ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/gclib/cuffcompare/gtf_tracking.h
Revision: 155
Committed: Wed Jan 25 21:06:46 2012 UTC (8 years, 2 months ago) by gpertea
File size: 45392 byte(s)
Log Message:
fix for a subtle XLocus building bug

Line User Rev File contents
1 gpertea 20 #ifndef GTF_TRACKING_H
2     #define GTF_TRACKING_H
3     /*
4     * gtf_tracking.h
5     * cufflinks
6     *
7     * Created by Cole Trapnell on 9/5/09.
8     * Copyright 2009 Geo Pertea. All rights reserved.
9     *
10     */
11    
12     #include "gff.h"
13     #include "GFaSeqGet.h"
14     #include "GFastaIndex.h"
15     #include "GStr.h"
16    
17    
18     #define MAX_QFILES 500
19    
20     extern bool gtf_tracking_verbose;
21    
22     extern bool gtf_tracking_largeScale;
23     //many input files, no accuracy stats are generated, no *.tmap
24     // and exon attributes are discarded
25    
26     int cmpByPtr(const pointer p1, const pointer p2);
27    
28     bool t_contains(GffObj& a, GffObj& b);
29     //returns true only IF b has fewer exons than a AND a "contains" b
30    
31     char* getGSeqName(int gseq_id);
32    
33     //genomic fasta sequence handling
34     class GFastaHandler {
35     public:
36     char* fastaPath;
37     GFastaIndex* faIdx;
38     char* getFastaFile(int gseq_id) {
39     if (fastaPath==NULL) return NULL;
40     GStr s(fastaPath);
41     s.trimR('/');
42     s.appendfmt("/%s",getGSeqName(gseq_id));
43     GStr sbase(s);
44     if (!fileExists(s.chars())) s.append(".fa");
45     if (!fileExists(s.chars())) s.append("sta");
46     if (fileExists(s.chars())) return Gstrdup(s.chars());
47     else {
48     GMessage("Warning: cannot find genomic sequence file %s{.fa,.fasta}\n",sbase.chars());
49     return NULL;
50     }
51     }
52    
53     GFastaHandler(const char* fpath=NULL) {
54     fastaPath=NULL;
55     faIdx=NULL;
56     if (fpath!=NULL && fpath[0]!=0) init(fpath);
57     }
58    
59     void init(const char* fpath) {
60     if (fpath==NULL || fpath[0]==0) return;
61     if (!fileExists(fpath))
62     GError("Error: file/directory %s does not exist!\n",fpath);
63     fastaPath=Gstrdup(fpath);
64     if (fastaPath!=NULL) {
65     if (fileExists(fastaPath)>1) { //exists and it's not a directory
66     GStr fainame(fastaPath);
67     //the .fai name might have been given directly
68     if (fainame.rindex(".fai")==fainame.length()-4) {
69     //.fai index file given directly
70     fastaPath[fainame.length()-4]=0;
71     if (!fileExists(fastaPath))
72     GError("Error: cannot find fasta file for index %s !\n", fastaPath);
73     }
74     else fainame.append(".fai");
75     //fainame.append(".fai");
76     faIdx=new GFastaIndex(fastaPath,fainame.chars());
77     GStr fainamecwd(fainame);
78     int ip=-1;
79     if ((ip=fainamecwd.rindex('/'))>=0)
80     fainamecwd.cut(0,ip+1);
81     if (!faIdx->hasIndex()) { //could not load index
82     //try current directory
83     if (fainame!=fainamecwd) {
84     if (fileExists(fainamecwd.chars())>1) {
85     faIdx->loadIndex(fainamecwd.chars());
86     }
87     }
88     } //tried to load index
89     if (!faIdx->hasIndex()) {
90     GMessage("No fasta index found for %s. Rebuilding, please wait..\n",fastaPath);
91     faIdx->buildIndex();
92     if (faIdx->getCount()==0) GError("Error: no fasta records found!\n");
93     GMessage("Fasta index rebuilt.\n");
94     FILE* fcreate=fopen(fainame.chars(), "w");
95     if (fcreate==NULL) {
96     GMessage("Warning: cannot create fasta index %s! (permissions?)\n", fainame.chars());
97     if (fainame!=fainamecwd) fcreate=fopen(fainamecwd.chars(), "w");
98     if (fcreate==NULL)
99     GError("Error: cannot create fasta index %s!\n", fainamecwd.chars());
100     }
101     if (faIdx->storeIndex(fcreate)<faIdx->getCount())
102     GMessage("Warning: error writing the index file!\n");
103     } //index created and attempted to store it
104     } //multi-fasta
105     } //genomic sequence given
106     }
107     GFaSeqGet* fetch(int gseq_id, bool checkFasta=false) {
108     if (fastaPath==NULL) return NULL;
109     //genomic sequence given
110     GFaSeqGet* faseq=NULL;
111     if (faIdx!=NULL) { //fastaPath was the multi-fasta file name
112     char* gseqname=getGSeqName(gseq_id);
113     GFastaRec* farec=faIdx->getRecord(gseqname);
114     if (farec!=NULL) {
115     faseq=new GFaSeqGet(fastaPath,farec->seqlen, farec->fpos,
116     farec->line_len, farec->line_blen);
117     faseq->loadall(); //just cache the whole sequence, it's faster
118     }
