Commit b4625612 authored by Michael R. Crusoe's avatar Michael R. Crusoe 🏳️‍🌈
Browse files

New upstream version 0.11.3

parent f4619388

GBase.h

+1 −1
Original line number Diff line number Diff line 
#ifndef G_BASE_DEFINED

#define G_BASE_DEFINED

#define GCLIB_VERSION "0.11.2"

#define GCLIB_VERSION "0.11.3"



#ifdef HAVE_CONFIG_H

#include "config.h"

GVec.hh

+4 −4
Original line number Diff line number Diff line
@@ -64,7 +64,7 @@ template <class OBJ> class GVec { 
    GVec(int init_count, const OBJ init_val);

    GVec(int init_count, OBJ* init_val, bool delete_initval=true); //convenience constructor for complex vectors

    GVec(const GVec<OBJ>& array); //copy constructor

    const GVec<OBJ>& operator=(GVec<OBJ>& array); //copy operator

    const GVec<OBJ>& operator=(const GVec<OBJ>& array); //copy operator

    virtual ~GVec();

    void Insert(int idx, OBJ item) { Insert(idx, &item); }

    void Insert(int idx, OBJ* item);
@@ -148,7 +148,7 @@ template <class OBJ> class GPVec { 
    GPVec(bool free_elements);

    GPVec(GPVec<OBJ>& list); //copy constructor?

    GPVec(GPVec<OBJ>* list); //kind of a copy constructor

    const GPVec<OBJ>& operator=(GPVec<OBJ>& list);

    const GPVec<OBJ>& operator=(const GPVec<OBJ>& list);

    inline OBJ* Get(int i) {

    	TEST_INDEX(i);

        return fList[i];
@@ -246,7 +246,7 @@ template <class OBJ> GVec<OBJ>::GVec(const GVec<OBJ>& array) { //copy constructo 
 this->fCount=array.fCount;

 }



template <class OBJ> const GVec<OBJ>& GVec<OBJ>::operator=(GVec<OBJ>& array) {

template <class OBJ> const GVec<OBJ>& GVec<OBJ>::operator=(const GVec<OBJ>& array) {

 if (&array==this) return *this;

 Clear();

 fCapacity=array.fCapacity;
@@ -580,7 +580,7 @@ template <class OBJ> GPVec<OBJ>::GPVec(GPVec* plist) { //another copy constructo 
  }

}



template <class OBJ> const GPVec<OBJ>& GPVec<OBJ>::operator=(GPVec& list) {

template <class OBJ> const GPVec<OBJ>& GPVec<OBJ>::operator=(const GPVec& list) {

 if (&list!=this) {

     Clear();

     fFreeProc=list.fFreeProc;

gff.cpp

+37 −2
Original line number Diff line number Diff line
@@ -31,6 +31,7 @@ void gffnames_unref(GffNames* &n) { 
  if (n->numrefs==0) { delete n; n=NULL; }

}



const int CLASSCODE_OVL_RANK = 15;

int classcode_rank(char c) {

	switch (c) {

		case '=': return 0; //intron chain match or full exon chain match if strict matching is enabled
@@ -42,6 +43,7 @@ int classcode_rank(char c) { 
		case 'j': return 6; // multi-exon transfrag with at least one junction match

		case 'e': return 12; // single exon transfrag partially overlapping an intron of reference (possible pre-mRNA fragment)

		case 'o': return 14; // other generic exon overlap

	//****  >15 = no-overlaps (not on the same strand) from here on *****

		case 's': return 16; //"shadow" - an intron overlaps with a ref intron on the opposite strand (wrong strand mapping?)

		case 'x': return 18; // generic overlap on opposite strand (usually wrong strand mapping)

		case 'i': return 20; // intra-intron (transfrag fully contained within a reference intron)
@@ -2439,6 +2441,17 @@ void GffObj::printExonList(FILE* fout) { 
	}

}



void GffObj::printCDSList(FILE* fout) {

	//print comma delimited list of CDS intervals

	if (!hasCDS()) return;

	GVec<GffExon> cds;

	this->getCDSegs(cds); //also uses/prepares the CDS phase for each CDS segment

	for (int i=0;i<cds.Count();i++) {

		if (i>0) fprintf(fout, ",");

		fprintf(fout, "%d-%d", cds[i].start, cds[i].end);

	}

}



void BED_addAttribute(FILE* fout, int& acc, const char* format,... ) {

	++acc;

	if (acc==1) fprintf(fout, "\t");
@@ -2708,6 +2721,26 @@ char* GffObj::getUnspliced(GFaSeqGet* faseq, int* rlen, GMapSegments* seglst) { 
    return unspliced;

