/usr/include/gff.h is in libgff-dev 1.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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#define GFF_H
#include "GBase.h"
#include "gdna.h"
#include "codons.h"
#include "GFaSeqGet.h"
#include "GList.hh"
#include "GHash.hh"
//#include <boost/crc.hpp> // for boost::crc_32_type
/*
const byte exMskMajSpliceL = 0x01;
const byte exMskMajSpliceR = 0x02;
const byte exMskMinSpliceL = 0x04;
const byte exMskMinSpliceR = 0x08;
const byte exMskTag = 0x80;
*/
//reserved Gffnames::feats entries -- basic feature types
extern const int gff_fid_mRNA; // "mRNA" feature name
extern const int gff_fid_transcript; // *RNA, *transcript feature name
extern const int gff_fid_exon;
extern const uint GFF_MAX_LOCUS;
extern const uint GFF_MAX_EXON;
extern const uint GFF_MAX_INTRON;
extern const uint gfo_flag_CHILDREN_PROMOTED;
extern const uint gfo_flag_HAS_ERRORS;
extern const uint gfo_flag_IS_GENE;
extern const uint gfo_flag_HAS_GFF_ID; //found a GFF3 formatted main feature with its own ID
extern const uint gfo_flag_BY_EXON; //created by subfeature (exon) directly
//(GTF2 and some chado gff3 dumps with exons given before their mRNA)
extern const uint gfo_flag_IS_TRANSCRIPT; //recognized as '*RNA' or '*transcript'
extern const uint gfo_flag_DISCARDED; //should not be printed under the "transcriptsOnly" directive
extern const uint gfo_flag_LST_KEEP; //GffObj from GffReader::gflst is to be kept (not deallocated)
//when GffReader is destroyed
extern const uint gfo_flag_LEVEL_MSK; //hierarchical level: 0 = no parent
extern const byte gfo_flagShift_LEVEL;
extern bool gff_show_warnings;
#define GFF_LINELEN 2048
#define ERR_NULL_GFNAMES "Error: GffObj::%s requires a non-null GffNames* names!\n"
enum GffExonType {
exgffIntron=-1, // useless "intron" feature
exgffNone=0, //not a recognizable exon or CDS segment
exgffStart, //from "start_codon" feature (within CDS)
exgffStop, //from "stop_codon" feature (may be outside CDS)
exgffCDS, //from "CDS" feature
exgffUTR, //from "UTR" feature
exgffCDSUTR, //from a merge of UTR and CDS feature
exgffExon, //from "exon" feature
};
const char* strExonType(char xtype);
class GffReader;
class GffLine {
char* _parents; //stores a copy of the Parent attribute value,
//with commas replaced by \0
int _parents_len;
public:
char* dupline; //duplicate of original line
char* line; //this will have tabs replaced by \0
int llen;
char* gseqname;
char* track;
char* ftype; //feature name: mRNA/gene/exon/CDS
char* info; //the last, attributes' field, unparsed
uint fstart;
uint fend;
uint qstart; //overlap coords on query, if available
uint qend;
uint qlen; //query len, if given
double score;
char strand;
bool skip;
bool is_gff3; //if the line appears to be in GFF3 format
bool is_cds; //"cds" and "stop_codon" features
bool is_exon; //"exon" and "utr" features
char exontype; // gffExonType
bool is_transcript; //if current feature is *RNA or *transcript
bool is_gene; //if current feature is *gene
char phase; // '.' , '0', '1' or '2'
// -- allocated strings:
char* gene_name; //value of gene_name attribute (GTF) if present or Name attribute of a gene feature (GFF3)
char* gene_id; //value of gene_id attribute (GTF) if present or ID attribute of a gene feature (GFF3)
//
char** parents; //for GTF only parents[0] is used
int num_parents;
char* ID; // if a ID=.. attribute was parsed, or a GTF with 'transcript' line (transcript_id)
GffLine(GffReader* reader, const char* l); //parse the line accordingly
void discardParent() {
GFREE(_parents);
_parents_len=0;
num_parents=0;
parents=NULL;
}
char* extractAttr(const char* pre, bool caseStrict=false, bool enforce_GTF2=false);
GffLine(GffLine* l):_parents(NULL), _parents_len(0),
dupline(NULL), line(NULL), llen(0), gseqname(NULL), track(NULL),
ftype(NULL), info(NULL), fstart(0), fend(0), qstart(0), qend(0), qlen(0),
score(0), strand(0), skip(true), is_gff3(false), is_cds(false), is_exon(false),
exontype(0), is_transcript(false), is_gene(false), phase(0),
gene_name(NULL), gene_id(NULL),
parents(NULL), num_parents(0), ID(NULL) { //a copy constructor
if (l==NULL || l->line==NULL)
GError("Error: invalid GffLine(l)\n");
memcpy((void*)this, (void*)l, sizeof(GffLine));
GMALLOC(line, llen+1);
memcpy(line, l->line, llen+1);
GMALLOC(dupline, llen+1);