119     else {
120     GMessage("Warning: couldn't find fasta record for '%s'!\n",gseqname);
121     return NULL;
122     }
123     }
124     else //if (fileExists(fastaPath)==1)
125     {
126     char* sfile=getFastaFile(gseq_id);
127     if (sfile!=NULL) {
128     //if (gtf_tracking_verbose)
129     // GMessage("Processing sequence from fasta file '%s'\n",sfile);
130     faseq=new GFaSeqGet(sfile,checkFasta);
131     faseq->loadall();
132     GFREE(sfile);
133     }
134     } //one fasta file per contig
135     return faseq;
136     }
137    
138     ~GFastaHandler() {
139     GFREE(fastaPath);
140     delete faIdx;
141     }
142     };
143    
144    
145    
146     bool betterRef(GffObj* a, GffObj* b); //for better CovLink reference ranking
147    
148     class GLocus;
149    
150     class COvLink {
151     public:
152     static int coderank(char c) {
153     switch (c) {
154     case '=': return 0; //ichain match
155     case 'c': return 2; //containment (ichain fragment)
156     case 'j': return 4; // overlap with at least a junction match
157     case 'e': return 6; // single exon transfrag overlapping an intron of reference (possible pre-mRNA)
158     case 'o': return 8; // generic exon overlap
159     case 's': return 16; //"shadow" - an intron overlaps with a ref intron on the opposite strand
160     case 'x': return 18; // exon overlap on opposite strand (usually wrong strand mapping)
161     case 'i': return 20; // intra-intron
162     case 'p': return 90; //polymerase run
163     case 'r': return 92; //repeats
164     case 'u': return 94; //intergenic
165     case 0 : return 100;
166     default: return 96;
167     }
168     }
169     char code;
170     int rank;
171     GffObj* mrna;
172     int ovlen;
173     COvLink(char c=0,GffObj* m=NULL, int ovl=0) {
174     code=c;
175     mrna=m;
176     ovlen=ovl;
177     rank=coderank(c);
178     }
179     bool operator<(COvLink& b) {
180     if (rank==b.rank)
181     return (ovlen==b.ovlen)? betterRef(mrna, b.mrna) : (ovlen>b.ovlen);
182     else return rank<b.rank;
183     }
184     bool operator==(COvLink& b) {
185     return (rank==b.rank && mrna==b.mrna);
186     }
187     };
188    
189     class GISeg: public GSeg {
190     public:
191     GffObj* t; //pointer to the largest transcript with a segment this exact exon coordinates
192     GISeg(uint s=0,uint e=0, GffObj* ot=NULL):GSeg(s,e) { t=ot; }
193     };
194    
195     class GIArray:public GArray<GISeg> {
196     public:
197     GIArray(bool uniq=true):GArray<GISeg>(true,uniq) { }
198     int IAdd(GISeg* item) {
199     if (item==NULL) return -1;
200     int result=-1;
201     if (Found(*item, result)) {
202     if (fUnique) {
203     //cannot add a duplicate, return index of existing item
204     if (item->t!=NULL && fArray[result].t!=NULL &&
205     item->t->covlen>fArray[result].t->covlen)
206     fArray[result].t=item->t;
207     return result;
208     }
209     }
210     //Found sets result to the position where the item should be
211     idxInsert(result, *item);
212     return result;
213     }
214    
215     };
216    
217     class CEqList: public GList<GffObj> {
218     public:
219     GffObj* head;
220     CEqList():GList<GffObj>((GCompareProc*)cmpByPtr, (GFreeProc*)NULL, true) {
221     head=NULL;
222     }
223     };
224    
225     class CTData { //transcript associated data
226     public:
227     GffObj* mrna; //owner transcript
228     GLocus* locus;
229     GList<COvLink> ovls; //overlaps with other transcripts (ref vs query)
230     //-- just for ichain match tracking:
231     GffObj* eqref; //ref transcript having an ichain match
232     int qset; //qry set index (qfidx), -1 means reference dataset
233     //GffObj* eqnext; //next GffObj in the linked list of matching transfrags
234     CEqList* eqlist; //keep track of matching transfrags
235     //int eqdata; // flags for EQ list (is it a list head?)
236     // Cufflinks specific data:
237     double FPKM;
238     double conf_hi;
239     double conf_lo;
240     double cov;
241     char classcode; //the best/final classcode
242     CTData(GffObj* m=NULL, GLocus* l=NULL):ovls(true,true,true) {
243     mrna=m;
244     if (mrna!=NULL) mrna->uptr=this;
245     locus=l;
246     classcode=0;
247     eqref=NULL;
248     //eqnext=NULL;
249     eqlist=NULL;
250     //eqdata=0;
251     qset=-2;
252     FPKM=0;
253     conf_lo=0;
254     conf_hi=0;
255     cov=0;
256     }
257    
258     ~CTData() {
259     ovls.Clear();
260     //if ((eqdata & EQHEAD_TAG)!=0) delete eqlist;
