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root/gclib/gclib/gff.cpp
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# Line 7 | Line 7
7  
8   const uint GFF_MAX_LOCUS = 7000000; //longest known gene in human is ~2.2M, UCSC claims a gene for mouse of ~ 3.1 M
9   const uint GFF_MAX_EXON  =   30000; //longest known exon in human is ~11K
10 < const uint GFF_MAX_INTRON= 6000000;
10 > const uint GFF_MAX_INTRON= 6000000; //Ensembl shows a >5MB human intron
11   bool gff_show_warnings = false; //global setting, set by GffReader->showWarnings()
12   const int gff_fid_mRNA=0;
13   const int gff_fid_transcript=1;
# Line 17 | Line 17
17   const uint gfo_flag_CHILDREN_PROMOTED= 0x00000002;
18   const uint gfo_flag_IS_GENE          = 0x00000004;
19   const uint gfo_flag_IS_TRANSCRIPT    = 0x00000008;
20 < const uint gfo_flag_FROM_GFF3        = 0x00000010;
20 > const uint gfo_flag_HAS_GFF_ID       = 0x00000010; //found GFF3 feature line with its own ID
21   const uint gfo_flag_BY_EXON          = 0x00000020; //created by subfeature (exon) directly
22   const uint gfo_flag_DISCARDED        = 0x00000100;
23   const uint gfo_flag_LST_KEEP         = 0x00000200;
# Line 52 | Line 52
52               else return (int)(g1.gseq_id-g2.gseq_id);
53   }
54  
55 < char* GffLine::extractAttr(const char* pre, bool caseStrict, bool enforce_GTF2) {
55 > char* GffLine::extractAttr(const char* attr, bool caseStrict, bool enforce_GTF2) {
56   //parse a key attribute and remove it from the info string
57   //(only works for attributes that have values following them after ' ' or '=')
58   static const char GTF2_ERR[]="Error parsing attribute %s ('\"' required) at GTF line:\n%s\n";
59 < int lpre=strlen(pre);
60 < char cend=pre[lpre-1];
61 < char* pos = (caseStrict) ? strstr(info, pre) : strifind(info, pre);
62 < if (pos==NULL) return NULL;
63 < char* findstart=info;
64 < //require word boundary on the left:
65 < while (pos!=NULL && pos!=info && *(pos-1)!=';' && *(pos-1)!=' ') {
66 <    findstart=pos+lpre;
67 <    pos = (caseStrict) ? strstr(findstart, pre) : strifind(findstart, pre);
68 <    }
69 < if (pos==NULL) return NULL;
70 < if (cend!=' ' && cend!='=') {
71 <    //require word boundary on the right:
72 <    while (pos!=NULL && *(pos+lpre)!=' ' && *(pos+lpre)!='=') {
73 <       findstart=pos+lpre;
74 <       pos = (caseStrict) ? strstr(findstart, pre) : strifind(findstart, pre);
75 <       }
76 <    }
77 < if (pos==NULL) return NULL;
78 < char* vp=pos+lpre;
59 > int attrlen=strlen(attr);
60 > char cend=attr[attrlen-1];
61 > //char* pos = (caseStrict) ? strstr(info, attr) : strifind(info, attr);
62 > //must make sure attr is not found in quoted text
63 > char* pos=info;
64 > char prevch=0;
65 > bool in_str=false;
66 > bool notfound=true;
67 > int (*strcmpfn)(const char*, const char*, int) = caseStrict ? Gstrcmp : Gstricmp;
68 > while (notfound && *pos) {
69 >   char ch=*pos;
70 >   if (ch=='"') {
71 >     in_str=!in_str;
72 >     pos++;
73 >     prevch=ch;
74 >     continue;
75 >     }
76 >   if (!in_str && (prevch==0 || prevch==' ' || prevch == ';')
77 >          && strcmpfn(attr, pos, attrlen)==0) {
78 >      //attr match found
79 >      //check for word boundary on right
80 >      char* epos=pos+attrlen;
81 >      if (cend=='=' || cend==' ' || *epos==0 || *epos==' ') {
82 >        notfound=false;
83 >        break;
84 >        }
85 >      //not a perfect match, move on
86 >      pos=epos;
87 >      prevch=*(pos-1);
88 >      continue;
89 >      }
90 >   //not a match or in_str
91 >   prevch=ch;
92 >   pos++;
93 >   }
94 > if (notfound) return NULL;
95 > char* vp=pos+attrlen;
96   while (*vp==' ') vp++;