memcpy(dupline, l->dupline, llen+1);
//--offsets within line[]
gseqname=line+(l->gseqname-l->line);
track=line+(l->track-l->line);
ftype=line+(l->ftype-l->line);
info=line+(l->info-l->line);
if (num_parents>0 && parents) {
parents=NULL; //re-init, just copied earlier
GMALLOC(parents, num_parents*sizeof(char*));
//_parents_len=l->_parents_len; copied above
_parents=NULL; //re-init, forget pointer copy
GMALLOC(_parents, _parents_len);
memcpy(_parents, l->_parents, _parents_len);
for (int i=0;i<num_parents;i++) {
parents[i]=_parents+(l->parents[i] - l->_parents);
}
}
//-- allocated string copies:
ID=Gstrdup(l->ID);
if (l->gene_name!=NULL)
gene_name=Gstrdup(l->gene_name);
if (l->gene_id!=NULL)
gene_id=Gstrdup(l->gene_id);
}
GffLine():_parents(NULL), _parents_len(0),
dupline(NULL), line(NULL), llen(0), gseqname(NULL), track(NULL),
ftype(NULL), info(NULL), fstart(0), fend(0), qstart(0), qend(0), qlen(0),
score(0), strand(0), skip(true), is_gff3(false), is_cds(false), is_exon(false),
exontype(0), is_transcript(false), is_gene(false), phase(0),
gene_name(NULL), gene_id(NULL),
parents(NULL), num_parents(0), ID(NULL) {
}
~GffLine() {
GFREE(dupline);
GFREE(line);
GFREE(_parents);
GFREE(parents);
GFREE(ID);
GFREE(gene_name);
GFREE(gene_id);
}
};
class GffAttr {
public:
int attr_id;
char* attr_val;
GffAttr(int an_id, const char* av=NULL) {
attr_id=an_id;
attr_val=NULL;
setValue(av);
}
~GffAttr() {
GFREE(attr_val);
}
void setValue(const char* av) {
if (attr_val!=NULL) {
GFREE(attr_val);
}
if (av==NULL || av[0]==0) return;
//trim spaces
const char* vstart=av;
while (*vstart==' ') av++;
const char* vend=vstart;
bool keep_dq=false;
while (vend[1]!=0) {
if (*vend==' ' && vend[1]!=' ') keep_dq=true;
else if (*vend==';') keep_dq=true;
vend++;
}
//remove spaces at the end:
while (*vend==' ' && vend!=vstart) vend--;
//practical clean-up: if it doesn't have any internal spaces just strip those useless double quotes
if (!keep_dq && *vstart=='"' && *vend=='"') {
vend--;
vstart++;
}
attr_val=Gstrdup(vstart, vend);
}
bool operator==(GffAttr& d){
return (this==&d);
}
bool operator>(GffAttr& d){
return (this>&d);
}
bool operator<(GffAttr& d){
return (this<&d);
}
};
class GffNameList;
class GffNames;
class GffNameInfo {
friend class GffNameList;
public:
int idx;
char* name;
GffNameInfo(const char* n=NULL):idx(-1),name(NULL) {
if (n) name=Gstrdup(n);
}
~GffNameInfo() {
GFREE(name);
}
bool operator==(GffNameInfo& d){
return (strcmp(this->name, d.name)==0);
}
bool operator<(GffNameInfo& d){
return (strcmp(this->name, d.name)<0);
}
};
class GffNameList:public GList<GffNameInfo> {
friend class GffNameInfo;
friend class GffNames;
protected:
GHash<GffNameInfo> byName;//hash with shared keys
int idlast; //fList index of last added/reused name
void addStatic(const char* tname) {// fast add
GffNameInfo* f=new GffNameInfo(tname);
idlast=this->Add(f);
f->idx=idlast;
byName.shkAdd(f->name,f);
}
public:
GffNameList(int init_capacity=6):GList<GffNameInfo>(init_capacity, false,true,true), byName(false) {
idlast=-1;
setCapacity(init_capacity);
}
char* lastNameUsed() { return idlast<0 ? NULL : Get(idlast)->name; }
int lastNameId() { return idlast; }
char* getName(int nid) { //retrieve name by its ID
if (nid<0 || nid>=fCount)
GError("GffNameList Error: invalid index (%d)\n",nid);
return fList[nid]->name;
}
int addName(const char* tname) {//returns or create an id for the given name
//check idlast first, chances are it's the same feature name checked
/*if (idlast>=0 && strcmp(fList[idlast]->name,tname)==0)
return idlast;*/
GffNameInfo* f=byName.Find(tname);
int fidx=-1;
if (f!=NULL) fidx=f->idx;
else {//add new entry
f=new GffNameInfo(tname);
fidx=this->Add(f);
f->idx=fidx;
byName.shkAdd(f->name,f);
}
idlast=fidx;
return fidx;
}
int addNewName(const char* tname) {
GffNameInfo* f=new GffNameInfo(tname);
int fidx=this->Add(f);
f->idx=fidx;
byName.shkAdd(f->name,f);
return fidx;
}
int getId(const char* tname) { //only returns a name id# if found
GffNameInfo* f=byName.Find(tname);
if (f==NULL) return -1;
return f->idx;
}
int removeName() {
GError("Error: removing names from GffNameList not allowed!\n");
return -1;
}
};
class GffNames {
public:
int numrefs;
GffNameList tracks;
GffNameList gseqs;
GffNameList attrs;
GffNameList feats; //feature names: 'mRNA', 'exon', 'CDS' etc.
