static void end_element_handler(void *info, const XML_Char *name)
{
Parseinfo *parseinfo = (Parseinfo*) info;
GthSA *sa = parseinfo->currentSA;
GtUword datalength;
double retdouble;
GtWord ret;
char *data;
/* save data and data length */
data = gt_str_get(parseinfo->databuf);
datalength = gt_str_length(parseinfo->databuf);
/* perform actions depending on end tag */
if (strcmp(name, SPLICEDALIGNMENT_TAG) == 0) {
/* before we store the spliced alignment we have to reverse its edit
operations */
gt_assert(sa && gth_sa_backtrace_path(sa));
gth_backtrace_path_reverse(gth_sa_backtrace_path(sa));
/* ensure that before an intron which is not in phase the edit operation
has length 1 (only for protein spliced alignments) */
gth_backtrace_path_ensure_length_1_before_introns(
gth_sa_backtrace_path(sa));
if (parseinfo->saprocessfunc(parseinfo->data , sa,
parseinfo->outputfilename, parseinfo->err)) {
/* XXX */
fprintf(stderr, "error: %s\n", gt_error_get(parseinfo->err));
exit(EXIT_FAILURE);
}
/* reset current spliced alignment */
parseinfo->currentSA = NULL;
}
else if (strcmp(name, REFERENCEALPHATYPE_TAG) == 0) {
if (strcmp(data, "DNA_ALPHA") == 0)
gth_sa_set_alphatype(sa, DNA_ALPHA);
else if (strcmp(data, "PROTEIN_ALPHA") == 0) {
gth_sa_set_alphatype(sa, PROTEIN_ALPHA);
}
else {
ILLEGAL_DATA;
}
}
else if (strcmp(name, DNA_EOP_TYPE_TAG) == 0) {
if (strcmp(data, "match") == 0)
parseinfo->eoptype = EOP_TYPE_MATCH;
else if (strcmp(data, "deletion") == 0)
parseinfo->eoptype = EOP_TYPE_DELETION;
else if (strcmp(data, "insertion") == 0)
parseinfo->eoptype = EOP_TYPE_INSERTION;
else if (strcmp(data, "mismatch") == 0)
parseinfo->eoptype = EOP_TYPE_MISMATCH;
else if (strcmp(data, "intron") == 0)
parseinfo->eoptype = EOP_TYPE_INTRON;
else {
ILLEGAL_DATA;
}
}
else if (strcmp(name, DNA_EOP_LENGTH_TAG) == 0) {
SCANUINT;
gth_backtrace_path_add_eop(gth_sa_backtrace_path(sa), parseinfo->eoptype,
ret);
}
else if (strcmp(name, PROTEIN_EOP_TYPE_TAG) == 0) {
if (strcmp(data, "match") == 0)
parseinfo->eoptype = EOP_TYPE_MATCH;
else if (strcmp(data, "deletion") == 0)
parseinfo->eoptype = EOP_TYPE_DELETION;
else if (strcmp(data, "insertion") == 0)
parseinfo->eoptype = EOP_TYPE_INSERTION;
else if (strcmp(data, "mismatch") == 0)
parseinfo->eoptype = EOP_TYPE_MISMATCH;
else if (strcmp(data, "intron") == 0)
parseinfo->eoptype = EOP_TYPE_INTRON;
else if (strcmp(data, "mismatch_with_1_gap") == 0)
parseinfo->eoptype = EOP_TYPE_MISMATCH_WITH_1_GAP;
else if (strcmp(data, "mismatch_with_2_gaps") == 0)
parseinfo->eoptype = EOP_TYPE_MISMATCH_WITH_2_GAPS;
else if (strcmp(data, "deletion_with_1_gap") == 0)
parseinfo->eoptype = EOP_TYPE_DELETION_WITH_1_GAP;
else if (strcmp(data, "deletion_with_2_gaps") == 0)
parseinfo->eoptype = EOP_TYPE_DELETION_WITH_2_GAPS;
else if (strcmp(data, "intron_with_1_base_left") == 0)
parseinfo->eoptype = EOP_TYPE_INTRON_WITH_1_BASE_LEFT;
else if (strcmp(data, "intron_with_2_bases_left") == 0)
parseinfo->eoptype = EOP_TYPE_INTRON_WITH_2_BASES_LEFT;
else {
ILLEGAL_DATA;
}
}
else if (strcmp(name, PROTEIN_EOP_LENGTH_TAG) == 0) {
SCANUINT;
gth_backtrace_path_add_eop(gth_sa_backtrace_path(sa), parseinfo->eoptype,
ret);
}
else if (strcmp(name, INDELCOUNT_TAG) == 0) {
SCANUINT;
/* ignore indelcount, gets recomputed anyway */