261     if (isEqHead()) delete eqlist;
262     }
263    
264     //inline bool eqHead() { return ((eqdata & EQHEAD_TAG)!=0); }
265     bool isEqHead() {
266     if (eqlist==NULL) return false;
267     return (eqlist->head==this->mrna);
268     }
269    
270     void joinEqList(GffObj* m) { //add list from m
271     //list head is set to the transfrag with the lower qset#
272     CTData* md=(CTData*)(m->uptr);
273     //ASSERT(md);
274     if (eqlist==NULL) {
275     if (md->eqlist!=NULL) {
276     eqlist=md->eqlist;
277     eqlist->Add(this->mrna);
278     CTData* md_head_d=(CTData*)(md->eqlist->head->uptr);
279     if (this->qset < md_head_d->qset)
280     eqlist->head=this->mrna;
281     }
282     else { //m was not in an EQ list
283     //eqlist=new GList<GffObj>((GCompareProc*)cmpByPtr, (GFreeProc*)NULL, true);
284     eqlist=new CEqList();
285     eqlist->Add(this->mrna);
286     eqlist->Add(m);
287     md->eqlist=eqlist;
288     if (qset<md->qset) eqlist->head=this->mrna;
289     else eqlist->head=m;
290     }
291     }//no eqlist before
292     else { //merge two eqlists
293     if (eqlist==md->eqlist) //already in the same eqlist, nothing to do
294     return;
295     if (md->eqlist!=NULL) { //copy elements of m's eqlist
296     //copy the smaller list into the larger one
297     CEqList* srclst, *destlst;
298     if (md->eqlist->Count()<eqlist->Count()) {
299     srclst=md->eqlist;
300     destlst=eqlist;
301     }
302     else {
303     srclst=eqlist;
304     destlst=md->eqlist;
305     }
306     for (int i=0;i<srclst->Count();i++) {
307     destlst->Add(srclst->Get(i));
308     CTData* od=(CTData*)((*srclst)[i]->uptr);
309     od->eqlist=destlst;
310     //od->eqdata=od->qset+1;
311     }
312     this->eqlist=destlst;
313     CTData* s_head_d=(CTData*)(srclst->head->uptr);
314     CTData* d_head_d=(CTData*)(destlst->head->uptr);
315     if (s_head_d->qset < d_head_d->qset )
316     this->eqlist->head=srclst->head;
317     delete srclst;
318     }
319     else { //md->eqlist==NULL
320     eqlist->Add(m);
321     md->eqlist=eqlist;
322     CTData* head_d=(CTData*)(eqlist->head->uptr);
323     if (md->qset<head_d->qset)
324     eqlist->head=m;
325     }
326     }
327     }
328    
329     void addOvl(char code,GffObj* target=NULL, int ovlen=0) {
330     ovls.AddIfNew(new COvLink(code, target, ovlen));
331     }
332     char getBestCode() {
333     return (ovls.Count()>0) ? ovls[0]->code : 0 ;
334     }
335     bool operator<(CTData& b) { return (mrna < b.mrna); }
336     bool operator==(CTData& b) { return (mrna==b.mrna); }
337     };
338    
339     class GSuperLocus;
340     class GTrackLocus;
341     class GXLocus;
342    
343     //Data structure holding a query locus data (overlapping mRNAs on the same strand)
344     // and also the accuracy data of all mRNAs of a query locus
345     // (against all reference loci overlapping the same region)
346     class GLocus:public GSeg {
347     public:
348     int gseq_id; //id of underlying genomic sequence
349     int qfidx; // for locus tracking
350     GTrackLocus* t_ptr; //for locus tracking cluster
351     GffObj* mrna_maxcov; //transcript with maximum coverage (for main "ref" transcript)
352     GffObj* mrna_maxscore; //transcript with maximum gscore (for major isoform)
353     GList<GffObj> mrnas; //list of transcripts (isoforms) for this locus
354     GArray<GSeg> uexons; //list of unique exons (covered segments) in this region
355     GArray<GSeg> mexons; //list of merged exons in this region
356     GIArray introns;
357     GList<GLocus> cmpovl; //temp list of overlapping qry/ref loci to compare to (while forming superloci)
358    
359     //only for reference loci --> keep track of all superloci found for each qry dataset
360     // which contain this reference locus
361     GList<GSuperLocus>* superlst;
362     GXLocus* xlocus; //superlocus formed by exon overlaps across all qry datasets
363     // -- if genomic sequence was given:
364     int spl_major; // number of GT-AG splice site consensi
365     int spl_rare; // number of GC-AG, AT-AC and other rare splice site consensi
366     int spl_wrong; //number of "wrong" (unrecognized) splice site consensi
367     int ichains; //number of multi-exon mrnas
368     int ichainTP;
369     int ichainATP;
370     int mrnaTP;
371     int mrnaATP;
372     int v; //user flag/data
373     GLocus(GffObj* mrna=NULL, int qidx=-1):mrnas(true,false,false),uexons(true,true),mexons(true,true),
374     introns(), cmpovl(true,false,true) {
375     //this will NOT free mrnas!