GffNames():tracks(),gseqs(),attrs(), feats() {
numrefs=0;
//the order below is critical!
//has to match: gff_fid_mRNA, gff_fid_exon
feats.addStatic("mRNA");//index 0=gff_fid_mRNA
feats.addStatic("transcript");//index 1=gff_fid_transcript
feats.addStatic("exon");//index 1=gff_fid_exon
//feats.addStatic("CDS"); //index 2=gff_fid_CDS
}
};
void gffnames_ref(GffNames* &n);
void gffnames_unref(GffNames* &n);
enum GffPrintMode {
pgtfAny, //print record as read
pgtfExon,
pgtfCDS,
pgffAny, //print record as read
pgffExon,
pgffCDS,
pgffBoth,
};
class GffAttrs:public GList<GffAttr> {
public:
GffAttrs():GList<GffAttr>(false,true,false) { }
void add_or_update(GffNames* names, const char* attrname, const char* val) {
int aid=names->attrs.getId(attrname);
if (aid>=0) {
//attribute found in the dictionary
for (int i=0;i<Count();i++) {
//do we have it?
if (aid==Get(i)->attr_id) {
//update the value
Get(i)->setValue(val);
return;
}
}
}
else {
aid=names->attrs.addNewName(attrname);
}
this->Add(new GffAttr(aid, val));
}
char* getAttr(GffNames* names, const char* attrname) {
int aid=names->attrs.getId(attrname);
if (aid>=0)
for (int i=0;i<Count();i++)
if (aid==Get(i)->attr_id) return Get(i)->attr_val;
return NULL;
}
char* getAttr(int aid) {
if (aid>=0)
for (int i=0;i<Count();i++)
if (aid==Get(i)->attr_id) return Get(i)->attr_val;
return NULL;
}
};
class GffExon : public GSeg {
public:
void* uptr; //for later extensions
GffAttrs* attrs; //other attributes kept for this exon
double score; // gff score column
char phase; //GFF phase column - for CDS segments only
// '.' = undefined (UTR), '0','1','2' for CDS exons
char exontype; // 1="exon" 2="cds" 3="utr" 4="stop_codon"
int qstart; // for mRNA/protein exon mappings: coordinates on query
int qend;
GffExon(int s=0, int e=0, double sc=0, char fr=0, int qs=0, int qe=0, char et=0) {
uptr=NULL;
attrs=NULL;
if (s<e) {
start=s;
end=e;
}
else {
start=e;
end=s;
}
if (qs<qe) {
qstart=qs;
qend=qe;
} else {
qstart=qe;
qend=qs;
}
score=sc;
phase=fr;
exontype=et;
} //constructor
char* getAttr(GffNames* names, const char* atrname) {
if (attrs==NULL || names==NULL || atrname==NULL) return NULL;
return attrs->getAttr(names, atrname);
}
char* getAttr(int aid) {
if (attrs==NULL) return NULL;
return attrs->getAttr(aid);
}
~GffExon() { //destructor
if (attrs!=NULL) delete attrs;
}
};
class GffCDSeg:public GSeg {
public:
char phase;
int exonidx;
};
//one GFF mRNA object -- e.g. a mRNA with its exons and/or CDS segments
class GffObj:public GSeg {
//utility segment-merging function for addExon()
void expandExon(int xovl, uint segstart, uint segend,
char exontype, double sc, char fr, int qs, int qe);
protected:
//coordinate transformation data:
uint xstart; //absolute genomic coordinates of reference region
uint xend;
char xstatus; //coordinate transform status:
//0 : (start,end) coordinates are absolute
//'+' : (start,end) coords are relative to xstart..xend region
//'-' : (start,end) are relative to the reverse complement of xstart..xend region
//--
char* gffID; // ID name for mRNA (parent) feature
char* gene_name; //value of gene_name attribute (GTF) if present or Name attribute of the parent gene feature (GFF3)
char* geneID; //value of gene_id attribute (GTF) if present or ID attribute of a parent gene feature (GFF3)
unsigned int flags;
//-- friends:
friend class GffReader;
friend class GffExon;
public:
static GffNames* names; // dictionary storage that holds the various attribute names etc.