}
else if (strcmp(name, GENOMICLENGTHDP_TAG) == 0) {
SCANUINT;
gth_sa_set_gen_dp_length(sa, ret);
}
else if (strcmp(name, GENOMICLENGTHTOTAL_TAG) == 0) {
SCANUINT;
gth_sa_set_gen_total_length(sa, ret);
}
else if (strcmp(name, GENOMICOFFSET_TAG) == 0) {
SCANUINT;
gth_sa_set_gen_offset(sa, ret);
}
else if (strcmp(name, REFERENCELENGTH_TAG) == 0) {
SCANUINT;
gth_sa_set_ref_total_length(sa, ret);
}
else if (strcmp(name, DPSTARTPOS_TAG) == 0) {
SCANUINT;
gth_sa_set_gen_dp_start(sa, ret);
}
else if (strcmp(name, DPENDPOS_TAG) == 0) {
SCANUINT;
/* ignore DP end pos, gets recomputed from gen_dp_length anyway */
gt_assert(gth_sa_gen_dp_end(sa) == ret);
}
else if (strcmp(name, GENOMICFILENAME_TAG) == 0) {
/* save genomic file name */
gt_str_append_cstr_nt(parseinfo->genomicfilename, data, datalength);
}
else if (strcmp(name, GENOMICFILEHASH_TAG) == 0) {
gth_sa_set_gen_file_num(sa, process_file(parseinfo->input,
gt_str_get(parseinfo->genomicfilename), data, false,
UNDEF_ALPHA));
/* reset genomic filename */
gt_str_reset(parseinfo->genomicfilename);
}
else if (strcmp(name, GENOMICSEQNUM_TAG) == 0) {
SCANUINT;
gth_sa_set_gen_seq_num(sa, ret);
}
else if (strcmp(name, REFERENCEFILENAME_TAG) == 0) {
/* save reference file name */
gt_str_append_cstr_nt(parseinfo->referencefilename, data, datalength);
}
else if (strcmp(name, REFERENCEFILEHASH_TAG) == 0) {
gth_sa_set_ref_file_num(sa, process_file(parseinfo->input,
gt_str_get(parseinfo->referencefilename),
data, true,
gth_sa_alphatype(sa)));
/* reset reference filename */
gt_str_reset(parseinfo->referencefilename);
}
else if (strcmp(name, REFERENCESEQNUM_TAG) == 0) {
SCANUINT;
gth_sa_set_ref_seq_num(sa, ret);
}
else if (strcmp(name, GENOMICID_TAG) == 0)
gth_sa_set_gen_id(sa, data);
else if (strcmp(name, REFERENCEID_TAG) == 0)
gth_sa_set_ref_id(sa, data);
else if (strcmp(name, GENOMICSTRANDISFORWARD_TAG) == 0)
gth_sa_set_gen_strand(sa, parse_boolean(data, parseinfo));
else if (strcmp(name, REFERENCESTRANDISFORWARD_TAG) == 0)
gth_sa_set_ref_strand(sa, parse_boolean(data, parseinfo));
else if (strcmp(name, GENOMICCUTOFF_TAG) == 0) {
SCANUINT;
parseinfo->cutoffs.genomiccutoff = ret;
}
else if (strcmp(name, REFERENCECUTOFF_TAG) == 0) {
SCANUINT;
parseinfo->cutoffs.referencecutoff = ret;
}
else if (strcmp(name, EOPCUTOFF_TAG) == 0) {
SCANUINT;
parseinfo->cutoffs.eopcutoff = ret;
}
else if (strcmp(name, CUTOFFSSTART_TAG) == 0)
gth_sa_set_cutoffs_start(sa, &parseinfo->cutoffs);
else if (strcmp(name, CUTOFFSEND_TAG) == 0)
gth_sa_set_cutoffs_end(sa, &parseinfo->cutoffs);
else if (strcmp(name, LEFTGENOMICEXONBORDER_TAG) == 0) {
SCANUINT;
parseinfo->exoninfo.leftgenomicexonborder = ret;
}
else if (strcmp(name, RIGHTGENOMICEXONBORDER_TAG) == 0) {
SCANUINT;
parseinfo->exoninfo.rightgenomicexonborder = ret;
}
else if (strcmp(name, LEFTREFERENCEEXONBORDER_TAG) == 0) {
SCANUINT;
parseinfo->exoninfo.leftreferenceexonborder = ret;
}
else if (strcmp(name, RIGHTREFERENCEEXONBORDER_TAG) == 0) {
SCANUINT;
parseinfo->exoninfo.rightreferenceexonborder = ret;
}
else if (strcmp(name, EXONSCORE_TAG) == 0) {
SCANDOUBLE;
parseinfo->exoninfo.exonscore = retdouble;
}
else if (strcmp(name, EXONINFO_TAG) == 0)
gth_sa_add_exon(sa, &parseinfo->exoninfo);
