Vector *IntronSupportingEvidenceAdaptor_objectsFromStatementHandle(IntronSupportingEvidenceAdaptor *isea,
StatementHandle *sth,
AssemblyMapper *assMapper,
Slice *destSlice) {
SliceAdaptor *sa = DBAdaptor_getSliceAdaptor(isea->dba);
AnalysisAdaptor *aa = DBAdaptor_getAnalysisAdaptor(isea->dba);
Vector *features = Vector_new();
IDHash *sliceHash = IDHash_new(IDHASH_SMALL);
/* Unneccesary
my %analysis_hash;
my %sr_name_hash;
my %sr_cs_hash;
*/
/* Unused
my $asm_cs;
my $cmp_cs;
my $asm_cs_vers;
my $asm_cs_name;
my $cmp_cs_vers;
my $cmp_cs_name;
if($mapper) {
$asm_cs = $mapper->assembled_CoordSystem();
$cmp_cs = $mapper->component_CoordSystem();
$asm_cs_name = $asm_cs->name();
$asm_cs_vers = $asm_cs->version();
$cmp_cs_name = $cmp_cs->name();
$cmp_cs_vers = $cmp_cs->version();
}
*/
long destSliceStart;
long destSliceEnd;
int destSliceStrand;
long destSliceLength;
//CoordSystem *destSliceCs;
char * destSliceSrName;
IDType destSliceSrId = 0;
//AssemblyMapperAdaptor *asma;
if (destSlice) {
destSliceStart = Slice_getStart(destSlice);
destSliceEnd = Slice_getEnd(destSlice);
destSliceStrand = Slice_getStrand(destSlice);
destSliceLength = Slice_getLength(destSlice);
//??destSliceCs = Slice_getCoordSystem(destSlice);
destSliceSrName = Slice_getSeqRegionName(destSlice);
destSliceSrId = Slice_getSeqRegionId(destSlice);
//??asma = DBAdaptor_getAssemblyMapperAdaptor(ea->dba);
}
ResultRow *row;
while ((row = sth->fetchRow(sth))) {
IDType id = row->getLongLongAt(row,0);
IDType analysisId = row->getLongLongAt(row,1);
IDType seqRegionId = row->getLongLongAt(row,2);
long seqRegionStart = row->getLongAt(row,3);
long seqRegionEnd = row->getLongAt(row,4);
int seqRegionStrand = row->getIntAt(row,5);
char *hitName = row->getStringAt(row,6);
double score = row->getDoubleAt(row,7);
char *scoreType = row->getStringAt(row,8);
int spliceCanonical = row->getIntAt(row,9);
// get the analysis object
Analysis *analysis = AnalysisAdaptor_fetchByDbID(aa, analysisId);
/*
// need to get the internal_seq_region, if present
$seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
#get the slice object
my $slice = $slice_hash{"ID:".$seq_region_id};
if(!$slice) {
$slice = $sa->fetch_by_seq_region_id($seq_region_id);
$slice_hash{"ID:".$seq_region_id} = $slice;
$sr_name_hash{$seq_region_id} = $slice->seq_region_name();
$sr_cs_hash{$seq_region_id} = $slice->coord_system();
}
my $sr_name = $sr_name_hash{$seq_region_id};
my $sr_cs = $sr_cs_hash{$seq_region_id};
*/
if (! IDHash_contains(sliceHash, seqRegionId)) {
IDHash_add(sliceHash, seqRegionId, SliceAdaptor_fetchBySeqRegionId(sa, seqRegionId, POS_UNDEF, POS_UNDEF, STRAND_UNDEF));
}
Slice *slice = IDHash_getValue(sliceHash, seqRegionId);
Slice *iseSlice = slice;
char *srName = Slice_getSeqRegionName(slice);
CoordSystem *srCs = Slice_getCoordSystem(slice);
//
// remap the feature coordinates to another coord system
// if a mapper was provided
//
if (assMapper != NULL) {
MapperRangeSet *mrs;
// Slightly suspicious about need for this if statement so left in perl statements for now
if (destSlice != NULL &&
assMapper->objectType == CLASS_CHAINEDASSEMBLYMAPPER) {
mrs = ChainedAssemblyMapper_map(assMapper, srName, seqRegionStart, seqRegionEnd, seqRegionStrand, srCs, 1, destSlice);
} else {
mrs = AssemblyMapper_fastMap(assMapper, srName, seqRegionStart, seqRegionEnd, seqRegionStrand, srCs, NULL);
}
// skip features that map to gaps or coord system boundaries
//next FEATURE if (!defined($seq_region_id));
if (MapperRangeSet_getNumRange(mrs) == 0) {
continue;
}
MapperRange *range = MapperRangeSet_getRangeAt(mrs, 0);
if (range->rangeType == MAPPERRANGE_GAP) {
fprintf(stderr,"Got a mapper gap in gene obj_from_sth - not sure if this is allowed\n");
exit(1);
} else {
MapperCoordinate *mc = (MapperCoordinate *)range;
seqRegionId = mc->id;
seqRegionStart = mc->start;
seqRegionEnd = mc->end;
seqRegionStrand = mc->strand;
}
MapperRangeSet_free(mrs);
/* Was - but identical if and else so why test???