97   if (*vp==';' || *vp==0)
98 <      GError("Error parsing value of GFF attribute \"%s\", line:\n%s\n", pre, dupline);
98 >      GError("Error parsing value of GFF attribute \"%s\", line:\n%s\n", attr, dupline);
99   bool dq_enclosed=false; //value string enclosed by double quotes
100   if (*vp=='"') {
101       dq_enclosed=true;
102       vp++;
103       }
104   if (enforce_GTF2 && !dq_enclosed)
105 <      GError(GTF2_ERR,pre, dupline);
105 >      GError(GTF2_ERR,attr, dupline);
106   char* vend=vp;
107   if (dq_enclosed) {
108      while (*vend!='"' && *vend!=';' && *vend!=0) vend++;
# Line 94 | Line 111
111      while (*vend!=';' && *vend!=0) vend++;
112      }
113   if (enforce_GTF2 && *vend!='"')
114 <     GError(GTF2_ERR, pre, dupline);
114 >     GError(GTF2_ERR, attr, dupline);
115   char *r=Gstrdup(vp, vend-1);
116   //-- now remove this attribute from the info string
117   while (*vend!=0 && (*vend=='"' || *vend==';' || *vend==' ')) vend++;
# Line 159 | Line 176
176   ftype=t[2];
177   info=t[8];
178   char* p=t[3];
179 < if (!parseUInt(p,fstart))
180 <   GError("Error parsing start coordinate from GFF line:\n%s\n",l);
179 > if (!parseUInt(p,fstart)) {
180 >   //FIXME: chromosome_band entries in Flybase
181 >   GMessage("Warning: invalid start coordinate at line:\n%s\n",l);
182 >   return;
183 >   }
184   p=t[4];
185 < if (!parseUInt(p,fend))
186 <   GError("Error parsing end coordinate from GFF line:\n%s\n",l);
187 < if (fend<fstart) swap(fend,fstart); //make sure fstart>=fend, always
185 > if (!parseUInt(p,fend)) {
186 >   GMessage("Warning: invalid end coordinate at line:\n%s\n",l);
187 >   return;
188 >   }
189 > if (fend<fstart) Gswap(fend,fstart); //make sure fstart>=fend, always
190   p=t[5];
191   if (p[0]=='.' && p[1]==0) {
192    score=0;
# Line 188 | Line 210
210     is_exon=true;
211     is_t_data=true;
212     }
213 <  else if (strstr(fnamelc, "exon")!=NULL) {
213 >  else if (endsWith(fnamelc, "exon")) {
214     exontype=exgffExon;
215     is_exon=true;
216     is_t_data=true;
# Line 229 | Line 251
251            }
252          return; //skip this line, unwanted feature name
253          }
254 < ID=extractAttr("ID=");
255 < char* Parent=extractAttr("Parent=");
254 > ID=extractAttr("ID=",true);
255 > char* Parent=extractAttr("Parent=",true);
256   is_gff3=(ID!=NULL || Parent!=NULL);
257   if (is_gff3) {
258     //parse as GFF3
259      if (ID!=NULL) {
260         //has ID attr so it's likely to be a parent feature
261         //look for explicit gene name
262 <       gene_name=extractAttr("gene_name=",false);
262 >       gene_name=extractAttr("gene_name=");
263         if (gene_name==NULL) {
264 <           gene_name=extractAttr("geneName=",false);
264 >           gene_name=extractAttr("geneName=");
265             if (gene_name==NULL) {
266 <               gene_name=extractAttr("gene_sym=",false);
266 >               gene_name=extractAttr("gene_sym=");
267                 if (gene_name==NULL) {
268 <                   gene_name=extractAttr("gene=",false);
268 >                   gene_name=extractAttr("gene=");
269                     }
270                 }
271             }
272 <       gene_id=extractAttr("geneID=",false);
272 >       gene_id=extractAttr("geneID=");
273         if (gene_id==NULL) {
274 <          gene_id=extractAttr("gene_id=",false);
274 >          gene_id=extractAttr("gene_id=");
275            }
276         if (is_gene) {
277           //special case: keep the Name and ID attributes of the gene feature
# Line 294 | Line 316
316           } //has Parent field
317     } //GFF3
318    else { // GTF-like expected
319 <   Parent=extractAttr("transcript_id");