376     ichains=0;
377     gseq_id=-1;
378     qfidx=qidx;
379     t_ptr=NULL;
380     creset();
381     xlocus=NULL;
382     mrna_maxcov=NULL;
383     mrna_maxscore=NULL;
384     superlst=new GList<GSuperLocus>(true,false,false);
385     if (mrna!=NULL) {
386     start=mrna->exons.First()->start;
387     end=mrna->exons.Last()->end;;
388     gseq_id=mrna->gseq_id;
389     GISeg seg;
390     for (int i=0;i<mrna->exons.Count();i++) {
391     seg.start=mrna->exons[i]->start;
392     seg.end=mrna->exons[i]->end;
393     uexons.Add(seg);
394     mexons.Add(seg);
395     if (i>0) {
396     seg.start=mrna->exons[i-1]->end+1;
397     seg.end=mrna->exons[i]->start-1;
398     seg.t=mrna;
399     introns.Add(seg);
400     }
401     }
402     mrnas.Add(mrna);
403     if (mrna->exons.Count()>1) ichains++;
404     ((CTData*)(mrna->uptr))->locus=this;
405     mrna_maxscore=mrna;
406     mrna_maxcov=mrna;
407     }
408     }
409     ~GLocus() {
410     delete superlst;
411     }
412     void creset() {
413     spl_major=0;spl_rare=0;spl_wrong=0;
414     v=0; //visited/other data
415     ichainTP=0;
416     ichainATP=0;
417     mrnaTP=0;
418     mrnaATP=0;
419     cmpovl.Clear();
420     }
421    
422     void addMerge(GLocus& locus, GffObj* lnkmrna) {
423     //add all the elements of the other locus (merging)
424     //-- merge mexons
425     GArray<int> ovlexons(true,true); //list of locus.mexons indexes overlapping existing mexons
426     int i=0; //index of first mexons with a merge
427     int j=0; //index current mrna exon
428     while (i<mexons.Count() && j<locus.mexons.Count()) {
429     uint istart=mexons[i].start;
430     uint iend=mexons[i].end;
431     uint jstart=locus.mexons[j].start;
432     uint jend=locus.mexons[j].end;
433     if (iend<jstart) { i++; continue; }
434     if (jend<istart) { j++; continue; }
435     //if (mexons[i].overlap(jstart, jend)) {
436     //exon overlap was found :
437     ovlexons.Add(j);
438     //extend mexons[i] as needed
439     if (jstart<istart) mexons[i].start=jstart;
440     if (jend>iend) { //mexons[i] end extend
441     mexons[i].end=jend;
442     //now this could overlap the next mexon(s), so we have to merge them all
443     while (i<mexons.Count()-1 && mexons[i].end>mexons[i+1].start) {
444     uint nextend=mexons[i+1].end;
445     mexons.Delete(i+1);
446     if (nextend>mexons[i].end) {
447     mexons[i].end=nextend;
448     break; //no need to check next mexons
449     }
450     } //while next mexons merge
451     } // mexons[i] end extend
452     // } //exon overlap
453     j++; //check the next locus.mexon
454     }
455     //-- add the rest of the non-overlapping mexons:
456     GSeg seg;
457     for (int i=0;i<locus.mexons.Count();i++) {
458     seg.start=locus.mexons[i].start;
459     seg.end=locus.mexons[i].end;
460     if (!ovlexons.Exists(i)) mexons.Add(seg);
461     }
462     // -- merge uexons
463     //add to uexons:
464     for (int i=0;i<locus.uexons.Count();i++) {
465     uexons.Add(locus.uexons[i]);
466     }
467     for (int i=0;i<locus.introns.Count();i++) {
468     introns.IAdd(&(locus.introns[i]));
469     }
470    
471     // -- add locus.mrnas
472     for (int i=0;i<locus.mrnas.Count();i++) {
473     ((CTData*)(locus.mrnas[i]->uptr))->locus=this;
474     if (locus.mrnas[i]!=lnkmrna) {
475     mrnas.Add(locus.mrnas[i]);
476     if (locus.mrnas[i]->exons.Count()>1) ichains++;
477     }
478     }
479     // -- adjust start/end as needed
480     if (start>locus.start) start=locus.start;
481     if (end<locus.end) end=locus.end;
482     if (mrna_maxcov->covlen<locus.mrna_maxcov->covlen)
483     mrna_maxcov=locus.mrna_maxcov;
484     if (mrna_maxscore->gscore<locus.mrna_maxscore->gscore)
485     mrna_maxscore=locus.mrna_maxscore;
486     }
487    
488    
489     bool exonOverlap(GLocus& loc) {
490     //check if any mexons overlap!
491     int i=0;
492     int j=0;
493     while (i<mexons.Count() && j<loc.mexons.Count()) {
494     uint istart=mexons[i].start;
495     uint iend=mexons[i].end;
496     uint jstart=loc.mexons[j].start;
497     uint jend=loc.mexons[j].end;
498     if (iend<jstart) { i++; continue; }
499     if (jend<istart) { j++; continue; }
500     //exon overlap found if we're here:
501     return true;
502     }
503     return false;
504     }
505    
506     bool add_mRNA(GffObj* mrna) {
507     if (mrnas.Count()>0 && mrna->gseq_id!=gseq_id) return false; //mrna must be on the same genomic seq
508     //check for exon overlap with existing mexons
509     //also update uexons and mexons accordingly, if mrna is added
510     uint mrna_start=mrna->exons.First()->start;
511     uint mrna_end=mrna->exons.Last()->end;
512     if (mrna_start>end || start>mrna_end) return false;
513     bool hasovl=false;
514     int i=0; //index of first mexons with a merge
515     int j=0; //index current mrna exon
516     GArray<int> ovlexons(true,true); //list of mrna exon indexes overlapping mexons
517     while (i<mexons.Count() && j<mrna->exons.Count()) {
518     uint istart=mexons[i].start;
519     uint iend=mexons[i].end;
520     uint jstart=mrna->exons[j]->start;
521     uint jend=mrna->exons[j]->end;
522     if (iend<jstart) { i++; continue; }
523     if (jend<istart) { j++; continue; }
524     //exon overlap found if we're here:
525     ovlexons.Add(j);
526     hasovl=true;
527     //extend mexons[i] as needed
528     if (jstart<istart) mexons[i].start=jstart;
529     if (jend>iend) { //mexon stretch up
530     mexons[i].end=jend;
531     //now this could overlap the next mexon(s), so we have to merge them all
532     while (i<mexons.Count()-1 && mexons[i].end>mexons[i+1].start) {
533     uint nextend=mexons[i+1].end;
534     mexons.Delete(i+1);
535     if (nextend>mexons[i].end) {
536     mexons[i].end=nextend;
537     break; //no need to check next mexons
538     }
539     } //while next mexons merge
540     } //possible mexons merge
541    
542     j++; //check the next mrna exon
543     }//all vs all exon check loop
544     if (hasovl) {
545     GSeg seg;
546     //add the rest of the non-overlapping exons,
547     // and also to uexons etc.
