GtUword gt_bioseq_md5_to_index(GtBioseq *bs, const char *md5)
{
gt_assert(bs && md5 && gt_encseq_has_md5_support(bs->encseq));
if (!bs->md5_tab) {
bs->md5_tab = gt_encseq_get_md5_tab(bs->encseq, NULL);
}
return gt_md5_tab_map(bs->md5_tab, md5);
}
int gt_encseq_col_md5_to_sequence_length(GtSeqCol *sc, GtUword *len,
GtStr *md5_seqid, GtError *err)
{
GtUword seqnum = GT_UNDEF_UWORD;
int had_err = 0;
GtEncseqCol *esc;
esc = gt_encseq_col_cast(sc);
gt_error_check(err);
gt_assert(esc && len && md5_seqid && err);
gt_assert(gt_md5_seqid_has_prefix(gt_str_get(md5_seqid)));
seqnum = gt_md5_tab_map(esc->md5_tab, gt_str_get(md5_seqid) +
GT_MD5_SEQID_PREFIX_LEN);
if (seqnum != GT_UNDEF_UWORD) {
gt_assert(seqnum < gt_encseq_num_of_sequences(esc->encseq));
*len = gt_encseq_seqlength(esc->encseq, seqnum);
} else {
gt_error_set(err, "sequence %s not found", gt_str_get(md5_seqid));
had_err = -1;
}
return had_err;
}
static int gt_encseq_col_md5_to_seq(GtSeqCol *sc, char **seq,
GtUword start, GtUword end,
GtStr *md5_seqid, GtError *err)
{
GtUword seqnum = GT_UNDEF_UWORD;
char seqid[GT_MD5_SEQID_HASH_LEN + 1];
int had_err = 0;
GtEncseqCol *esc;
esc = gt_encseq_col_cast(sc);
gt_error_check(err);
gt_assert(esc && seq && start <= end && md5_seqid && err);
gt_assert(gt_md5_seqid_has_prefix(gt_str_get(md5_seqid)));
if (gt_str_length(md5_seqid) >= GT_MD5_SEQID_TOTAL_LEN) {
const char *cstrseqid = gt_str_get(md5_seqid);
if (cstrseqid[GT_MD5_SEQID_TOTAL_LEN-1] != GT_MD5_SEQID_SEPARATOR) {
gt_error_set(err, "MD5 sequence id %s not terminated with '%c'",
gt_str_get(md5_seqid), GT_MD5_SEQID_SEPARATOR);
had_err = -1;
}
if (!had_err) {
strncpy(seqid, cstrseqid + GT_MD5_SEQID_PREFIX_LEN,
GT_MD5_SEQID_HASH_LEN);
seqid[GT_MD5_SEQID_HASH_LEN] = '\0';
}
}
seqnum = gt_md5_tab_map(esc->md5_tab, seqid);
if (seqnum != GT_UNDEF_UWORD) {
GtUword startpos = gt_encseq_seqstartpos(esc->encseq, seqnum),
GT_UNUSED seqlength = gt_encseq_seqlength(esc->encseq,
seqnum);
*seq = gt_calloc(end - start + 1, sizeof (char));
gt_encseq_extract_decoded(esc->encseq, (char*) *seq, startpos + start,
startpos + end);
} else {
gt_error_set(err, "sequence %s not found", gt_str_get(md5_seqid));
had_err = -1;
}
return had_err;
}
static int gt_encseq_col_md5_to_description(GtSeqCol *sc, GtStr *desc,
GtStr *md5_seqid, GtError *err)
{
GtUword seqnum = GT_UNDEF_UWORD;
char seqid[GT_MD5_SEQID_HASH_LEN + 1];
int had_err = 0;
GtEncseqCol *esc;
esc = gt_encseq_col_cast(sc);
gt_error_check(err);
gt_assert(esc && desc && md5_seqid && err);
gt_assert(gt_md5_seqid_has_prefix(gt_str_get(md5_seqid)));
if (gt_str_length(md5_seqid) >= GT_MD5_SEQID_TOTAL_LEN) {
const char *cstrseqid = gt_str_get(md5_seqid);
if (cstrseqid[GT_MD5_SEQID_TOTAL_LEN-1] != GT_MD5_SEQID_SEPARATOR) {
gt_error_set(err, "MD5 sequence id %s not terminated with '%c'",
gt_str_get(md5_seqid), GT_MD5_SEQID_SEPARATOR);
had_err = -1;
}
if (!had_err) {
strncpy(seqid, cstrseqid + GT_MD5_SEQID_PREFIX_LEN,
GT_MD5_SEQID_HASH_LEN);
seqid[GT_MD5_SEQID_HASH_LEN] = '\0';
}
}
seqnum = gt_md5_tab_map(esc->md5_tab, seqid);
if (seqnum != GT_UNDEF_UWORD) {
const char *cdesc;
GtUword desc_len;
gt_assert(seqnum < gt_encseq_num_of_sequences(esc->encseq));
cdesc = gt_encseq_description(esc->encseq, &desc_len, seqnum);
gt_str_append_cstr_nt(desc, cdesc, desc_len);
} else {
gt_error_set(err, "sequence %s not found", gt_str_get(md5_seqid));
had_err = -1;
}
return had_err;
}
