_read = readnum;
hcr_dec->seq_dec->cur_read = 0;
}
}
for (idx = 0; idx < reads_to_read; idx++) {
if (hcr_next_seq_qual(hcr_dec->seq_dec, seq,qual, err) == -1) {
gt_assert(gt_error_is_set(err));
return -1;
}
gt_log_log("seq:\n%s\nqual:\n%s", seq, qual);
}
if (hcr_next_seq_qual(hcr_dec->seq_dec, seq, qual, err) == -1) {
gt_assert(gt_error_is_set(err));
return -1;
}
}
if (hcr_dec->encdesc != NULL) {
if (gt_encdesc_decode(hcr_dec->encdesc, readnum, desc, err) == -1) {
gt_error_set(err, "cannot retrieve description with number "GT_WU"."
"(%d)", readnum, __LINE__);
return -1;
}
}
return 0;
}
int gt_hcr_decoder_decode(GtHcrDecoder *hcr_dec, GtUword readnum,
char *seq, char *qual, GtStr *desc, GtError *err)
{
int had_err = 0;
GtUword nearestsample = 0,
reads_to_read = 0,
idx,
current_read = hcr_dec->seq_dec->cur_read ;
size_t startofnearestsample = 0;
GtSampling *sampling;
HcrHuffDataIterator *data_iter;
GtHuffmanDecoder *huff_dec;
gt_error_check(err);
gt_assert(hcr_dec);
gt_assert(readnum < hcr_dec->seq_dec->num_of_reads);
gt_assert(seq != NULL && qual != NULL);
if (current_read == readnum)
had_err = hcr_next_seq_qual(hcr_dec->seq_dec, seq, qual, err) == -1 ?
-1 : 0;
else {
sampling = hcr_dec->seq_dec->sampling;
data_iter = hcr_dec->seq_dec->data_iter;
huff_dec = hcr_dec->seq_dec->huff_dec;
if (sampling != NULL) {
gt_sampling_get_page(sampling,
readnum,
&nearestsample,
&startofnearestsample);
/* nearestsample <= cur_read < readnum: current sample is the right one */
if (nearestsample <= current_read && current_read <= readnum)
reads_to_read = readnum - current_read;
else { /* reset decoder to new sample */
reset_data_iterator_to_pos(data_iter, startofnearestsample);
had_err = gt_huffman_decoder_get_new_mem_chunk(huff_dec, err);
reads_to_read = readnum - nearestsample;
hcr_dec->seq_dec->cur_read = nearestsample;
}
gt_log_log("reads to read: "GT_WU", nearest sample: "GT_WU"",
reads_to_read,nearestsample);
gt_log_log("start of nearest: "GT_WU"", (GtUword) startofnearestsample);
}
else {
if (current_read <= readnum)
reads_to_read = readnum - current_read;
else {
reset_data_iterator_to_start(data_iter);
had_err = gt_huffman_decoder_get_new_mem_chunk(huff_dec, err);
reads_to_read = readnum;
hcr_dec->seq_dec->cur_read = 0;
}
}
for (idx = 0; !had_err && idx < reads_to_read; idx++)
had_err = hcr_next_seq_qual(hcr_dec->seq_dec, seq,qual, err) == -1 ?
-1 : 0;
if (!had_err)
had_err = hcr_next_seq_qual(hcr_dec->seq_dec, seq, qual, err) == -1 ?
-1 : 0;
}
if (had_err)
gt_assert(gt_error_is_set(err));
if (!had_err && hcr_dec->encdesc != NULL)
had_err = gt_encdesc_decode(hcr_dec->encdesc, readnum, desc, err);
if (had_err)
gt_assert(gt_error_is_set(err));
return had_err;
}