int track_id; // index of track name in names->tracks
int gseq_id; // index of genomic sequence name in names->gseqs
int ftype_id; // index of this record's feature name in names->feats, or the special gff_fid_mRNA value
int exon_ftype_id; //index of child subfeature name in names->feats (that subfeature stored in "exons")
//if ftype_id==gff_fid_mRNA then this value is ignored
GList<GffExon> exons; //for non-mRNA entries, these can be any subfeature of type subftype_id
GPVec<GffObj> children;
GffObj* parent;
int udata; //user data, flags etc.
void* uptr; //user pointer (to a parent object, cluster, locus etc.)
GffObj* ulink; //link to another GffObj (user controlled field)
// mRNA specific fields:
bool isCDS; //just a CDS, no UTRs
bool partial; //partial CDS
uint CDstart; //CDS start coord
uint CDend; //CDS end coord
char CDphase; //initial phase for CDS start
bool hasErrors() { return ((flags & gfo_flag_HAS_ERRORS)!=0); }
void hasErrors(bool v) {
if (v) flags |= gfo_flag_HAS_ERRORS;
else flags &= ~gfo_flag_HAS_ERRORS;
}
bool hasGffID() { return ((flags & gfo_flag_HAS_GFF_ID)!=0); }
void hasGffID(bool v) {
if (v) flags |= gfo_flag_HAS_GFF_ID;
else flags &= ~gfo_flag_HAS_GFF_ID;
}
bool createdByExon() { return ((flags & gfo_flag_BY_EXON)!=0); }
void createdByExon(bool v) {
if (v) flags |= gfo_flag_BY_EXON;
else flags &= ~gfo_flag_BY_EXON;
}
bool isGene() { return ((flags & gfo_flag_IS_GENE)!=0); }
void isGene(bool v) {
if (v) flags |= gfo_flag_IS_GENE;
else flags &= ~gfo_flag_IS_GENE;
}
bool isDiscarded() { return ((flags & gfo_flag_DISCARDED)!=0); }
void isDiscarded(bool v) {
if (v) flags |= gfo_flag_DISCARDED;
else flags &= ~gfo_flag_DISCARDED;
}
bool isUsed() { return ((flags & gfo_flag_LST_KEEP)!=0); }
void isUsed(bool v) {
if (v) flags |= gfo_flag_LST_KEEP;
else flags &= ~gfo_flag_LST_KEEP;
}
bool isTranscript() { return ((flags & gfo_flag_IS_TRANSCRIPT)!=0); }
void isTranscript(bool v) {
if (v) flags |= gfo_flag_IS_TRANSCRIPT;
else flags &= ~gfo_flag_IS_TRANSCRIPT;
}
bool promotedChildren() { return ((flags & gfo_flag_CHILDREN_PROMOTED)!=0); }
void promotedChildren(bool v) {
if (v) flags |= gfo_flag_CHILDREN_PROMOTED;
else flags &= ~gfo_flag_CHILDREN_PROMOTED;
}
void setLevel(byte v) {
if (v==0) flags &= ~gfo_flag_LEVEL_MSK;
else flags &= ~(((uint)v) << gfo_flagShift_LEVEL);
}
byte incLevel() {
uint v=((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL);
v++;
flags &= ~(v << gfo_flagShift_LEVEL);
return v;
}
byte getLevel() {
return ((byte)((flags & gfo_flag_LEVEL_MSK) >> gfo_flagShift_LEVEL));
}
bool isValidTranscript() {
//return (ftype_id==gff_fid_mRNA && exons.Count()>0);
return (isTranscript() && exons.Count()>0);
}
int addExon(uint segstart, uint segend, double sc=0, char fr='.',
int qs=0, int qe=0, bool iscds=false, char exontype=0);
int addExon(GffReader* reader, GffLine* gl, bool keepAttr=false, bool noExonAttr=true);
void removeExon(int idx);
void removeExon(GffExon* p);
char strand; //true if features are on the reverse complement strand
double gscore;
double uscore; //custom, user-computed score, if needed
int covlen; //total coverage of reference genomic sequence (sum of maxcf segment lengths)
//--------- optional data:
int qlen; //query length, start, end - if available
int qstart;
int qend;
int qcov; //query coverage - percent
GffAttrs* attrs; //other gff3 attributes found for the main mRNA feature
//constructor by gff line parsing:
