int gt_region_mapping_get_sequence_length(GtRegionMapping *rm,
unsigned long *length, GtStr *seqid,
GtError *err)
{
unsigned long filenum, seqnum;
int had_err;
gt_error_check(err);
GT_UNUSED GtRange range;
gt_assert(rm && seqid);
if (rm->userawseq) {
return rm->rawlength;
}
had_err = update_seq_col_if_necessary(rm, seqid, err);
if (!had_err) {
if (gt_md5_seqid_has_prefix(gt_str_get(seqid))) {
had_err = gt_seq_col_md5_to_sequence_length(rm->seq_col, length, seqid,
err);
}
else if (rm->usedesc) {
gt_assert(rm->seqid2seqnum_mapping);
had_err = gt_seqid2seqnum_mapping_map(rm->seqid2seqnum_mapping,
gt_str_get(seqid), &range, &seqnum,
&filenum, NULL, err);
if (!had_err)
*length = gt_seq_col_get_sequence_length(rm->seq_col, filenum, seqnum);
}
else if (rm->matchdesc) {
had_err = gt_seq_col_grep_desc_sequence_length(rm->seq_col, length,
seqid, err);
}
else if (rm->useseqno) {
unsigned long seqno = GT_UNDEF_ULONG;
gt_assert(rm->encseq);
if (1 != sscanf(gt_str_get(seqid), "seq%lu", &seqno)) {
gt_error_set(err, "seqid '%s' does not have the form 'seqX' "
"where X is a sequence number in the encoded "
"sequence", gt_str_get(seqid));
had_err = -1;
}
gt_assert(had_err || seqno != GT_UNDEF_ULONG);
if (!had_err && seqno >= gt_encseq_num_of_sequences(rm->encseq)) {
gt_error_set(err, "trying to access sequence %lu, but encoded "
"sequence contains only %lu sequences",
seqno, gt_encseq_num_of_sequences(rm->encseq));
had_err = -1;
}
if (!had_err) {
*length = gt_encseq_seqlength(rm->encseq, seqno);
}
}
else
*length = gt_seq_col_get_sequence_length(rm->seq_col, 0, 0);
}
return had_err;
}
static int gt_encseq_col_grep_desc_sequence_length(GtSeqCol *sc,
GtUword *length,
GtStr *seqid,
GtError *err)
{
GtUword filenum = 0, seqnum = 0;
int had_err;
GtEncseqCol *esc;
esc = gt_encseq_col_cast(sc);
gt_error_check(err);
gt_assert(esc && length && seqid);
had_err = gt_encseq_col_do_grep_desc(esc, &filenum, &seqnum, seqid, err);
if (!had_err)
*length = gt_seq_col_get_sequence_length(sc, seqnum, filenum);
return had_err;
}
int gt_region_mapping_get_sequence(GtRegionMapping *rm, char **seq,
GtStr *seqid, unsigned long start,
unsigned long end, GtError *err)
{
int had_err = 0;
unsigned long offset = 1;
GtRange range = {GT_UNDEF_ULONG, GT_UNDEF_ULONG};
gt_error_check(err);
gt_assert(rm && seq && seqid && gt_str_length(seqid) > 0);
/* handle rawseq access first */
if (rm->userawseq) {
gt_assert(!rm->seqid2seqnum_mapping);
*seq = gt_calloc(end - start + 1, sizeof (char));
strncpy(*seq, rm->rawseq + start - 1, (end - start + 1) * sizeof (char));
return 0;
}
/* make sure that correct sequence is loaded */
had_err = update_seq_col_if_necessary(rm, seqid, err);
/* MD5 sequence id */
if (!had_err) {
if (gt_md5_seqid_has_prefix(gt_str_get(seqid))) {
had_err = gt_seq_col_md5_to_seq(rm->seq_col, seq, start - offset,
end - offset, seqid, err);
return had_err;
}
}
/* ``regular'' sequence ID */
if (!had_err) {
gt_assert(!rm->usedesc || rm->seqid2seqnum_mapping);
gt_assert(rm->mapping || rm->seq_col);
if (rm->usedesc) {
unsigned long seqnum, filenum;
gt_assert(rm->seqid2seqnum_mapping);
range.start = start;
range.end = end;
had_err = gt_seqid2seqnum_mapping_map(rm->seqid2seqnum_mapping,
gt_str_get(seqid), &range, &seqnum,
&filenum, &offset, err);
if (!had_err) {
if (range.end != GT_UNDEF_ULONG && range.start != GT_UNDEF_ULONG &&
range.end >= gt_seq_col_get_sequence_length(rm->seq_col, filenum,
seqnum)
+ offset) {
gt_error_set(err, "trying to extract range %lu-%lu on sequence "
"``%s'' which is not covered by that sequence (with "
"boundaries %lu-%lu). Has the sequence-region "
"to sequence mapping been defined correctly?",
start, end, gt_str_get(seqid),
range.start, range.end);
had_err = -1;
}
}
if (!had_err) {
*seq = gt_seq_col_get_sequence(rm->seq_col, filenum, seqnum,
start - offset, end - offset);
}
} else if (rm->matchdesc) {
gt_assert(!rm->seqid2seqnum_mapping);
gt_assert(rm->seq_col);
if (!had_err) {
had_err = gt_seq_col_grep_desc(rm->seq_col, seq, start - 1, end - 1,
seqid, err);
}
} else if (rm->useseqno) {
unsigned long seqno = GT_UNDEF_ULONG;
gt_assert(rm->encseq);
if (1 != sscanf(gt_str_get(seqid), "seq%lu", &seqno)) {
gt_error_set(err, "seqid '%s' does not have the form 'seqX' "
"where X is a sequence number in the encoded "
"sequence", gt_str_get(seqid));
had_err = -1;
}
gt_assert(had_err || seqno != GT_UNDEF_ULONG);
if (!had_err && seqno >= gt_encseq_num_of_sequences(rm->encseq)) {
gt_error_set(err, "trying to access sequence %lu, but encoded "
"sequence contains only %lu sequences",
seqno, gt_encseq_num_of_sequences(rm->encseq));
had_err = -1;
}
if (!had_err) {
unsigned long seqlength = gt_encseq_seqlength(rm->encseq, seqno);
if (start > seqlength || end > seqlength) {
gt_error_set(err, "trying to extract range %lu-%lu on sequence "
"``%s'' which is not covered by that sequence (only "
"%lu characters in size). Has the sequence-region "
"to sequence mapping been defined correctly?",
start, end, gt_str_get(seqid), seqlength);
had_err = -1;
}
}
if (!had_err) {
unsigned long seqstartpos;
*seq = gt_calloc(end - start + 1, sizeof (char));
seqstartpos = gt_encseq_seqstartpos(rm->encseq, seqno);
gt_encseq_extract_decoded(rm->encseq, *seq, seqstartpos + start - 1,
seqstartpos + end - 1);
}
} else if (rm->userawseq) {
gt_assert(!rm->seqid2seqnum_mapping);
*seq = gt_calloc(end - start + 1, sizeof (char));
strncpy(*seq, rm->rawseq + start - 1, (end - start + 1) * sizeof (char));
} else {
gt_assert(rm->seq_col);
if (!had_err) {
unsigned long seqlength = gt_seq_col_get_sequence_length(rm->seq_col,
0, 0);
if (start > seqlength || end > seqlength) {
had_err = -1;
gt_error_set(err, "trying to extract range %lu-%lu on sequence "
"``%s'' which is not covered by that sequence (only "
"%lu 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_seq_col_get_sequence(rm->seq_col, 0, 0, start - offset,
end - offset);
}
}
}
}
return had_err;
}