319 >   Parent=extractAttr("transcript_id",true);
320     if (Parent!=NULL) { //GTF2 format detected
321       if (is_transcript) {
322           // atypical GTF with a parent transcript line declared
# Line 302 | Line 324
324           Parent=NULL;
325           }
326       gene_id=extractAttr("gene_id"); // for GTF this is the only attribute accepted as geneID
327 +     if (gene_id==NULL)
328 +       gene_id=extractAttr("geneid");
329       gene_name=extractAttr("gene_name");
330       if (gene_name==NULL) {
331 +
332             gene_name=extractAttr("gene_sym");
333 <           if (gene_name==NULL)
333 >           if (gene_name==NULL) {
334                 gene_name=extractAttr("gene");
335 +               if (gene_name==NULL)
336 +                  gene_name=extractAttr("genesymbol");
337 +               }
338             }
339       //prepare for parseAttr by adding '=' character instead of spaces for all attributes
340       //after the attribute name
# Line 526 | Line 554
554       isCDS=false;
555       }
556    if (qs || qe) {
557 <    if (qs>qe) swap(qs,qe);
557 >    if (qs>qe) Gswap(qs,qe);
558      if (qs==0) qs=1;
559          }
560    int ovlen=0;
# Line 758 | Line 786
786    isCDS=gffline->is_cds; //for now
787    isGene(gffline->is_gene);
788    isTranscript(gffline->is_transcript || gffline->exontype!=0);
789 <  fromGff3(gffline->is_gff3);
789 >  //fromGff3(gffline->is_gff3);
790  
791    if (gffline->parents!=NULL) {
792      //GTF style -- create a GffObj directly by subfeature
# Line 771 | Line 799
799         //make this GffObj of the same feature type
800         ftype_id=names->feats.addName(gffline->ftype);
801         }
802 <    if (gffline->ID==NULL) { //typical GTF
802 >    if (gffline->ID==NULL) { //typical GTF2 without "transcript" line
803          gffID=Gstrdup(gffline->parents[0]);
804          this->createdByExon(true);
805          //this is likely the first exon/segment of the feature
806          addExon(gfrd, gffline, keepAttr, noExonAttr);
807          }
808 <      else { //a parented feature with an ID -- probably an orphan GFF3 line
808 >      else { //a parented feature with an ID -- probably an orphan or premature GFF3 subfeature line
809          if (gffline->is_gff3 && gffline->exontype!=0) {
810               //premature exon given before its parent transcript
811               //create the transcript entry here
# Line 797 | Line 825
825      gscore=gffline->score;
826      if (gffline->ID==NULL || gffline->ID[0]==0)
827        GError("Error: no ID found for GFF record start\n");
828 +    this->hasGffID(true);
829      gffID=Gstrdup(gffline->ID); //there must be an ID here
830      //if (gffline->is_transcript) ftype_id=gff_fid_mRNA;
831        //else
# Line 854 | Line 883
883   return gffline;
884   }
885  
886 +
887   char* GffReader::gfoBuildId(const char* id, const char* ctg) {
888   //caller must free the returned pointer
889   char* buf=NULL;
# Line 864 | Line 894
894   strcpy(buf+idlen+1, ctg);
895   return buf;
896   }
897 <
897 > /*
898   void GffReader::gfoRemove(const char* id, const char* ctg) {
899   char* buf=gfoBuildId(id,ctg);
900   phash.Remove(buf);
901   GFREE(buf);
902   }
903 <
903 > */
904   //Warning: if gflst gets altered, idx becomes obsolete
905 < GfoHolder* GffReader::gfoAdd(const char* id, const char* ctg, GffObj* gfo, int idx) {
906 < char* buf=gfoBuildId(id,ctg);
877 < GfoHolder* r=new GfoHolder(gfo,idx);
878 < phash.Add(buf, r);
879 < GFREE(buf);
880 < return r;
881 < }
905 > GfoHolder* GffReader::gfoAdd(GffObj* gfo, int idx) {
906 > //TODO: must make sure the gfo ID isn't there already.