GffObj(GffReader* gfrd, GffLine* gffline, bool keepAttrs=false, bool noExonAttr=true);
//if gfline->Parent!=NULL then this will also add the first sub-feature
// otherwise, only the main feature is created
void copyAttrs(GffObj* from);
void clearAttrs() {
if (attrs!=NULL) {
bool sharedattrs=(exons.Count()>0 && exons[0]->attrs==attrs);
delete attrs; attrs=NULL;
if (sharedattrs) exons[0]->attrs=NULL;
}
}
GffObj(char* anid=NULL):GSeg(0,0), exons(true,true,false), children(1,false) {
//exons: sorted, free, non-unique
gffID=NULL;
uptr=NULL;
ulink=NULL;
flags=0;
udata=0;
parent=NULL;
ftype_id=-1;
exon_ftype_id=-1;
if (anid!=NULL) gffID=Gstrdup(anid);
gffnames_ref(names);
qlen=0;
qstart=0;
qend=0;
qcov=0;
partial=true;
isCDS=false;
CDstart=0; // hasCDS <=> CDstart>0
CDend=0;
CDphase=0;
gseq_id=-1;
track_id=-1;
xstart=0;
xend=0;
xstatus=0;
strand='.';
gscore=0;
uscore=0;
attrs=NULL;
covlen=0;
gene_name=NULL;
geneID=NULL;
}
~GffObj() {
GFREE(gffID);
GFREE(gene_name);
GFREE(geneID);
clearAttrs();
gffnames_unref(names);
}
//--------------
GffObj* finalize(GffReader* gfr, bool mergeCloseExons=false,
bool keepAttrs=false, bool noExonAttr=true);
//complete parsing: must be called in order to merge adjacent/close proximity subfeatures
void parseAttrs(GffAttrs*& atrlist, char* info, bool isExon=false);
const char* getSubfName() { //returns the generic feature type of the entries in exons array
//int sid=exon_ftype_id;
//if (sid==gff_fid_exon && isCDS) sid=gff_fid_CDS;
return names->feats.getName(exon_ftype_id);
}
void addCDS(uint cd_start, uint cd_end, char phase=0);
bool monoFeature() {
return (exons.Count()==0 ||
(exons.Count()==1 && //exon_ftype_id==ftype_id &&
exons[0]->end==this->end && exons[0]->start==this->start));
}
bool hasCDS() { return (CDstart>0); }
const char* getFeatureName() {
return names->feats.getName(ftype_id);
}
void setFeatureName(const char* feature);
void addAttr(const char* attrname, const char* attrvalue);
int removeAttr(const char* attrname, const char* attrval=NULL);
int removeAttr(int aid, const char* attrval=NULL);
int removeExonAttr(GffExon& exon, const char* attrname, const char* attrval=NULL);
int removeExonAttr(GffExon& exon, int aid, const char* attrval=NULL);
const char* getAttrName(int i) {
if (attrs==NULL) return NULL;
return names->attrs.getName(attrs->Get(i)->attr_id);
}
char* getAttr(const char* attrname, bool checkFirstExon=false) {
if (names==NULL || attrname==NULL) return NULL;
char* r=NULL;
if (attrs==NULL) {
if (!checkFirstExon) return NULL;
}
else r=attrs->getAttr(names, attrname);
if (r!=NULL) return r;
if (checkFirstExon && exons.Count()>0) {
r=exons[0]->getAttr(names, attrname);
}
return r;
}
char* getExonAttr(GffExon* exon, const char* attrname) {
if (exon==NULL || attrname==NULL) return NULL;
return exon->getAttr(names, attrname);
}
char* getExonAttr(int exonidx, const char* attrname) {
if (exonidx<0 || exonidx>=exons.Count() || attrname==NULL) return NULL;
return exons[exonidx]->getAttr(names, attrname);
}
char* getAttrValue(int i) {
if (attrs==NULL) return NULL;
return attrs->Get(i)->attr_val;
}
const char* getGSeqName() {
return names->gseqs.getName(gseq_id);
}
const char* getRefName() {
return names->gseqs.getName(gseq_id);
}
void setRefName(const char* newname);
const char* getTrackName() {
return names->tracks.getName(track_id);
}
bool exonOverlap(uint s, uint e) {//check if ANY exon overlaps given segment
//ignores strand!