}



 void GffObj::addPadding(int padLeft, int padRight) {

	 this->start-=padLeft;

	 this->end+=padRight;

	 if (exons.Count()>0) {

		 exons[0]->start-=padLeft;

		 exons.Last()->end+=padRight;

	 }

	 covlen+=padLeft+padRight;

 }



 void GffObj::removePadding(int padLeft, int padRight) {

	 this->start+=padLeft;

	 this->end-=padRight;

	 if (exons.Count()>0) {

		 exons[0]->start+=padLeft;

		 exons.Last()->end-=padRight;

	 }

	 covlen-=padLeft+padRight;

 }



char* GffObj::getSpliced(GFaSeqGet* faseq, bool CDSonly, int* rlen, uint* cds_start, uint* cds_end,

          GMapSegments* seglst, bool cds_open) {

	//cds_open only makes sense when CDSonly is true by overriding CDS 3'end such that the end of
@@ -2729,7 +2762,8 @@ char* GffObj::getSpliced(GFaSeqGet* faseq, bool CDSonly, int* rlen, uint* cds_st 
  if (gsubseq==NULL) {

        GError("Error getting subseq for %s (%d..%d)!\n", gffID, start, end);

  }

  if (fspan<(int)(end-start+1)) { //special case: stop coordinate was extended past the gseq length, must adjust

  if (fspan<(int)(end-start+1)) {

	  //special case: stop coordinate was extended past the gseq length, must adjust

     int endadj=end-start+1-fspan;

     uint prevend=end;

     end-=endadj;
@@ -2744,7 +2778,7 @@ char* GffObj::getSpliced(GFaSeqGet* faseq, bool CDSonly, int* rlen, uint* cds_st 
     }

  }

  char* spliced=NULL;

  GMALLOC(spliced, covlen+1); //allocate more here

  GMALLOC(spliced, covlen+1); //IMPORTANT: covlen must be correct here!

  uint g_start=0, g_end=0;

  int cdsadj=0;

  if (CDphase=='1' || CDphase=='2') {
@@ -3216,6 +3250,7 @@ void GffObj::getCDSegs(GVec<GffExon>& cds) { 
       cds.Add(cdseg);

       } //for each exon

   } // + strand



}



//-- transcript overlap classification functions

gff.h

+16 −5
Original line number Diff line number Diff line
@@ -22,7 +22,7 @@ extern int gff_fid_exon; 
extern const uint GFF_MAX_LOCUS;

extern const uint GFF_MAX_EXON;

extern const uint GFF_MAX_INTRON;



extern const int CLASSCODE_OVL_RANK;

//extern const uint gfo_flag_LEVEL_MSK; //hierarchical level: 0 = no parent

//extern const byte gfo_flagShift_LEVEL;
@@ -651,13 +651,18 @@ class GffExon : public GSeg { 


  } //constructor





  GffExon(const GffExon& ex):GSeg(ex.start, ex.end) { //copy constructor

	  (*this)=ex; //use the default copy operator

      if (ex.attrs!=NULL) {

      (*this)=ex; //use the default (shallow!) copy operator

      if (ex.attrs!=NULL) { //make a deep copy here

        attrs=new GffAttrs();

        attrs->copyAttrs(ex.attrs);

      }

  }



  GffExon& operator=(const GffExon& o) = default; //prevent gcc 9 warnings:

                                           //yes, I want a shallow copy here



  ~GffExon() { //destructor

     if (attrs!=NULL && !sharedAttrs) delete attrs;

  }
@@ -1015,6 +1020,8 @@ public: 
         printGxf(fout, showCDS ? pgffBoth : pgffExon, tlabel, gfparent, cvtChars);

      }

   void printExonList(FILE* fout); //print comma delimited list of exon intervals

   void printCDSList(FILE* fout); //print comma delimited list of CDS intervals



   void printBED(FILE* fout, bool cvtChars, char* dbuf, int dbuf_len);

       //print a BED-12 line + GFF3 attributes in 13th field

   void printSummary(FILE* fout=NULL);
@@ -1023,6 +1030,10 @@ public: 
           uint* cds_start=NULL, uint* cds_end=NULL, GMapSegments* seglst=NULL,

		   bool cds_open=false);

    char* getUnspliced(GFaSeqGet* faseq, int* rlen, GMapSegments* seglst=NULL);



    void addPadding(int padLeft, int padRight); //change exons to include this padding on the sides

    void removePadding(int padLeft, int padRight);



   //bool validCDS(GFaSeqGet* faseq); //has In-Frame Stop Codon ?

   bool empty() { return (start==0); }

};