548     for (int i=0;i<mrna->exons.Count();i++) {
549     seg.start=mrna->exons[i]->start;
550     seg.end=mrna->exons[i]->end;
551     if (!ovlexons.Exists(i)) mexons.Add(seg);
552     uexons.Add(seg);
553     GISeg iseg;
554     if (i>0) {
555     iseg.start=mrna->exons[i-1]->end+1;
556     iseg.end=mrna->exons[i]->start-1;
557     iseg.t=mrna;
558     introns.Add(iseg);
559     }
560     }
561    
562     mrnas_add(mrna);
563     // add to mrnas
564     ((CTData*)mrna->uptr)->locus=this;
565     gseq_id=mrna->gseq_id;
566     if (mrna->exons.Count()>1) ichains++;
567     }
568     return hasovl;
569     }
570    
571     //simpler,basic adding of a mrna
572     void mrnas_add(GffObj* mrna) {
573     mrnas.Add(mrna);
574     // adjust start/end
575     if (start>mrna->start) start=mrna->start;
576     if (end<mrna->end) end=mrna->end;
577     if (mrna_maxcov->covlen<mrna->covlen) mrna_maxcov=mrna;
578     if (mrna_maxscore->gscore<mrna->gscore) mrna_maxscore=mrna;
579     }
580     };
581    
582     class GSuperLocus;
583     class GTrackLocus;
584    
585     class GSuperLocus : public GSeg {
586     public:
587     int qfidx; //index of query dataset/file for which this superlocus was created
588     GList<GLocus> qloci;
589     GList<GLocus> rloci;
590     GList<GffObj> qmrnas; //list of transcripts (isoforms) for this locus
591     GArray<GSeg> qmexons; //list of merged exons in this region
592     GArray<GSeg> quexons; //list of unique exons (covered segments) in this region
593     GIArray qintrons; //list of unique exons (covered segments) in this region
594     //same lists for reference:
595     GList<GffObj> rmrnas; //list of transcripts (isoforms) for this locus
596     GArray<GSeg> rmexons; //list of merged exons in this region
597     GArray<GSeg> ruexons; //list of unique exons (covered segments) in this region
598     GArray<GISeg> rintrons; //list of unique exons (covered segments) in this region
599     // store problematic introns for printing:
600     GIArray i_missed; //missed reference introns (not overlapped by any qry intron)
601     GIArray i_notp; //wrong ref introns (one or both ends not matching any qry intron)
602     //
603     GIArray i_qwrong; //totally wrong qry introns (not overlapped by any ref intron)
604     GIArray i_qnotp; //imperfect qry introns (may overlap but has no "perfect" match)
605    
606    
607     int qbases_all;
608     int rbases_all; //in fact, it's all ref bases overlapping any query loci
609     int in_rmrnas; //count of ALL ref mrnas and loci given for this region
610     int in_rloci; //not just those overlapping qry data
611     // this will keep track of total qry loci, mrnas and exons in an area
612     int total_superloci;
613     int total_qloci;
614     int total_qloci_alt; //total qloci with multiple transcripts
615    
616     int total_qmrnas;
617     int total_qichains; //multi exon mrnas
618     int total_qexons; //unique exons
619     int total_qmexons;
620     int total_qintrons; //unique introns
621     // these ref totals are in fact only limited to data from
622     // loci overlapping any of qry loci
623     int total_rmexons;
624     int total_richains; //multi exon mrnas
625     int total_rloci;
626     int total_rmrnas;
627     int total_rexons;
628     int total_rintrons; //unique introns
629    
630     //--- accuracy data after compared to ref loci:
631 gpertea 118 int locusQTP;
632     int locusTP;
633     int locusAQTP;
634 gpertea 20 int locusATP; // 1 if ichainATP + mrnaATP > 0
635     int locusFP;
636     int locusAFP;
637     int locusAFN;
638     int locusFN;
639     //---transcript level accuracy -- all exon coordinates should match (most stringent)
640     int mrnaTP; // number of qry mRNAs with perfect match with ref transcripts
641     int mrnaFP; // number of qry mRNAs with no perfect match with a ref transcript
642     int mrnaFN; // number of ref mRNAs in this region having no perfect match with a qry transcript
643     int mrnaATP;
644     int mrnaAFN;
645     int mrnaAFP;
646     //---intron level accuracy (comparing the ordered set of splice sites):
647     int ichainTP; // number of qry intron chains covering a reference intron chain
648     // (covering meaning that the ordered set of reference splice sites
649     // is the same with a ordered subset of the query splice sites)
650     int ichainFP; // number of qry intron chains not covering a reference intron chain
651     int ichainFN; // number of ref intron chains in this region not being covered by a reference intron chain
652     // same as above, but approximate -- allowing a 10bp distance error for splice sites
653     int ichainATP;
654     int ichainAFP;
655     int ichainAFN;
656     //---projected features ---
657     //---exon level accuracy:
658     int exonTP; //number of perfectly overlapping exons (true positives)
659     int exonFP; //number of exons of query with no perfect match with a reference exon
660     int exonFN; //number of exons of reference with no perfect match with a query exon
661     // same as the above but with acceptable approximation (10bp error window):
662     int exonATP;
663     int exonAFP;
664     int exonAFN;
665    
666     int intronTP; //number of perfectly overlapping introns (true positives)
667     int intronFP; //number of introns of query with no perfect match with a reference intron