else if (strcmp(name, DONORSITEPROBABILITY_TAG) == 0) {
SCANDOUBLE;
parseinfo->introninfo.donorsiteprobability = (GthFlt) retdouble;
}
else if (strcmp(name, ACCEPTORSITEPROBABILITY_TAG) == 0) {
SCANDOUBLE;
parseinfo->introninfo.acceptorsiteprobability = (GthFlt) retdouble;
}
else if (strcmp(name, DONORSITESCORE_TAG) == 0) {
SCANDOUBLE;
parseinfo->introninfo.donorsitescore = retdouble;
}
else if (strcmp(name, ACCEPTORSITESCORE_TAG) == 0) {
SCANDOUBLE;
parseinfo->introninfo.acceptorsitescore = retdouble;
}
else if (strcmp(name, INTRONINFO_TAG) == 0)
gth_sa_add_intron(sa, &parseinfo->introninfo);
else if (strcmp(name, POLYASTART_TAG) == 0) {
SCANUINT;
gth_sa_set_polyAtail_start(sa, ret);
}
else if (strcmp(name, POLYAEND_TAG) == 0) {
SCANUINT;
gth_sa_set_polyAtail_stop(sa, ret);
}
else if (strcmp(name, ALIGNMENTSCORE_TAG) == 0) {
SCANDOUBLE;
gth_sa_set_score(sa, retdouble);
}
else if (strcmp(name, COVERAGE_TAG) == 0) {
SCANDOUBLE;
gth_sa_set_coverage(sa, retdouble);
}
else if (strcmp(name, COVERAGEOFGENOMICSEGMENTISHIGHEST_TAG) == 0) {
gth_sa_set_highest_cov(sa, parse_boolean(data, parseinfo));
}
else if (strcmp(name, CUMULATIVELENGTHOFSCOREDEXONS_TAG) == 0) {
SCANUINT;
gth_sa_set_cumlen_scored_exons(sa, ret);
}
}
static int call_dna_DP(bool directmatches, GthCallInfo *call_info,
GthInput *input, GthStat *stat,
GthSACollection *sa_collection, GthSA *saA,
GtUword gen_file_num,
GtUword ref_file_num,
GtUword gen_total_length,
GtUword gen_offset,
const GtRange *gen_seq_bounds,
const GtRange *gen_seq_bounds_rc,
GtUword ref_total_length, GtUword ref_offset,
GtUword chainctr,
GtUword num_of_chains, GthMatchInfo *match_info,
const unsigned char *ref_seq_tran,
const unsigned char *ref_seq_orig,
const unsigned char *ref_seq_tran_rc,
const unsigned char *ref_seq_orig_rc,
GthChain *chain,
GthDNACompletePathMatrixJT dna_complete_path_matrix_jt,
GthProteinCompletePathMatrixJT
protein_complete_path_matrix_jt)
{
int rval;
bool bothstrandsanalyzed, firstdp = true,
GT_UNUSED gs2outdirectmatches = directmatches;
GthSA *saB = NULL;
GtFile *outfp = call_info->out->outfp;
if (directmatches ? gth_input_forward(input)
: gth_input_reverse(input)) {
/* calculate alignment */
rval = callsahmt(true, saA, directmatches, gen_file_num, ref_file_num,
chain, gen_total_length, gen_offset, gen_seq_bounds,
gen_seq_bounds_rc,
ref_seq_tran, ref_seq_orig, ref_total_length, ref_offset,
input, &call_info->simfilterparam.introncutoutinfo, stat,
chainctr, num_of_chains, call_info->translationtable,
directmatches, call_info->proteinexonpenal,
call_info->splice_site_model, call_info->dp_options_core,
call_info->dp_options_est, call_info->dp_options_postpro,
dna_complete_path_matrix_jt,
protein_complete_path_matrix_jt, call_info->out);
if (rval && rval != GTH_ERROR_SA_COULD_NOT_BE_DETERMINED) {
/* ^ this error is treated below */
return rval;
}
firstdp = false;
bothstrandsanalyzed = gth_input_both(input);
if (rval == GTH_ERROR_SA_COULD_NOT_BE_DETERMINED ||
isunsuccessfulalignment(saA, call_info->out->comments, outfp)) {
match_info->call_number--;
/* if the spliced alignment was unsuccessful, it is deleted and the
next hit is considered. */
gth_sa_delete(saA);
return 0; /* continue */
}
/* if not both strands are analyzed, we can save this alignment now.
