static int md5_to_seqid(GtGenomeNode *gn, GtRegionMapping *region_mapping,
GtError *err)
{
GtStr *seqid;
int had_err = 0;
gt_error_check(err);
gt_assert(gn && region_mapping);
seqid = gt_genome_node_get_seqid(gn);
if (gt_md5_seqid_has_prefix(gt_str_get(seqid))) {
/* seqid is a MD5 seqid -> change id */
GtStr *desc = gt_str_new();
had_err = gt_region_mapping_get_description(region_mapping, desc, seqid,
err);
if (!had_err) {
GtStr *new_seqid = gt_str_new();
gt_regular_seqid_save(new_seqid, desc);
if (gt_feature_node_try_cast(gn)) {
M2IChangeSeqidInfo info;
info.new_seqid = new_seqid;
info.region_mapping = region_mapping;
had_err = gt_feature_node_traverse_children((GtFeatureNode*) gn, &info,
m2i_change_seqid, true,
err);
}
else
gt_genome_node_change_seqid(gn, new_seqid);
gt_str_delete(new_seqid);
}
gt_str_delete(desc);
}
return had_err;
}
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;
}
int gt_bioseq_col_md5_to_sequence_length(GtSeqCol *sc, GtUword *len,
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 && len && 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);
*len = gt_bioseq_get_sequence_length(bioseq, seqnum);
}
return had_err;
}
static int gt_bioseq_col_md5_to_description(GtSeqCol *sc, GtStr *desc,
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 && desc && 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);
gt_str_append_cstr(desc, gt_bioseq_get_description(bioseq, seqnum));
}
return had_err;
}
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;
}
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;
}
const char* gt_region_mapping_get_md5_fingerprint(GtRegionMapping *rm,
GtStr *seqid,
const GtRange *range,
unsigned long *offset,
GtError *err)
{
const char *md5 = NULL;
int had_err;
unsigned long filenum, seqnum;
gt_error_check(err);
gt_assert(rm && seqid);
gt_assert(!rm->userawseq); /* not implemented */
gt_assert(!gt_md5_seqid_has_prefix(gt_str_get(seqid))); /* not implemented */
had_err = update_seq_col_if_necessary(rm, seqid, err);
if (!had_err) {
if (rm->usedesc) {
gt_assert(rm->seqid2seqnum_mapping);
had_err = gt_seqid2seqnum_mapping_map(rm->seqid2seqnum_mapping,
gt_str_get(seqid), range, &seqnum,
&filenum, offset, err);
if (!had_err)
md5 = gt_seq_col_get_md5_fingerprint(rm->seq_col, filenum, seqnum);
}
else if (rm->matchdesc) {
if (!rm->seq_col) {
if (rm->encseq) {
if (!(rm->seq_col = gt_encseq_col_new(rm->encseq, err)))
had_err = -1;
} else {
if (!(rm->seq_col = gt_bioseq_col_new(rm->sequence_filenames, err)))
had_err = -1;
}
}
if (!had_err)
(void) gt_seq_col_grep_desc_md5(rm->seq_col, &md5, seqid, err);
*offset = 1;
}
else if (rm->useseqno) {
GtMD5Tab *tab = NULL;
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) {
tab = gt_encseq_get_md5_tab(rm->encseq, err);
if (!tab)
had_err = -1;
}
*offset = 1;
if (!had_err)
return gt_md5_tab_get(tab, seqno);
else
return NULL;
}
else {
if (!had_err)
md5 = gt_seq_col_get_md5_fingerprint(rm->seq_col, 0, 0);
*offset = 1;
}
}
return md5;
}
int gt_region_mapping_get_description(GtRegionMapping *rm, GtStr *desc,
GtStr *seqid, GtError *err)
{
int had_err = 0;
