static int gt_bioseq_col_grep_desc(GtSeqCol *sc, char **seq,
GtUword start, GtUword end,
GtStr *seqid, GtError *err)
{
GtUword filenum = 0, seqnum = 0, seqlength;
int had_err;
GtBioseqCol *bsc;
bsc = gt_bioseq_col_cast(sc);
gt_error_check(err);
gt_assert(bsc && seq && seqid);
had_err = grep_desc(bsc, &filenum, &seqnum, seqid, err);
if (!had_err) {
seqlength = gt_bioseq_get_sequence_length(bsc->bioseqs[filenum], seqnum);
if (start > seqlength - 1 || end > seqlength - 1) {
had_err = -1;
gt_error_set(err, "trying to extract range "GT_WU"-"GT_WU" on sequence "
"``%s'' which is not covered by that sequence (only "
""GT_WU" characters in size). Has the sequence-region "
"to sequence mapping been defined correctly?",
start, end, gt_str_get(seqid), seqlength);
}
}
if (!had_err) {
*seq = gt_bioseq_get_sequence_range(bsc->bioseqs[filenum], seqnum,
start, end);
}
return had_err;
}
static char* gt_bioseq_col_get_sequence(const GtSeqCol *sc,
GtUword filenum,
GtUword seqnum,
GtUword start,
GtUword end)
{
GtBioseqCol *bsc;
bsc = gt_bioseq_col_cast(sc);
gt_assert(bsc && filenum < bsc->num_of_seqfiles);
return gt_bioseq_get_sequence_range(bsc->bioseqs[filenum], seqnum, start,
end);
}
GtSeq* gt_bioseq_get_seq_range(GtBioseq *bs, GtUword idx,
GtUword start, GtUword end)
{
GtSeq *seq;
gt_assert(bs);
gt_assert(idx < gt_encseq_num_of_sequences(bs->encseq));
gt_assert(end >= start);
gt_assert(end - start + 1 > gt_encseq_seqlength(bs->encseq, idx));
seq = gt_seq_new_own(gt_bioseq_get_sequence_range(bs, idx, start, end),
end - start + 1,
gt_encseq_alphabet(bs->encseq));
gt_seq_set_description(seq, gt_bioseq_get_description(bs, idx));
return seq;
}
static int gt_bioseq_col_md5_to_seq(GtSeqCol *sc, char **seq,
GtUword start, GtUword end,
GtStr *md5_seqid, GtError *err)
{
GtUword seqnum = GT_UNDEF_UWORD;
GtBioseq *bioseq = NULL;
GtBioseqCol *bsc;
int had_err = 0;
bsc = gt_bioseq_col_cast(sc);
gt_error_check(err);
gt_assert(bsc && seq && md5_seqid && err);
gt_assert(gt_md5_seqid_has_prefix(gt_str_get(md5_seqid)));
if (!(had_err = md5_to_index(&bioseq, &seqnum, bsc, md5_seqid, err))) {
gt_assert(seqnum != GT_UNDEF_UWORD);
*seq = gt_bioseq_get_sequence_range(bioseq, seqnum, start, end);
}
return had_err;
}
static char* generate_fragment(GtShredder *shredder,
unsigned long *fragment_length,
GtStr *desc)
{
gt_assert(shredder && fragment_length);
if (shredder->seqnum < gt_bioseq_number_of_sequences(shredder->bioseq)) {
unsigned long seqlen, fraglen;
char *frag;
seqlen = gt_bioseq_get_sequence_length(shredder->bioseq, shredder->seqnum);
fraglen = (shredder->maxlength == shredder->minlength
? 0 : gt_rand_max(shredder->maxlength - shredder->minlength))
+ shredder->minlength;
gt_assert(fraglen >= shredder->minlength);
if (shredder->pos + fraglen > seqlen)
fraglen = seqlen - shredder->pos;
*fragment_length = fraglen;
gt_str_reset(desc);
gt_str_append_cstr(desc, gt_bioseq_get_description(shredder->bioseq,
shredder->seqnum));
gt_assert(shredder->pos + fraglen <= seqlen);
frag = gt_bioseq_get_sequence_range(shredder->bioseq, shredder->seqnum,
shredder->pos,
shredder->pos + fraglen -1);
if (shredder->pos + fraglen == seqlen) { /* last fragment */
shredder->seqnum++;
shredder->pos = 0;
}
else {
if (fraglen > shredder->overlap)
shredder->pos += fraglen - shredder->overlap;
else
shredder->pos++; /* go at least one base further each step */
}
return frag;
}
return NULL;
}