if (s>e) Gswap(s,e);
for (int i=0;i<exons.Count();i++) {
if (exons[i]->overlap(s,e)) return true;
}
return false;
}
bool exonOverlap(GffObj& m) {//check if ANY exon overlaps given segment
//if (gseq_id!=m.gseq_id) return false;
// ignores strand and gseq_id, must check in advance
for (int i=0;i<exons.Count();i++) {
for (int j=0;j<m.exons.Count();j++) {
if (exons[i]->start>m.exons[j]->end) continue;
if (m.exons[j]->start>exons[i]->end) break;
//-- overlap if we are here:
return true;
}
}
return false;
}
int exonOverlapIdx(uint s, uint e, int* ovlen=NULL) {
//return the exons' index for the overlapping OR ADJACENT exon
//ovlen, if given, will return the overlap length
if (s>e) Gswap(s,e);
s--;e++; //to also catch adjacent exons
for (int i=0;i<exons.Count();i++) {
if (exons[i]->start>e) break;
if (s>exons[i]->end) continue;
//-- overlap if we are here:
if (ovlen!=NULL) {
s++;e--;
int ovlend= (exons[i]->end>e) ? e : exons[i]->end;
*ovlen= ovlend - ((s>exons[i]->start)? s : exons[i]->start)+1;
}
return i;
} //for each exon
*ovlen=0;
return -1;
}
int exonOverlapLen(GffObj& m) {
if (start>m.end || m.start>end) return 0;
int i=0;
int j=0;
int ovlen=0;
while (i<exons.Count() && j<m.exons.Count()) {
uint istart=exons[i]->start;
uint iend=exons[i]->end;
uint jstart=m.exons[j]->start;
uint jend=m.exons[j]->end;
if (istart>jend) { j++; continue; }
if (jstart>iend) { i++; continue; }
//exon overlap
uint ovstart=GMAX(istart,jstart);
if (iend<jend) {
ovlen+=iend-ovstart+1;
i++;
}
else {
ovlen+=jend-ovstart+1;
j++;
}
}//while comparing exons
return ovlen;
}
bool exonOverlap(GffObj* m) {
return exonOverlap(*m);
}
//---------- coordinate transformation
void xcoord(uint grstart, uint grend, char xstrand='+') {
//relative coordinate transform, and reverse-complement transform if xstrand is '-'
//does nothing if xstatus is the same already
if (xstatus) {
if (xstatus==xstrand && grstart==xstart && grend==xend) return;
unxcoord();//restore original coordinates
}
xstatus=xstrand;
xstart=grstart;
xend=grend;
if (CDstart>0) xcoordseg(CDstart, CDend);
for (int i=0;i<exons.Count();i++) {
xcoordseg(exons[i]->start, exons[i]->end);
}
if (xstatus=='-') {
exons.Reverse();
int flen=end-start;
start=xend-end+1;
end=start+flen;
}
else {
start=start-xstart+1;
end=end-xstart+1;
}
}
//transform an arbitrary segment based on current xstatus/xstart-xend
void xcoordseg(uint& segstart, uint &segend) {
if (xstatus==0) return;
if (xstatus=='-') {
int flen=segend-segstart;
segstart=xend-segend+1;
segend=segstart+flen;
return;
}
else {
segstart=segstart-xstart+1;
segend=segend-xstart+1;
}
}
void unxcoord() { //revert back to absolute genomic/gff coordinates if xstatus==true
if (xstatus==0) return; //nothing to do, no transformation appplied
if (CDstart>0) unxcoordseg(CDstart, CDend);
//restore all GffExon intervals too
for (int i=0;i<exons.Count();i++) {
unxcoordseg(exons[i]->start, exons[i]->end);
}
if (xstatus=='-') {
exons.Reverse();
int flen=end-start;
start=xend-end+1;
end=start+flen;
}
else {
start=start+xstart-1;
end=end+xstart-1;
}
xstatus=0;
}
void unxcoordseg(uint& astart, uint &aend) {
//restore an arbitrary interval -- does NOT change the transform state!
if (xstatus==0) return;
if (xstatus=='-') {
int flen=aend-astart;
astart=xend-aend+1;
aend=astart+flen;
}
else {
astart=astart+xstart-1;
aend=aend+xstart-1;
}
}
//---------------------
bool operator==(GffObj& d){
return (gseq_id==d.gseq_id && start==d.start && end==d.end && strcmp(gffID, d.gffID)==0);
}
bool operator>(GffObj& d){
if (gseq_id!=d.gseq_id) return (gseq_id>d.gseq_id);
if (start==d.start) {
if (getLevel()==d.getLevel()) {
if (end==d.end) return (strcmp(gffID, d.gffID)>0);
else return (end>d.end);
} else return (getLevel()>d.getLevel());
} else return (start>d.start);
}
bool operator<(GffObj& d){
if (gseq_id!=d.gseq_id) return (gseq_id<d.gseq_id);
if (start==d.start) {
if (getLevel()==d.getLevel()) {
if (end==d.end) return strcmp(gffID, d.gffID)<0;