907  
908 < GfoHolder* GffReader::gfoFind(const char* id, const char* ctg) {
909 < char* buf=gfoBuildId(id,ctg);
910 < GfoHolder* r=phash.Find(buf);
911 < GFREE(buf);
912 < return r;
908 > GVec<GfoHolder>* glst=phash.Find(gfo->gffID);
909 > if (glst==NULL)
910 >         glst=new GVec<GfoHolder>(1);
911 > GfoHolder gh(gfo,idx);
912 > int i=glst->Add(gh);
913 > phash.Add(gfo->gffID, glst);
914 > return &(glst->Get(i));
915 > }
916 >
917 > GfoHolder* GffReader::gfoAdd(GVec<GfoHolder>& glst, GffObj* gfo, int idx) {
918 > GfoHolder gh(gfo,idx);
919 > int i=glst.Add(gh);
920 > return &(glst[i]);
921 > }
922 >
923 > GfoHolder* GffReader::gfoFind(const char* id, const char* ctg,
924 >                    GVec<GfoHolder>** glst, char strand, uint start, uint end) {
925 > GVec<GfoHolder>* gl=phash.Find(id);
926 > GfoHolder* gh=NULL;
927 > if (gl) {
928 >   for (int i=0;i<gl->Count();i++) {
929 >      GfoHolder& gfo = gl->Get(i);
930 >      if (ctg!=NULL && strcmp(ctg, gfo.gffobj->getGSeqName())!=0)
931 >           continue;
932 >      if (strand && strand != gfo.gffobj->strand)
933 >           continue;
934 >      if (start>0) {
935 >           if (abs((int)start-(int)gfo.gffobj->start)>GFF_MAX_LOCUS)
936 >               continue;
937 >           if (end>0 && (gfo.gffobj->start>end || gfo.gffobj->end<start))
938 >                   continue;
939 >           }
940 >      //must be the same transcript, according to given comparison criteria
941 >      gh=&gfo;
942 >      break;
943 >      }
944 >   }
945 > if (glst) *glst=gl;
946 > return gh;
947   }
948  
949   GfoHolder* GffReader::replaceGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr, int replaceidx) {
# Line 892 | Line 951
951    GfoHolder* r=NULL;
952    if (replaceidx>=0) {
953       gflst.Put(replaceidx,newgfo);
954 <     r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, replaceidx);
954 >     r=gfoAdd(newgfo, replaceidx);
955       }
956     else {
957       int gfoidx=gflst.Add(newgfo);
958 <     r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, gfoidx);
958 >     r=gfoAdd(newgfo, gfoidx);
959       }
960 +  /*
961    if (gff_warns) {
962      int* pcount=tids.Find(newgfo->gffID);
963      if (pcount!=NULL) {
964 <       if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
964 >      if (gff_warns) GMessage("Warning: duplicate GFF ID: %s\n", newgfo->gffID);
965         (*pcount)++;
966         }
967       else {
968         tids.Add(newgfo->gffID,new int(1));
969         }
970      }
971 +   */
972    return r;
973   }
974  
# Line 928 | Line 989
989   }
990  
991   GfoHolder* GffReader::newGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr,
992 <                          GffObj* parent, GffExon* pexon) {
992 >                          GffObj* parent, GffExon* pexon, GVec<GfoHolder>* glst) {
993    GffObj* newgfo=new GffObj(this, gffline, keepAttr, noExonAttr);
994    GfoHolder* r=NULL;
995    int gfoidx=gflst.Add(newgfo);
996 <  r=gfoAdd(newgfo->gffID, gffline->gseqname, newgfo, gfoidx);
996 >  r=(glst) ? gfoAdd(*glst, newgfo, gfoidx) : gfoAdd(newgfo, gfoidx);
997    if (parent!=NULL) {
998      updateParent(r, parent);
999      if (pexon!=NULL) parent->removeExon(pexon);
1000      }
1001 +  /*
1002    if (gff_warns) {
1003      int* pcount=tids.Find(newgfo->gffID);
1004      if (pcount!=NULL) {
# Line 947 | Line 1009
1009         tids.Add(newgfo->gffID,new int(1));
1010         }
1011      }
1012 +  */
1013    return r;
1014   }
1015  
1016   GfoHolder* GffReader::updateGffRec(GfoHolder* prevgfo, GffLine* gffline,