gt_error_check(err);
gt_assert(rm && desc && seqid);
if (rm->userawseq) {
gt_str_append_cstr(desc, "<rawseq>");
return 0;
}
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_description(rm->seq_col, desc, seqid,
err);
}
return had_err;
}
if (!had_err) {
if (rm->usedesc) {
unsigned long filenum, seqnum;
gt_assert(rm->seqid2seqnum_mapping);
had_err = gt_seqid2seqnum_mapping_map(rm->seqid2seqnum_mapping,
gt_str_get(seqid), NULL, &seqnum,
&filenum, NULL, err);
if (!had_err) {
char *cdesc;
cdesc = gt_seq_col_get_description(rm->seq_col, filenum, seqnum);
gt_assert(cdesc);
gt_str_append_cstr(desc, cdesc);
gt_free(cdesc);
}
}
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 desclen;
const char *edesc;
edesc = gt_encseq_description(rm->encseq, &desclen, seqno);
gt_str_append_cstr_nt(desc, edesc, desclen);
}
} else if (rm->matchdesc) {
const char *md5;
/* XXX: not beautiful, but works -- this may be LOTS faster */
had_err = gt_seq_col_grep_desc_md5(rm->seq_col, &md5, seqid, err);
if (!had_err) {
GtStr *md5_seqid = gt_str_new_cstr(md5);
had_err = gt_seq_col_md5_to_description(rm->seq_col, desc, md5_seqid,
err);
gt_str_delete(md5_seqid);
}
} else {
if (!had_err) {
char *cdesc;
cdesc = gt_seq_col_get_description(rm->seq_col, 0, 0);
gt_assert(cdesc);
gt_str_append_cstr(desc, cdesc);
gt_free(cdesc);
}
}
}
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;
}
static int update_seq_col_if_necessary(GtRegionMapping *rm, GtStr *seqid,
GtError *err)
{
int had_err = 0;
gt_error_check(err);
gt_assert(rm && seqid);
/* for mappings, we need to load the changed sequence, if needed... */
if (rm->mapping) {
if (!rm->sequence_file || (gt_str_cmp(rm->sequence_name, seqid))) {
gt_str_delete(rm->sequence_file);
/* ignore MD5 hashes when using region mappings */
if (gt_md5_seqid_has_prefix(gt_str_get(seqid))) {
rm->sequence_file = region_mapping_map(rm,
gt_str_get(seqid)
+GT_MD5_SEQID_TOTAL_LEN,
err);
} else
rm->sequence_file = region_mapping_map(rm, gt_str_get(seqid), err);
if (!rm->sequence_file)
had_err = -1;
else {
/* load new seqcol */
if (!rm->sequence_filenames)
rm->sequence_filenames = gt_str_array_new();
else
gt_str_array_reset(rm->sequence_filenames);
gt_str_array_add(rm->sequence_filenames, rm->sequence_file);
if (!rm->sequence_name)
rm->sequence_name = gt_str_new();
else
gt_str_reset(rm->sequence_name);
gt_str_append_str(rm->sequence_name, seqid);
gt_seq_col_delete(rm->seq_col);
rm->seq_col = gt_bioseq_col_new(rm->sequence_filenames, err);
if (!rm->seq_col)
had_err = -1;
}
}
} else {
/* ...otherwise, just make sure the seqcol is loaded */
if (!rm->seq_col) {
if (rm->encseq) {
if (!(rm->seq_col = gt_encseq_col_new(rm->encseq, err)))
had_err = -1;
} else {
gt_assert(rm->sequence_filenames);
if (!(rm->seq_col = gt_bioseq_col_new(rm->sequence_filenames, err)))
had_err = -1;
}
}
if (!had_err && rm->usedesc) {
if (rm->seqid2seqnum_mapping)
gt_seqid2seqnum_mapping_delete(rm->seqid2seqnum_mapping);
rm->seqid2seqnum_mapping =
gt_seqid2seqnum_mapping_new_seqcol(rm->seq_col, err);
if (!rm->seqid2seqnum_mapping) {
had_err = -1;
}
}
}
return had_err;
}