668     int intronFN; //number of introns of reference with no perfect match with a query intron
669     // same as the above but with acceptable approximation (10bp error window):
670     int intronATP;
671     int intronAFP;
672     int intronAFN;
673    
674     //-- EGASP added these too:
675     int m_exons; //number of exons totally missed (not overlapped *at all* by any query exon)
676     int w_exons; //numer of totally wrong exons (query exons not overlapping *at all* any reference exon)
677     int m_introns; //number of introns totally missed (not overlapped *at all* by any query intron)
678     int w_introns; //numer of totally wrong introns (query introns not overlapping *at all* any reference intron)
679     int m_loci; //missed loci
680     int w_loci; //novel/wrong loci
681     //---base level accuracy
682     int baseTP; //number of overlapping bases
683     int baseFP; //number of qry bases not overlapping reference
684     int baseFN; //number of ref bases not overlapping qry
685     // sorted,free,unique sorted,unique
686     GSuperLocus(uint lstart=0,uint lend=0):qloci(true,false,false),rloci(true,false,false),
687     qmrnas(true,false,false), qmexons(true,false), quexons(true,false), qintrons(false),
688     rmrnas(true,false,false), rmexons(true,false), ruexons(true,false), rintrons(false),
689     i_missed(false),i_notp(false), i_qwrong(false), i_qnotp(false){
690     qfidx=-1;
691     start=lstart;
692     end=lend;
693     qbases_all=0;
694     rbases_all=0;
695     baseTP=0;baseFP=0;baseFN=0;
696 gpertea 118 locusTP=0;locusQTP=0; locusAQTP=0; locusATP=0;
697 gpertea 20 locusFP=0;locusAFP=0;locusAFN=0;
698     locusFN=0;
699     in_rmrnas=0;
700     in_rloci=0;
701     w_loci=0;
702     m_loci=0;
703     total_superloci=0;
704     mrnaTP=0;mrnaFP=0;mrnaFN=0;
705     mrnaATP=0;mrnaAFP=0;mrnaAFN=0;
706     ichainTP=0;ichainFP=0;ichainFN=0;
707     ichainATP=0;ichainAFP=0;ichainAFN=0;
708     exonTP=0;exonFP=0;exonFN=0;
709     exonATP=0;exonAFP=0;exonAFN=0;
710     intronTP=0;intronFP=0;intronFN=0;
711     intronATP=0;intronAFP=0;intronAFN=0;
712     total_rmexons=0;
713     total_qmexons=0;
714     total_qexons=0;total_qloci=0;total_qmrnas=0;
715     total_qloci_alt=0;
716     total_qintrons=0;total_qichains=0;
717     total_rexons=0;total_rloci=0;total_rmrnas=0;
718     total_rintrons=0;total_richains=0;
719     w_exons=0;
720     m_exons=0;
721     w_introns=0;
722     m_introns=0;
723     }
724     void addQlocus(GLocus& loc) {
725     if (start==0 || start>loc.start) start=loc.start;
726     if (end<loc.end) end=loc.end;
727     qloci.Add(&loc);
728     total_qloci++;
729     if (loc.ichains>0 && loc.mrnas.Count()>1)
730     total_qloci_alt++;
731     qmrnas.Add(loc.mrnas);
732     total_qmrnas+=loc.mrnas.Count();
733     total_qichains+=loc.ichains;
734     qmexons.Add(loc.mexons);
735     total_qmexons+=loc.mexons.Count();
736     quexons.Add(loc.uexons);
737     total_qexons+=loc.uexons.Count();
738     qintrons.Add(loc.introns);
739     total_qintrons+=loc.introns.Count();
740     }
741     void addRlocus(GLocus& loc) {
742     if (start==0 || start>loc.start) start=loc.start;
743     if (end<loc.end) end=loc.end;
744     rloci.Add(&loc);
745     total_rloci++;
746     rmrnas.Add(loc.mrnas);
747     total_rmrnas+=loc.mrnas.Count();
748     total_richains+=loc.ichains;
749     rmexons.Add(loc.mexons);
750     total_rmexons+=loc.mexons.Count();
751     ruexons.Add(loc.uexons);
752     total_rexons+=loc.uexons.Count();
753     rintrons.Add(loc.introns);
754     total_rintrons+=loc.introns.Count();
755     }
756    
757     void calcF() {
758     // base level
759     baseFP=qbases_all-baseTP;
760     baseFN=rbases_all-baseTP;
761     //exon level:
762     exonAFP=total_qexons-exonATP;
763     exonFP=total_qexons-exonTP;
764     exonAFN=total_rexons-exonATP;
765     exonFN=total_rexons-exonTP;
766     //intron stats
767     intronAFP=total_qintrons-intronATP;
768     intronFP=total_qintrons-intronTP;
769     intronAFN=total_rintrons-intronATP;
770     intronFN=total_rintrons-intronTP;
771    
772     // ichain and transcript levels:
773     ichainAFP=total_qichains-ichainATP;
774     ichainFP=total_qichains-ichainTP;
775     ichainAFN=total_richains-ichainATP;
776     ichainFN=total_richains-ichainTP;
777     mrnaFP=total_qmrnas-mrnaTP;
778     mrnaFN=total_rmrnas-mrnaTP;
779     mrnaAFP=total_qmrnas-mrnaATP;
780     mrnaAFN=total_rmrnas-mrnaATP;
781     // locus/gene level:
782 gpertea 118 locusAFP=total_qloci-locusAQTP;
783     locusFP=total_qloci-locusQTP;
784 gpertea 20 locusAFN=total_rloci-locusATP;
785     locusFN=total_rloci-locusTP;
786     }
787    
788     void addStats(GSuperLocus& s) {
789     in_rmrnas+=s.in_rmrnas;
790     in_rloci+=s.in_rloci;
791     baseTP+=s.baseTP;
792     exonTP+=s.exonTP;
793     exonATP+=s.exonATP;
794     intronTP+=s.intronTP;
795     intronATP+=s.intronATP;
796     ichainTP+=s.ichainTP;
797     ichainATP+=s.ichainATP;
798     mrnaTP+=s.mrnaTP;
799     mrnaATP+=s.mrnaATP;
800     locusTP+=s.locusTP;
801 gpertea 118 locusQTP+=s.locusQTP;
802 gpertea 20 locusATP+=s.locusATP;
803 gpertea 118 locusAQTP+=s.locusAQTP;
804 gpertea 20 m_exons+=s.m_exons;
805     w_exons+=s.w_exons;
806     m_introns+=s.m_introns;
807     w_introns+=s.w_introns;
808     if (s.total_superloci==0 && s.qloci.Count()>0) s.total_superloci=1;