1017                                           bool keepAttr) {
1018   if (prevgfo==NULL) return NULL;
1019 < prevgfo->gffobj->createdByExon(false);
1019 > //prevgfo->gffobj->createdByExon(false);
1020   prevgfo->gffobj->ftype_id=prevgfo->gffobj->names->feats.addName(gffline->ftype);
1021   prevgfo->gffobj->start=gffline->fstart;
1022   prevgfo->gffobj->end=gffline->fend;
1023   prevgfo->gffobj->isGene(gffline->is_gene);
1024   prevgfo->gffobj->isTranscript(gffline->is_transcript || gffline->exontype!=0);
1025 < prevgfo->gffobj->fromGff3(gffline->is_gff3);
1025 > prevgfo->gffobj->hasGffID(gffline->ID!=NULL);
1026   if (keepAttr) {
1027     if (prevgfo->gffobj->attrs!=NULL) prevgfo->gffobj->attrs->Clear();
1028     prevgfo->gffobj->parseAttrs(prevgfo->gffobj->attrs, gffline->info);
# Line 971 | Line 1034
1034   bool GffReader::addExonFeature(GfoHolder* prevgfo, GffLine* gffline, GHash<CNonExon>& pex, bool noExonAttr) {
1035    bool r=true;
1036    if (gffline->strand!=prevgfo->gffobj->strand) {
1037 <     GMessage("GFF Error: duplicate GFF ID '%s' (exons found on different strands of %s)\n",
1038 <        prevgfo->gffobj->gffID, prevgfo->gffobj->getGSeqName());
1039 <      r=false;
1040 <     }
1037 >     //TODO: add support for trans-splicing and even inter-chromosomal fusions
1038 >        if (prevgfo->gffobj->strand=='.') {
1039 >            prevgfo->gffobj->strand=gffline->strand;
1040 >        }
1041 >     else {
1042 >       GMessage("GFF Error at %s (%c): exon %d-%d (%c) found on different strand; discarded.\n",
1043 >       prevgfo->gffobj->gffID, prevgfo->gffobj->strand,
1044 >       gffline->fstart, gffline->fend, gffline->strand, prevgfo->gffobj->getGSeqName());
1045 >       //r=false;
1046 >       return true; //FIXME: split trans-spliced mRNAs by strand
1047 >       }
1048 >   }
1049    int gdist=(gffline->fstart>prevgfo->gffobj->end) ? gffline->fstart-prevgfo->gffobj->end :
1050                        ((gffline->fend<prevgfo->gffobj->start)? prevgfo->gffobj->start-gffline->fend :
1051                           0 );
# Line 1028 | Line 1099
1099   }
1100  
1101   //have to parse the whole file because exons can be scattered all over
1102 + //trans-splicing and fusions are only accepted in proper GFF3 format, with a single parent feature ID entry
1103   void GffReader::readAll(bool keepAttr, bool mergeCloseExons, bool noExonAttr) {
1104    bool validation_errors = false;
1105    //loc_debug=false;
1106    GHash<CNonExon> pex; //keep track of any "exon"-like features that have an ID
1107                       //and thus could become promoted to parent features
1108    while (nextGffLine()!=NULL) {
1037       //seen this gff ID before?
1109       GfoHolder* prevseen=NULL;
1110 <     if (gffline->ID) //GFF3
1111 <         prevseen=gfoFind(gffline->ID, gffline->gseqname);
1112 <     if (prevseen!=NULL) {
1113 <            if (prevseen->gffobj->createdByExon()) {
1114 <                updateGffRec(prevseen, gffline, keepAttr);
1115 <                }
1116 <             else {
1117 <                GMessage("Error: duplicate GFF ID '%s' encountered!\n",gffline->ID);
1118 <                validation_errors = true;
1119 <                if (gff_warns) {
1120 <                       delete gffline; gffline=NULL; continue;
1121 <                       }
1122 <                   else exit(1);
1123 <                }
1124 <            }
1110 >     GVec<GfoHolder>* prevgflst=NULL;
1111 >     if (gffline->ID && gffline->exontype==0) {
1112 >         //>>>>> for a parent-like IDed feature (mRNA, gene, etc.)