else return end<d.end;
} else return (getLevel()<d.getLevel());
} else return (start<d.start);
}
char* getID() { return gffID; }
char* getGeneID() { return geneID; }
char* getGeneName() { return gene_name; }
void setGeneName(const char* gname) {
GFREE(gene_name);
if (gname) gene_name=Gstrdup(gname);
}
void setGeneID(const char* gene_id) {
GFREE(geneID);
if (gene_id) geneID=Gstrdup(gene_id);
}
int addSeg(GffLine* gfline);
int addSeg(int fnid, GffLine* gfline);
void getCDSegs(GArray<GffCDSeg>& cds);
void updateExonPhase(); //for CDS-only features, updates GExon::phase
void printGxfLine(FILE* fout, const char* tlabel, const char* gseqname,
bool iscds, uint segstart, uint segend, int exidx, char phase, bool gff3, bool cvtChars=false);
void printGxf(FILE* fout, GffPrintMode gffp=pgffExon,
const char* tlabel=NULL, const char* gfparent=NULL, bool cvtChars=false);
void printGtf(FILE* fout, const char* tlabel=NULL, bool cvtChars=false) {
printGxf(fout, pgtfAny, tlabel, NULL, cvtChars);
}
void printGff(FILE* fout, const char* tlabel=NULL,
const char* gfparent=NULL, bool cvtChars=false) {
printGxf(fout, pgffAny, tlabel, gfparent, cvtChars);
}
void printTranscriptGff(FILE* fout, char* tlabel=NULL,
bool showCDS=false, const char* gfparent=NULL, bool cvtChars=false) {
if (isValidTranscript())
printGxf(fout, showCDS ? pgffBoth : pgffExon, tlabel, gfparent, cvtChars);
}
void printSummary(FILE* fout=NULL);
void getCDS_ends(uint& cds_start, uint& cds_end);
void mRNA_CDS_coords(uint& cds_start, uint& cds_end);
char* getSpliced(GFaSeqGet* faseq, bool CDSonly=false, int* rlen=NULL,
uint* cds_start=NULL, uint* cds_end=NULL, GList<GSeg>* seglst=NULL);
char* getUnspliced(GFaSeqGet* faseq, int* rlen, GList<GSeg>* seglst);
char* getSplicedTr(GFaSeqGet* faseq, bool CDSonly=true, int* rlen=NULL);
//bool validCDS(GFaSeqGet* faseq); //has In-Frame Stop Codon ?
bool empty() { return (start==0); }
};
typedef bool GffRecFunc(GffObj* gobj, void* usrptr1, void* usrptr2);
//user callback after parsing a mapping object:
// Returns: "done with it" status:
// TRUE if gobj is no longer needed so it's FREEd upon return
// FALSE if the user needs the gobj pointer and is responsible for
// collecting and freeing all GffObj objects
//GSeqStat: collect basic stats about a common underlying genomic sequence
// for multiple GffObj
class GSeqStat {
public:
int gseqid; //gseq id in the global static pool of gseqs
char* gseqname; //just a pointer to the name of gseq
int fcount;//number of features on this gseq
uint mincoord;
uint maxcoord;
uint maxfeat_len; //maximum feature length on this genomic sequence
GffObj* maxfeat;
GSeqStat(int id=-1, char* name=NULL) {
gseqid=id;
gseqname=name;
fcount=0;
mincoord=MAXUINT;
maxcoord=0;
maxfeat_len=0;
maxfeat=NULL;
}
bool operator>(GSeqStat& g) {
return (gseqid>g.gseqid);
}
bool operator<(GSeqStat& g) {
return (gseqid<g.gseqid);
}
bool operator==(GSeqStat& g) {
return (gseqid==g.gseqid);
}
};
int gfo_cmpByLoc(const pointer p1, const pointer p2);
class GfList: public GList<GffObj> {
//just adding the option to sort by genomic sequence and coordinate
bool mustSort;
public:
GfList(bool sortbyloc=false):GList<GffObj>(false,false,false) {
//GffObjs in this list are NOT deleted when the list is cleared
//-- for deallocation of these objects, call freeAll() or freeUnused() as needed
mustSort=sortbyloc;
}
void sortedByLoc(bool v=true) {
bool prev=mustSort;
mustSort=v;
if (fCount>0 && mustSort && !prev) {
this->setSorted((GCompareProc*)gfo_cmpByLoc);
}
}
void finalize(GffReader* gfr, bool mergeCloseExons,
bool keepAttrs=false, bool noExonAttr=true);
void freeAll() {
for (int i=0;i<fCount;i++) {
delete fList[i];
fList[i]=NULL;
}
Clear();
}
void freeUnused() {
for (int i=0;i<fCount;i++) {
if (fList[i]->isUsed()) continue;
//inform the children
for (int c=0;c<fList[i]->children.Count();c++) {
fList[i]->children[c]->parent=NULL;
}
delete fList[i];
fList[i]=NULL;
}
Clear();
}
};
/*