#get a slice in the coord system we just mapped to
if($asm_cs == $sr_cs || ($cmp_cs != $sr_cs && $asm_cs->equals($sr_cs))) {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
} else {
$slice = $slice_hash{"ID:".$seq_region_id} ||=
$sa->fetch_by_seq_region_id($seq_region_id);
}
*/
// Instead...
if (! IDHash_contains(sliceHash, seqRegionId)) {
IDHash_add(sliceHash, seqRegionId, SliceAdaptor_fetchBySeqRegionId(sa, seqRegionId, POS_UNDEF, POS_UNDEF, STRAND_UNDEF));
}
iseSlice = IDHash_getValue(sliceHash, seqRegionId);
}
//
// If a destination slice was provided convert the coords
// If the dest_slice starts at 1 and is foward strand, nothing needs doing
//
if (destSlice != NULL) {
if (destSliceStart != 1 || destSliceStrand != 1) {
if (destSliceStrand == 1) {
seqRegionStart = seqRegionStart - destSliceStart + 1;
seqRegionEnd = seqRegionEnd - destSliceStart + 1;
} else {
long tmpSeqRegionStart = seqRegionStart;
seqRegionStart = destSliceEnd - seqRegionEnd + 1;
seqRegionEnd = destSliceEnd - tmpSeqRegionStart + 1;
seqRegionStrand = -seqRegionStrand;
}
}
// throw away features off the end of the requested slice
if (seqRegionEnd < 1 || seqRegionStart > destSliceLength || (destSliceSrId != seqRegionId)) {
continue;
}
iseSlice = destSlice;
}
IntronSupportingEvidence *ise = IntronSupportingEvidence_new();
IntronSupportingEvidence_setStart (ise, seqRegionStart);
IntronSupportingEvidence_setEnd (ise, seqRegionEnd);
IntronSupportingEvidence_setStrand (ise, seqRegionStrand);
IntronSupportingEvidence_setSlice (ise, iseSlice);
IntronSupportingEvidence_setAnalysis (ise, analysis);
IntronSupportingEvidence_setAdaptor (ise, (BaseAdaptor *)isea);
IntronSupportingEvidence_setDbID (ise, id);
IntronSupportingEvidence_setHitName (ise, hitName);
IntronSupportingEvidence_setScore (ise, score);
IntronSupportingEvidence_setScoreType (ise, scoreType);
IntronSupportingEvidence_setIsSpliceCanonical(ise, spliceCanonical);
Vector_addElement(features, ise);
}
return features;
}
/*
=head2 _objs_from_sth
Arg [1] : DBI:st $sth
An executed DBI statement handle
Arg [2] : (optional) Bio::EnsEMBL::Mapper $mapper
An mapper to be used to convert contig coordinates
to assembly coordinates.
Arg [3] : (optional) Bio::EnsEMBL::Slice $slice
A slice to map the prediction transcript to.
Example : $p_transcripts = $self->_objs_from_sth($sth);
Description: Creates a list of Prediction transcripts from an executed DBI
statement handle. The columns retrieved via the statement
handle must be in the same order as the columns defined by the
_columns method. If the slice argument is provided then the
the prediction transcripts will be in returned in the coordinate
system of the $slice argument. Otherwise the prediction
transcripts will be returned in the RawContig coordinate system.
