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;
}
static void reset_data_iterator_to_start(HcrHuffDataIterator *data_iter)
{
gt_assert(data_iter);
reset_data_iterator_to_pos(data_iter, data_iter->start);
}
static int hcr_next_seq_qual(GtHcrSeqDecoder *seq_dec, char *seq, char *qual,
GtError *err)
{
enum state {
HCR_ERROR = -1,
END,
SUCCESS
};
unsigned char base;
GtUword i,
nearestsample,
*symbol;
size_t startofnearestsample = 0;
enum state status = END;
FastqFileInfo cur_read;
FastqFileInfo *fileinfo = NULL;
if (seq_dec->cur_read <= seq_dec->num_of_reads) {
status = SUCCESS;
if (seq_dec->symbols == NULL)
seq_dec->symbols = gt_array_new(sizeof (GtUword));
else
gt_array_reset(seq_dec->symbols);
cur_read.readnum = seq_dec->cur_read;
gt_log_log("cur_read: "GT_WU"",seq_dec->cur_read);
fileinfo = (FastqFileInfo *)gt_rbtree_next_key(seq_dec->file_info_rbt,
&cur_read,
hcr_cmp_FastqFileInfo,
NULL);
gt_assert(fileinfo);
/* reset huffman_decoder if next read is sampled */
if (gt_sampling_get_next_elementnum(seq_dec->sampling) ==
seq_dec->cur_read) {
gt_log_log("reset because sampled read is next");
(void) gt_sampling_get_next_sample(seq_dec->sampling,
&nearestsample,
&startofnearestsample);
reset_data_iterator_to_pos(seq_dec->data_iter, startofnearestsample);
(void) gt_huffman_decoder_get_new_mem_chunk(seq_dec->huff_dec, err);
if (gt_error_is_set(err))
status = HCR_ERROR;
}
if (status != HCR_ERROR) {
int ret;
ret = gt_huffman_decoder_next(seq_dec->huff_dec, seq_dec->symbols,
fileinfo->readlength, err);
if (ret != 1)
status = HCR_ERROR;
if (ret == 0)
gt_error_set(err, "reached end of file");
}
if (qual || seq) {
gt_log_log("set strings");
for (i = 0; i < gt_array_size(seq_dec->symbols); i++) {
symbol = (GtUword*) gt_array_get(seq_dec->symbols, i);
if (qual != NULL)
qual[i] = get_qual_from_symbol(seq_dec, *symbol);
if (seq != NULL) {
base = get_base_from_symbol(seq_dec, *symbol);
seq[i] = (char)toupper(gt_alphabet_decode(seq_dec->alpha,
(GtUchar) base));
}
}
if (qual != NULL)
qual[gt_array_size(seq_dec->symbols)] = '\0';
if (seq != NULL)
seq[gt_array_size(seq_dec->symbols)] = '\0';
}
seq_dec->cur_read++;
}
return (int) status;
}
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;
}