struct GfoHolder {
//int idx; //position in GffReader::gflst array
GffObj* gffobj;
GfoHolder(GffObj* gfo=NULL) { //, int i=0) {
//idx=i;
gffobj=gfo;
}
};
*/
class CNonExon { //utility class used in subfeature promotion
public:
//int idx;
GffObj* parent;
GffExon* exon;
GffLine* gffline;
//CNonExon(int i, GffObj* p, GffExon* e, GffLine* gl) {
CNonExon(GffObj* p, GffExon* e, GffLine* gl) {
parent=p;
exon=e;
//idx=i;
gffline=new GffLine(gl);
}
~CNonExon() {
delete gffline;
}
};
class GffReader {
friend class GffObj;
friend class GffLine;
char* linebuf;
off_t fpos;
int buflen;
protected:
bool gff_warns; //warn about duplicate IDs, etc. even when they are on different chromosomes
FILE* fh;
char* fname; //optional fasta file with the underlying genomic sequence to be attached to this reader
GffLine* gffline;
bool transcriptsOnly; //keep only transcripts w/ their exon/CDS features
GHash<int> discarded_ids; //for transcriptsOnly mode, keep track
// of discarded parent IDs
GHash< GPVec<GffObj> > phash; //transcript_id+contig (Parent~Contig) => [gflst index, GffObj]
//GHash<int> tids; //just for transcript_id uniqueness
char* gfoBuildId(const char* id, const char* ctg);
//void gfoRemove(const char* id, const char* ctg);
GffObj* gfoAdd(GffObj* gfo);
GffObj* gfoAdd(GPVec<GffObj>& glst, GffObj* gfo);
// const char* id, const char* ctg, char strand, GVec<GfoHolder>** glst, uint start, uint end
GffObj* gfoFind(const char* id, const char* ctg=NULL, GPVec<GffObj>** glst=NULL,
char strand=0, uint start=0, uint end=0);
CNonExon* subfPoolCheck(GffLine* gffline, GHash<CNonExon>& pex, char*& subp_name);
void subfPoolAdd(GHash<CNonExon>& pex, GffObj* newgfo);
GffObj* promoteFeature(CNonExon* subp, char*& subp_name, GHash<CNonExon>& pex,
bool keepAttr, bool noExonAttr);
GList<GSeqStat> gseqstats; //list of all genomic sequences seen by this reader, accumulates stats
//boost::crc_32_type _crc_result;
public:
GffNames* names; //just a pointer to the global static Gff names repository in GffObj
GfList gflst; //accumulate GffObjs being read
GffObj* newGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr,
GffObj* parent=NULL, GffExon* pexon=NULL, GPVec<GffObj>* glst=NULL);
//GffObj* replaceGffRec(GffLine* gffline, bool keepAttr, bool noExonAttr, int replaceidx);
GffObj* updateGffRec(GffObj* prevgfo, GffLine* gffline,
bool keepAttr);
GffObj* updateParent(GffObj* newgfh, GffObj* parent);
bool addExonFeature(GffObj* prevgfo, GffLine* gffline, GHash<CNonExon>& pex, bool noExonAttr);
GPVec<GSeqStat> gseqStats; //only populated after finalize()
GffReader(FILE* f=NULL, bool t_only=false, bool sortbyloc=false):discarded_ids(true),
phash(true), gseqstats(true,true,true), gflst(sortbyloc), gseqStats(1, false) {
gff_warns=gff_show_warnings;
names=NULL;
gffline=NULL;
transcriptsOnly=t_only;
fpos=0;
fname=NULL;
fh=f;
GMALLOC(linebuf, GFF_LINELEN);
buflen=GFF_LINELEN-1;
}
void init(FILE *f, bool t_only=false, bool sortbyloc=false) {
fname=NULL;
fh=f;
if (fh!=NULL) rewind(fh);
fpos=0;
transcriptsOnly=t_only;
gflst.sortedByLoc(sortbyloc);
}
GffReader(char* fn, bool t_only=false, bool sort=false):discarded_ids(true), phash(true),
gseqstats(true,true,true), gflst(sort), gseqStats(1,false) {
gff_warns=gff_show_warnings;
names=NULL;
fname=Gstrdup(fn);
transcriptsOnly=t_only;
fh=fopen(fname, "rb");
fpos=0;
gffline=NULL;
GMALLOC(linebuf, GFF_LINELEN);
buflen=GFF_LINELEN-1;
}
~GffReader() {
delete gffline;
gffline=NULL;
fpos=0;
gflst.freeUnused();
gflst.Clear();
discarded_ids.Clear();
phash.Clear();
gseqstats.Clear();
GFREE(fname);
GFREE(linebuf);
}
void showWarnings(bool v=true) {
gff_warns=v;
gff_show_warnings=v;
}
GffLine* nextGffLine();
// load all subfeatures, re-group them:
void readAll(bool keepAttr=false, bool mergeCloseExons=false, bool noExonAttr=true);
//boost::crc_32_type current_crc_result() const { return _crc_result; }
}; // end of GffReader
#endif
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