809     total_superloci+=s.total_superloci;
810     qbases_all+=s.qbases_all;
811     rbases_all+=s.rbases_all;
812     m_loci+=s.m_loci;
813     w_loci+=s.w_loci;
814     total_qexons+=s.total_qexons;
815     total_qintrons+=s.total_qintrons;
816     total_qmexons+=s.total_qmexons;
817     total_rexons+=s.total_rexons;
818     total_rintrons+=s.total_rintrons;
819     total_rmexons+=s.total_rmexons;
820     total_qmrnas+=s.total_qmrnas;
821     total_qichains+=s.total_qichains;
822     total_rmrnas+=s.total_rmrnas;
823     total_richains+=s.total_richains;
824     total_qloci+=s.total_qloci;
825     total_qloci_alt+=s.total_qloci_alt;
826     total_rloci+=s.total_rloci;
827     }
828     };
829    
830     class GSeqData {
831     int gseq_id;
832     public:
833     const char* gseq_name;
834     GList<GffObj> refs_f; //forward strand mRNAs
835     GList<GffObj> refs_r; //reverse strand mRNAs
836     GList<GffObj> mrnas_f; //forward strand mRNAs
837     GList<GffObj> mrnas_r; //reverse strand mRNAs
838     GList<GLocus> loci_f; //forward strand loci
839     GList<GLocus> loci_r; //reverse strand loci
840     //--> the fields below are not used by reference data --
841     GList<GSuperLocus> gstats_f; //stats for forward strand superloci
842     GList<GSuperLocus> gstats_r; //stats for reverse strand superloci
843     GList<GLocus> nloci_f; //"novel" loci on forward strand
844     GList<GLocus> nloci_r; //"novel" loci on reverse strand
845     GList<GffObj> umrnas; //unknown orientation mrnas
846     GList<GLocus> nloci_u; //"novel" loci with no orientation found
847    
848     GList<CTData> tdata; //transcript data (uptr holder for all mrnas here)
849    
850     int get_gseqid() { return gseq_id; }
851    
852     //--<
853     GSeqData(int gid=-1):mrnas_f(true,true,false),mrnas_r(true,true,false),
854     loci_f(true,true,true),loci_r(true,true,true),
855     gstats_f(true,true,false),gstats_r(true,true,false),
856     nloci_f(true,false,true), nloci_r(true,false,true),
857     umrnas(true,true,false), nloci_u(true,true,true), tdata(false,true,false) {
858     gseq_id=gid;
859     if (gseq_id>=0)
860     gseq_name=GffObj::names->gseqs.getName(gseq_id);
861     }
862     bool operator==(GSeqData& d){
863     return (gseq_id==d.gseq_id);
864     }
865     bool operator>(GSeqData& d){
866     return (gseq_id>d.gseq_id);
867     }
868     bool operator<(GSeqData& d){
869     return (gseq_id<d.gseq_id);
870     }
871     };
872    
873    
874     // a group of qry loci and a transcript cluster for a single qry dataset
875     class GQCluster : public GList<GffObj> {
876     public:
877     GffObj* mrna_maxcov; //transcript with maximum coverage (for largest transcript)
878     GffObj* mrna_maxscore; //transcript with maximum gscore ( = major isoform for Cufflinks)
879     uint start;
880     uint end;
881     GList<GLocus> qloci;
882     //GCluster cl; //just a more compact way of keeping all transcripts in these loci
883     GQCluster(GList<GLocus>* loci=NULL):GList<GffObj>(true,false,false),
884     qloci(true,false,false) {
885     mrna_maxcov=NULL;
886     mrna_maxscore=NULL;
887     start=0;
888     end=0;
889     if (loci!=NULL) {
890     qloci.Add(*loci);
891     for (int i=0;i<loci->Count();i++) {
892     addLocus(loci->Get(i),false);
893     }
894     }
895     }
896     void addLocus(GLocus* loc, bool toLoci=true) {
897     //check so we don't add locus duplicates
898     if (toLoci) {
899     for (int i=0;i<qloci.Count();i++) {
900     if (loc==qloci[i]) return;
901     }
902     qloci.Add(loc);
903     }
904     for (int m=0;m<loc->mrnas.Count();m++) {
905     GffObj* mrna=loc->mrnas[m];
906     Add(mrna);
907     if (start==0 || start>mrna->start) start=mrna->start;
908     if (end<mrna->end) end=mrna->end;
909     if (mrna_maxcov==NULL || mrna_maxcov->covlen<mrna->covlen) mrna_maxcov=mrna;
910     if (mrna_maxscore==NULL || mrna_maxscore->gscore<mrna->gscore) mrna_maxscore=mrna;
911     }
912     }
913     };
914    
915     //track a set of clustered qloci across multiple qry datasets
916     // the qloci in qcls[] overlap but not necessarily at exon level
917     // (so there can be multiple genes here in fact)
918     class GTrackLocus:public GSeg {
919     public:
920     char strand;
921     bool hasQloci;
922     //GLocus* rloc; //corresponding reference locus, if available
923     GList<GLocus> rloci; //ref loci found overlapping this region
924     GQCluster* qcls[MAX_QFILES]; //all qloci for this superlocus, grouped by dataset
925     GTrackLocus(GLocus* qloc=NULL, int q=-1):GSeg(0,0),rloci(true,false,true) {
926     strand='.';
927     for (int i=0;i<MAX_QFILES;i++) qcls[i]=NULL;
928     if (qloc!=NULL) addQLocus(qloc,q);
929     }
930    
931     void addRLocus(GLocus* rl) {
932     if (rl==NULL) return;
933     if (rl->qfidx>=0)
934     GError("Error: GTrackLocus::addRLocus called with a query locus (set# %d)\n",
935     rl->qfidx+1);
936     if (strand=='.') strand=rl->mrna_maxcov->strand;
937     if (start==0 || start>rl->start) start=rl->start;
938     if (end==0 || end<rl->end) end=rl->end;
939     rl->t_ptr=this;
940     rloci.Add(rl);
941     }
942    
943     void addQLocus(GLocus* loc, int q=-1) { //adding qry locus
944     if (loc==NULL) return;
945     if (strand=='.' && loc->mrna_maxcov->strand!='.')
