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root/gclib/gclib/gff.h
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# Line 29 | Line 29
29   extern const uint gfo_flag_CHILDREN_PROMOTED;
30   extern const uint gfo_flag_HAS_ERRORS;
31   extern const uint gfo_flag_IS_GENE;
32 < extern const uint gfo_flag_FROM_GFF3; //parsed from GFF3 formatted record
32 > extern const uint gfo_flag_HAS_GFF_ID; //found a GFF3 formatted main feature with its own ID
33   extern const uint gfo_flag_BY_EXON;  //created by subfeature (exon) directly
34                        //(GTF2 and some chado gff3 dumps with exons given before their mRNA)
35   extern const uint gfo_flag_IS_TRANSCRIPT; //recognized as '*RNA' or '*transcript'
# Line 472 | Line 472
472        if (v) flags |= gfo_flag_HAS_ERRORS;
473          else flags &= ~gfo_flag_HAS_ERRORS;
474        }
475 <  bool fromGff3() { return ((flags & gfo_flag_FROM_GFF3)!=0); }
476 <  void fromGff3(bool v) {
477 <      if (v) flags |= gfo_flag_FROM_GFF3;
478 <        else flags &= ~gfo_flag_FROM_GFF3;
475 >  bool hasGffID() { return ((flags & gfo_flag_HAS_GFF_ID)!=0); }
476 >  void hasGffID(bool v) {
477 >      if (v) flags |= gfo_flag_HAS_GFF_ID;
478 >        else flags &= ~gfo_flag_HAS_GFF_ID;
479        }
480    bool createdByExon() { return ((flags & gfo_flag_BY_EXON)!=0); }
481    void createdByExon(bool v) {
# Line 1018 | Line 1018
1018    GHash<int> discarded_ids; //for transcriptsOnly mode, keep track
1019                              // of discarded parent IDs
1020    GHash< GVec<GfoHolder> > phash; //transcript_id+contig (Parent~Contig) => [gflst index, GffObj]
1021 <  GHash<int> tids; //transcript_id uniqueness
1021 >  //GHash<int> tids; //just for transcript_id uniqueness
1022    char* gfoBuildId(const char* id, const char* ctg);
1023    //void gfoRemove(const char* id, const char* ctg);
1024    GfoHolder* gfoAdd(GffObj* gfo, int idx);
# Line 1040 | Line 1040
1040    bool addExonFeature(GfoHolder* prevgfo, GffLine* gffline, GHash<CNonExon>& pex, bool noExonAttr);
1041    GList<GSeqStat> gseqstats; //list of all genomic sequences seen by this reader, accumulates stats
1042    GffReader(FILE* f=NULL, bool t_only=false, bool sortbyloc=false):discarded_ids(true),
1043 <                       phash(true), tids(true), gflst(sortbyloc), gseqstats(true,true,true) {
1043 >                       phash(true), gflst(sortbyloc), gseqstats(true,true,true) {
1044        gff_warns=gff_show_warnings;
1045        names=NULL;
1046        gffline=NULL;
# Line 1060 | Line 1060
1060        gflst.sortedByLoc(sortbyloc);
1061        }
1062    GffReader(char* fn, bool t_only=false, bool sort=false):discarded_ids(true), phash(true),
1063 <                             tids(true),gflst(sort),gseqstats(true,true,true) {
1063 >                             gflst(sort),gseqstats(true,true,true) {
1064        gff_warns=gff_show_warnings;
1065        names=NULL;
1066        fname=Gstrdup(fn);

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