Returntype : reference to a list of Bio::EnsEMBL::PredictionTranscripts
Exceptions : none
Caller : superclass generic_fetch
Status : Stable
=cut
*/
Vector *PredictionTranscriptAdaptor_objectsFromStatementHandle(PredictionTranscriptAdaptor *pta,
StatementHandle *sth,
AssemblyMapper *assMapper,
Slice *destSlice) {
SliceAdaptor *sa = DBAdaptor_getSliceAdaptor(pta->dba);
AnalysisAdaptor *aa = DBAdaptor_getAnalysisAdaptor(pta->dba);
Vector *pTranscripts = Vector_new();
IDHash *sliceHash = IDHash_new(IDHASH_SMALL);
long destSliceStart;
long destSliceEnd;
int destSliceStrand;
long destSliceLength;
char * destSliceSrName;
IDType destSliceSrId = 0;
if (destSlice) {
destSliceStart = Slice_getStart(destSlice);
destSliceEnd = Slice_getEnd(destSlice);
destSliceStrand = Slice_getStrand(destSlice);
destSliceLength = Slice_getLength(destSlice);
destSliceSrName = Slice_getSeqRegionName(destSlice);
destSliceSrId = Slice_getSeqRegionId(destSlice);
}
ResultRow *row;
while ((row = sth->fetchRow(sth))) {
IDType predictionTranscriptId = row->getLongLongAt(row,0);
IDType seqRegionId = row->getLongLongAt(row,1);
long seqRegionStart = row->getLongAt(row,2);
long seqRegionEnd = row->getLongAt(row,3);
int seqRegionStrand = row->getIntAt(row,4);
IDType analysisId = row->getLongLongAt(row,5);
char *displayLabel = row->getStringAt(row,6);
// get the analysis object
Analysis *analysis = AnalysisAdaptor_fetchByDbID(aa, analysisId);
if (! IDHash_contains(sliceHash, seqRegionId)) {
IDHash_add(sliceHash, seqRegionId, SliceAdaptor_fetchBySeqRegionId(sa, seqRegionId, POS_UNDEF, POS_UNDEF, STRAND_UNDEF));
}
Slice *slice = IDHash_getValue(sliceHash, seqRegionId);
Slice *ptSlice = slice;
char *srName = Slice_getSeqRegionName(slice);
CoordSystem *srCs = Slice_getCoordSystem(slice);
//
// remap the feature coordinates to another coord system
// if a mapper was provided
//
if (assMapper != NULL) {
MapperRangeSet *mrs;
// Slightly suspicious about need for this if statement so left in perl statements for now
if (destSlice != NULL &&
assMapper->objectType == CLASS_CHAINEDASSEMBLYMAPPER) {
mrs = ChainedAssemblyMapper_map(assMapper, srName, seqRegionStart, seqRegionEnd, seqRegionStrand, srCs, 1, destSlice);
} else {
mrs = AssemblyMapper_fastMap(assMapper, srName, seqRegionStart, seqRegionEnd, seqRegionStrand, srCs, NULL);
}
// skip features that map to gaps or coord system boundaries
if (MapperRangeSet_getNumRange(mrs) == 0) {
continue;
}
MapperRange *range = MapperRangeSet_getRangeAt(mrs, 0);
if (range->rangeType == MAPPERRANGE_GAP) {
fprintf(stderr,"Got a mapper gap in gene obj_from_sth - not sure if this is allowed\n");
exit(1);
} else {
MapperCoordinate *mc = (MapperCoordinate *)range;
seqRegionId = mc->id;
seqRegionStart = mc->start;
seqRegionEnd = mc->end;
seqRegionStrand = mc->strand;
}
MapperRangeSet_free(mrs);
if (! IDHash_contains(sliceHash, seqRegionId)) {
IDHash_add(sliceHash, seqRegionId, SliceAdaptor_fetchBySeqRegionId(sa, seqRegionId, POS_UNDEF, POS_UNDEF, STRAND_UNDEF));
}
ptSlice = IDHash_getValue(sliceHash, seqRegionId);
}
//
// If a destination slice was provided convert the coords
// If the dest_slice starts at 1 and is foward strand, nothing needs doing
//
if (destSlice != NULL) {
if (destSliceStart != 1 || destSliceStrand != 1) {
if (destSliceStrand == 1) {
seqRegionStart = seqRegionStart - destSliceStart + 1;
seqRegionEnd = seqRegionEnd - destSliceStart + 1;
} else {
long tmpSeqRegionStart = seqRegionStart;
seqRegionStart = destSliceEnd - seqRegionEnd + 1;
seqRegionEnd = destSliceEnd - tmpSeqRegionStart + 1;
seqRegionStrand = -seqRegionStrand;
}
}
// throw away features off the end of the requested slice
if (seqRegionEnd < 1 || seqRegionStart > destSliceLength || (destSliceSrId != seqRegionId)) {
continue;
}
ptSlice = destSlice;
}
// Finally, create the new PredictionTranscript.