1113 >                 //look for same ID on the same chromosome/strand/locus
1114 >                 prevseen=gfoFind(gffline->ID, gffline->gseqname, &prevgflst, gffline->strand, gffline->fstart);
1115 >                 if (prevseen!=NULL) {
1116 >                                //same ID/chromosome combo encountered before
1117 >                                if (prevseen->gffobj->createdByExon() &&
1118 >                                          prevseen->gffobj->start>=gffline->fstart &&
1119 >                                          prevseen->gffobj->end<=gffline->fend) {
1120 >                                        //an exon of this ID was given before
1121 >                                        //this line has the main attributes for this ID
1122 >                                        updateGffRec(prevseen, gffline, keepAttr);
1123 >                                        }
1124 >                                 else {
1125 >                                        //- duplicate ID -- this must be a discontiguous feature
1126 >                                   //   e.g. a trans-spliced transcript
1127 >                                   if (prevseen->gffobj->overlap(gffline->fstart, gffline->fend)) {
1128 >                                          //overlapping with same ID not allowed
1129 >                                         GMessage("Error: duplicate GFF ID '%s' encountered!\n",gffline->ID);
1130 >                                         //validation_errors = true;
1131 >                                         if (gff_warns) {
1132 >                                                   delete gffline;
1133 >                                                   gffline=NULL;
1134 >                                                   continue;
1135 >                                                   }
1136 >                                         else exit(1);
1137 >                                     }
1138 >                                    //create a new entry with the same ID
1139 >                    prevseen=newGffRec(gffline, keepAttr, noExonAttr,
1140 >                            prevseen->gffobj->parent, NULL, prevgflst);
1141 >                                        } //duplicate ID on the same chromosome
1142 >                                } //prevseeen != NULL
1143 >        } //parent-like ID feature
1144      if (gffline->parents==NULL) {//start GFF3-like record with no parent (mRNA, gene)
1145 <       if (!prevseen) newGffRec(gffline, keepAttr, noExonAttr);
1145 >       if (!prevseen) newGffRec(gffline, keepAttr, noExonAttr, NULL, NULL, prevgflst);
1146         }
1147 <    else { //--- it's a parented feature (could still be a mRNA)
1147 >    else { //--- it's a child feature (exon/CDS but could still be a mRNA with gene(s) as parent)
1148         bool found_parent=false;
1149         GfoHolder* newgfo=prevseen;
1150 +       GVec<GfoHolder>* newgflst=NULL;
1151         for (int i=0;i<gffline->num_parents;i++) {
1152              if (transcriptsOnly && discarded_ids.Find(gffline->parents[i])!=NULL)
1153                  continue; //skipping discarded parent feature
1154 <            GfoHolder* parentgfo=gfoFind(gffline->parents[i], gffline->gseqname);
1154 >            GfoHolder* parentgfo=gfoFind(gffline->parents[i], gffline->gseqname,
1155 >                                          &newgflst, gffline->strand, gffline->fstart, gffline->fend);
1156              if (parentgfo!=NULL) { //parent GffObj parsed earlier
1157                     found_parent=true;
1158                     if (parentgfo->gffobj->isGene() && gffline->is_transcript
# Line 1077 | Line 1169
1169                         if (!addExonFeature(parentgfo, gffline, pex, noExonAttr))
1170                           validation_errors=true;
1171                         }
1172 <                   }
1172 >                   } //overlapping parent feature found
1173              } //for each parsed parent Id
1174         if (!found_parent) { //new GTF-like record starting here with a subfeature directly
1175               //or it could be some chado GFF3 barf with exons declared BEFORE their parent :(
# Line 1093 | Line 1185
1185                 }
1186                else { //no parent seen before, create one directly with this exon
1187                 //loc_debug=true;
1188 <               GfoHolder* newgfo=prevseen ? prevseen : newGffRec(gffline, keepAttr, noExonAttr);
1188 >               GfoHolder* ngfo=prevseen;
1189 >               if (ngfo==NULL)
1190 >                   ngfo=newGffRec(gffline, keepAttr, noExonAttr, NULL, NULL, newgflst);
1191                 if (gffline->ID!=NULL && gffline->exontype==0)
1192 <                     subfPoolAdd(pex, newgfo);
1192 >                     subfPoolAdd(pex, ngfo);
1193                 //even those with errors will be added here!
1194                 }
1195              GFREE(subp_name);
# Line 1109 | Line 1203
1203   // all gff records are now loaded in GList gflst
1204   // so we can free the hash
1205    phash.Clear();
1206 <  tids.Clear();
1206 >  //tids.Clear();
1207    if (validation_errors) {
1208      exit(1);
1209      }
# Line 1158 | Line 1252
1252       } //for each exon
1253     }
1254   //attribute reduction for GTF records
1255 < if (keepAttrs && !noExonAttr && !fromGff3()
1255 > if (keepAttrs && !noExonAttr && !hasGffID()
1256            && exons.Count()>0 && exons[0]->attrs!=NULL) {
1257     bool attrs_discarded=false;
1258     for (int a=0;a<exons[0]->attrs->Count();a++) {

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