Otherwise we have to calculate the alignment to the other strand
first and then save the better one. */
if (!bothstrandsanalyzed)
save_sa(sa_collection, saA, call_info->sa_filter, match_info, stat);
}
if (directmatches ? gth_input_reverse(input)
: gth_input_forward(input)) {
if ((firstdp || gth_sa_is_poor(saA, call_info->minaveragessp)) &&
!call_info->cdnaforwardonly) {
if (firstdp) {
/* space for first alignment is already allocated, bu we have to
change the direction of the genomic and the reference strand */
gth_sa_set_gen_strand(saA, !directmatches);
gth_sa_set_ref_strand(saA, false);
}
else {
/* allocating space for second alignment */
saB = gth_sa_new_and_set(!directmatches, false, input,
chain->gen_file_num, chain->gen_seq_num,
chain->ref_file_num, chain->ref_seq_num,
match_info->call_number, gen_total_length,
gen_offset, ref_total_length);
}
/* setting gs2outdirectmatches (for compatibility) */
gs2outdirectmatches = (bool) !directmatches;
/* calculate alignment */
rval = callsahmt(true, firstdp ? saA : saB, !directmatches,
gen_file_num, ref_file_num, chain, gen_total_length,
gen_offset, gen_seq_bounds, gen_seq_bounds_rc,
ref_seq_tran_rc, ref_seq_orig_rc, ref_total_length,
ref_offset, input,
&call_info->simfilterparam.introncutoutinfo, stat,
chainctr, num_of_chains, call_info->translationtable,
directmatches, call_info->proteinexonpenal,
call_info->splice_site_model, call_info->dp_options_core,
call_info->dp_options_est, call_info->dp_options_postpro,
dna_complete_path_matrix_jt,
protein_complete_path_matrix_jt, call_info->out);
if (rval && rval != GTH_ERROR_SA_COULD_NOT_BE_DETERMINED) {
/* ^ this error is treated below */
return rval;
}
if (firstdp) {
if (rval == GTH_ERROR_SA_COULD_NOT_BE_DETERMINED ||
isunsuccessfulalignment(saA, call_info->out->comments, outfp)) {
/* for compatibility with GS2 */
/* XXX: makes no sense. Possibly only if -gs2out is used. */
match_info->significant_match_found= true;
/* if the spliced alignment was unsuccessful, it is deleted and
the next hit is considered. */
gth_sa_delete(saA);
return 0; /* continue */
}
save_sa(sa_collection, saA, call_info->sa_filter, match_info, stat);
}
else /* !firstdp */
{
if (rval == GTH_ERROR_SA_COULD_NOT_BE_DETERMINED ||
isunsuccessfulalignment(saB, call_info->out->comments, outfp) ||
!gth_sa_B_is_better_than_A(saA, saB)) {
/* insert first SA */
save_sa(sa_collection, saA, call_info->sa_filter, match_info, stat);
/* discard second SA */
gth_sa_delete(saB);
}
else {
/* insert second SA */
save_sa(sa_collection, saB, call_info->sa_filter, match_info, stat);
/* free first SA */
gth_sa_delete(saA);
}
}
}
else
save_sa(sa_collection, saA, call_info->sa_filter, match_info, stat);
}
return 0;
}