PredictionTranscript *pt = PredictionTranscript_new();
PredictionTranscript_setStart (pt, seqRegionStart);
PredictionTranscript_setEnd (pt, seqRegionEnd);
PredictionTranscript_setStrand (pt, seqRegionStrand);
PredictionTranscript_setSlice (pt, ptSlice);
PredictionTranscript_setAnalysis (pt, analysis);
PredictionTranscript_setAdaptor (pt, (BaseAdaptor *)pta);
PredictionTranscript_setDbID (pt, predictionTranscriptId);
PredictionTranscript_setDisplayLabel(pt, displayLabel);
Vector_addElement(pTranscripts, pt);
}
IDHash_free(sliceHash, NULL);
return pTranscripts;
}
int calcCoverage(char *fName, Slice *slice, htsFile *in, hts_idx_t *idx, int flags) {
int ref;
int begRange;
int endRange;
char region[1024];
char region_name[512];
if (Slice_getChrStart(slice) != 1) {
fprintf(stderr, "Currently only allow a slice start position of 1\n");
return 1;
}
if (flags & M_UCSC_NAMING) {
sprintf(region,"chr%s", Slice_getSeqRegionName(slice));
} else {
sprintf(region,"%s", Slice_getSeqRegionName(slice));
}
bam_hdr_t *header = bam_hdr_init();
header = bam_hdr_read(in->fp.bgzf);
ref = bam_name2id(header, region);
if (ref < 0) {
fprintf(stderr, "Invalid region %s\n", region);
exit(1);
}
sprintf(region,"%s:%ld-%ld", region_name,
Slice_getSeqRegionStart(slice),
Slice_getSeqRegionEnd(slice));
if (hts_parse_reg(region, &begRange, &endRange) == NULL) {
fprintf(stderr, "Could not parse %s\n", region);
exit(2);
}
bam_hdr_destroy(header);
hts_itr_t *iter = sam_itr_queryi(idx, ref, begRange, endRange);
bam1_t *b = bam_init1();
Coverage *coverage = calloc(Slice_getLength(slice),sizeof(Coverage));
long counter = 0;
long overlapping = 0;
long bad = 0;
int startIndex = 0;
while (bam_itr_next(in, iter, b) >= 0) {
if (b->core.flag & (BAM_FUNMAP | BAM_FSECONDARY | BAM_FQCFAIL | BAM_FDUP)) {
bad++;
continue;
}
int end;
//end = bam_calend(&b->core, bam1_cigar(b));
end = bam_endpos(b);
// There is a special case for reads which have zero length and start at begRange (so end at begRange ie. before the first base we're interested in).
// That is the reason for the || end == begRange test
if (end == begRange) {
continue;
}
counter++;
if (!(counter%1000000)) {
if (verbosity > 1) { printf("."); }
fflush(stdout);
}
// Remember: b->core.pos is zero based!
int cigInd;
int refPos;
int readPos;
uint32_t *cigar = bam_get_cigar(b);
for (cigInd = readPos = 0, refPos = b->core.pos; cigInd < b->core.n_cigar; ++cigInd) {
int k;
int lenCigBlock = cigar[cigInd]>>4;
int op = cigar[cigInd]&0xf;
if (op == BAM_CMATCH || op == BAM_CEQUAL || op == BAM_CDIFF) {
for (k = 0; k < lenCigBlock; ++k) {
//if (ref[refPos+k] == 0) break; // out of boundary
coverage[refPos+k].coverage++;
}
if (k < lenCigBlock) break;
refPos += lenCigBlock; readPos += lenCigBlock;
} else if (op == BAM_CDEL) {
for (k = 0; k < lenCigBlock; ++k) {
// if (ref[refPos+k] == 0) break;
coverage[refPos+k].coverage++;
}
if (k < lenCigBlock) break;
refPos += lenCigBlock;
} else if (op == BAM_CSOFT_CLIP) {
readPos += lenCigBlock;
} else if (op == BAM_CHARD_CLIP) {
} else if (op == BAM_CINS) {
readPos += lenCigBlock;
} else if (op == BAM_CREF_SKIP) {
refPos += lenCigBlock;
}
}
#ifdef DONE
int j;
int done = 0;
int hadOverlap = 0;
for (j=startIndex; j < Vector_getNumElement(genes) && !done; j++) {
Gene *gene = Vector_getElementAt(genes,j);
if (!gene) {
continue;
}
// Remember: b->core.pos is zero based!
if (b->core.pos < Gene_getEnd(gene) && end >= Gene_getStart(gene)) {
int k;
int doneGene = 0;
for (k=0; k<Gene_getTranscriptCount(gene) && !doneGene; k++) {
Transcript *trans = Gene_getTranscriptAt(gene,k);
if (b->core.pos < Transcript_getEnd(trans) && end >= Transcript_getStart(trans)) {
int m;
for (m=0; m<Transcript_getExonCount(trans) && !doneGene; m++) {
Exon *exon = Transcript_getExonAt(trans,m);
if (b->core.pos < Exon_getEnd(exon) && end >= Exon_getStart(exon)) {
// Only count as overlapping once (could be that a read overlaps more than one gene)
if (!hadOverlap) {
overlapping++;
hadOverlap = 1;
}
gs = IDHash_getValue(geneCountsHash, Gene_getDbID(gene));
gs->score++;
doneGene = 1;
}
}
}
}
} else if (Gene_getStart(gene) > end) {
done = 1;
} else if (Gene_getEnd(gene) < b->core.pos+1) {
gs = IDHash_getValue(geneCountsHash, Gene_getDbID(gene));
printf("Gene %s (%s) score %ld\n",Gene_getStableId(gene),
Gene_getDisplayXref(gene) ? DBEntry_getDisplayId(Gene_getDisplayXref(gene)) : "",
gs->score);
if (verbosity > 1) {
printf("Removing gene %s (index %d) with extent %d to %d\n",
Gene_getStableId(gene),
gs->index,
Gene_getStart(gene),
Gene_getEnd(gene));
}
Vector_setElementAt(genes,j,NULL);
// Magic (very important for speed) - move startIndex to first non null gene
int n;
startIndex = 0;
for (n=0;n<Vector_getNumElement(genes);n++) {
void *v = Vector_getElementAt(genes,n);
if (v != NULL) {
break;
}
startIndex++;
}
if (verbosity > 1) {
printf("startIndex now %d\n",startIndex);
}
}
}
#endif
}
if (verbosity > 1) { printf("\n"); }
#ifdef DONE
// Print out read counts for what ever's left in the genes array
int n;
for (n=0;n<Vector_getNumElement(genes);n++) {
Gene *gene = Vector_getElementAt(genes,n);
if (gene != NULL) {
gs = IDHash_getValue(geneCountsHash, Gene_getDbID(gene));
printf("Gene %s (%s) score %ld\n",Gene_getStableId(gene),
Gene_getDisplayXref(gene) ? DBEntry_getDisplayId(Gene_getDisplayXref(gene)) : "",
gs->score);
}
}
#endif
printf("Read %ld reads. Number of bad reads (unmapped, qc fail, secondary, dup) %ld\n", counter, bad);
long i;
for (i=0; i< Slice_getLength(slice); i++) {
printf("%ld %ld\n", i+1, coverage[i].coverage);
}
sam_itr_destroy(iter);
bam_destroy1(b);
return 1;
}
Vector *PredictionTranscriptAdaptor_fetchAllBySlice(PredictionTranscriptAdaptor *pta, Slice *slice, char *logicName, int loadExons) {
//my $transcripts = $self->SUPER::fetch_all_by_Slice($slice,$logic_name);
Vector *transcripts = BaseFeatureAdaptor_fetchAllBySlice((BaseFeatureAdaptor *)pta, slice, logicName);
// if there are 0 or 1 transcripts still do lazy-loading
if ( ! loadExons || Vector_getNumElement(transcripts) < 2 ) {
return transcripts;
}
// preload all of the exons now, instead of lazy loading later
// faster than 1 query per transcript
// get extent of region spanned by transcripts
long minStart = 2000000000;
long maxEnd = -2000000000;
int i;
for (i=0; i<Vector_getNumElement(transcripts); i++) {
PredictionTranscript *t = Vector_getElementAt(transcripts, i);
if (PredictionTranscript_getSeqRegionStart((SeqFeature*)t) < minStart) {
minStart = PredictionTranscript_getSeqRegionStart((SeqFeature*)t);
}
if (PredictionTranscript_getSeqRegionEnd((SeqFeature*)t) > maxEnd) {
maxEnd = PredictionTranscript_getSeqRegionEnd((SeqFeature*)t);
}
}
Slice *extSlice;
if (minStart >= Slice_getStart(slice) && maxEnd <= Slice_getEnd(slice)) {
extSlice = slice;
} else {
SliceAdaptor *sa = DBAdaptor_getSliceAdaptor(pta->dba);
extSlice = SliceAdaptor_fetchByRegion(sa, Slice_getCoordSystemName(slice), Slice_getSeqRegionName(slice),
minStart, maxEnd, Slice_getStrand(slice), CoordSystem_getVersion(Slice_getCoordSystem(slice)), 0);
}
// associate exon identifiers with transcripts
IDHash *trHash = IDHash_new(IDHASH_MEDIUM);
for (i=0; i<Vector_getNumElement(transcripts); i++) {
PredictionTranscript *t = Vector_getElementAt(transcripts, i);
if ( ! IDHash_contains(trHash, PredictionTranscript_getDbID(t))) {
IDHash_add(trHash, PredictionTranscript_getDbID(t), t);
}
}
IDType *uniqueIds = IDHash_getKeys(trHash);
char tmpStr[1024];
char *qStr = NULL;
if ((qStr = (char *)calloc(655500,sizeof(char))) == NULL) {
fprintf(stderr,"Failed allocating qStr\n");
return transcripts;
}
int lenNum;
int endPoint = sprintf(qStr, "SELECT prediction_transcript_id, prediction_exon_id, exon_rank FROM prediction_exon WHERE prediction_transcript_id IN (");
for (i=0; i<IDHash_getNumValues(trHash); i++) {
if (i!=0) {
qStr[endPoint++] = ',';
qStr[endPoint++] = ' ';
}
lenNum = sprintf(tmpStr,IDFMTSTR,uniqueIds[i]);
memcpy(&(qStr[endPoint]), tmpStr, lenNum);
endPoint+=lenNum;
}
qStr[endPoint++] = ')';
qStr[endPoint] = '\0';
free(uniqueIds);
StatementHandle *sth = pta->prepare((BaseAdaptor *)pta,qStr,strlen(qStr));
sth->execute(sth);
IDHash *exTrHash = IDHash_new(IDHASH_MEDIUM);
ResultRow *row;
while ((row = sth->fetchRow(sth))) {
IDType trId = row->getLongLongAt(row,0);
IDType exId = row->getLongLongAt(row,1);
int rank = row->getIntAt(row,2);
if (! IDHash_contains(exTrHash, exId)) {
Vector *vec = Vector_new();
Vector_setFreeFunc(vec, PredictionTranscriptRankPair_free);
IDHash_add(exTrHash, exId, vec);
}
Vector *exVec = IDHash_getValue(exTrHash, exId);
PredictionTranscriptRankPair *trp = PredictionTranscriptRankPair_new(IDHash_getValue(trHash, trId), rank);
Vector_addElement(exVec, trp);
}
IDHash_free(trHash, NULL);
sth->finish(sth);
PredictionExonAdaptor *pea = DBAdaptor_getPredictionExonAdaptor(pta->dba);
Vector *exons = PredictionExonAdaptor_fetchAllBySlice(pea, extSlice);
// move exons onto transcript slice, and add them to transcripts
for (i=0; i<Vector_getNumElement(exons); i++) {
PredictionExon *ex = Vector_getElementAt(exons, i);
// Perl didn't have this line - it was in GeneAdaptor version so I think I'm going to keep it
if (!IDHash_contains(exTrHash, PredictionExon_getDbID(ex))) continue;
PredictionExon *newEx;
if (slice != extSlice) {
newEx = (PredictionExon*)PredictionExon_transfer((SeqFeature*)ex, slice);
if (newEx == NULL) {
fprintf(stderr, "Unexpected. Exon could not be transferred onto PredictionTranscript slice.\n");
exit(1);
}
} else {
newEx = ex;
}
Vector *exVec = IDHash_getValue(exTrHash, PredictionExon_getDbID(newEx));
int j;
for (j=0; j<Vector_getNumElement(exVec); j++) {
PredictionTranscriptRankPair *trp = Vector_getElementAt(exVec, j);
PredictionTranscript_addExon(trp->transcript, newEx, &trp->rank);
}
}
IDHash_free(exTrHash, Vector_free);
free(qStr);
return transcripts;
}