946     strand=loc->mrna_maxcov->strand;
947     if (loc->qfidx<0 && q<0)
948     GError("Error at GTrackLocus::addQLocus(): locus.qfidx not set and index not given!\n");
949     if (q>=0) loc->qfidx=q;
950     else q=loc->qfidx;
951     if (start==0 || start>loc->start) start=loc->start;
952     if (end==0 || end<loc->end) end=loc->end;
953     if (qcls[q]==NULL) qcls[q]=new GQCluster();
954     hasQloci=true;
955     loc->t_ptr = this;
956     qcls[q]->addLocus(loc);
957     }
958    
959     bool add_Locus(GLocus* loc) {
960     if (start==0 || overlap(*loc)) { //simple range overlap, not exon overlap
961     if (loc->qfidx<0) addRLocus(loc);
962     else addQLocus(loc);
963     return true;
964     }
965     return false;
966     }
967    
968    
969     void addQCl(int q, GQCluster* qcl, GLocus* lnkloc) {
970     for (int i=0;i<qcl->qloci.Count();i++) {
971     GLocus* loc=qcl->qloci[i];
972 gpertea 155 if (loc==lnkloc) continue; // or if loc->t_ptr==this ?
973 gpertea 20 hasQloci=true;
974     loc->t_ptr=this;
975     qcls[q]->addLocus(loc);
976     }
977     }
978    
979     void addMerge(GTrackLocus* loctrack, int qcount, GLocus* lnkloc) {
980     if (loctrack==NULL) return;
981     //merge qloci
982     for (int q=0; q < qcount; q++) {
983     if (qcls[q]==NULL) {
984     if (loctrack->qcls[q]!=NULL) {
985     qcls[q]=loctrack->qcls[q];
986     loctrack->qcls[q]=NULL; //just move pointer here
987     //set all t_ptr pointers for moved loci
988     for (int ql = 0; ql < qcls[q]->qloci.Count(); ql++) {
989     qcls[q]->qloci[ql]->t_ptr=this;
990     }
991     hasQloci=true;
992     }
993     }
994     else //existing qloci at q
995     if (loctrack->qcls[q]!=NULL) { //merge elements
996     addQCl(q, loctrack->qcls[q], lnkloc);
997     }
998     }//for each qset
999     //merge rloci, if any
1000     if (loctrack->rloci.Count()>0) {
1001     for (int l=0;l<loctrack->rloci.Count();l++) {
1002     if (loctrack->rloci[l]!=lnkloc && loctrack->rloci[l]->t_ptr!=this) {
1003     rloci.Add(loctrack->rloci[l]);
1004     loctrack->rloci[l]->t_ptr=this;
1005     }
1006     }
1007     }
1008     if (loctrack->start<start) start=loctrack->start;
1009     if (loctrack->end>end) end=loctrack->end;
1010     if (strand=='.' && loctrack->strand!='.') strand=loctrack->strand;
1011     }
1012    
1013     /*
1014     void add_QLoci(GList<GLocus>* loci, int q, GLocus& r) {
1015     // only add loci overlapping given refloc
1016     //rloc=&r;
1017     if (loci==NULL) return;
1018     for (int i=0;i<loci->Count();i++) {
1019     GLocus* loc=loci->Get(i);
1020     // if (!loc->exonOverlap(r)) continue; //do we really needed exon overlap?
1021     if (!loc->overlap(r)) continue;
1022     if (start==0 || start>loc->start) start=loc->start;
1023     if (end==0 || end<loc->end) end=loc->end;
1024     loc->t_ptr=this;
1025     loc->qfidx=q;
1026     if (qcls[q]==NULL) qcls[q]=new GQCluster();
1027     qcls[q]->addLocus(loc);
1028     }
1029     strand=r.mrnas[0]->strand;
1030     }
1031     */
1032     ~GTrackLocus() {
1033     for (int q=0;q<MAX_QFILES;q++)
1034     if (qcls[q]!=NULL) { delete qcls[q]; qcls[q]=NULL; }
1035     }
1036    
1037     GQCluster* operator[](int q) {
1038     if (q<0 || q>=MAX_QFILES)
1039     GError("Error: qfidx index out of bounds (%d) for GTrackLocus!\n",q);
1040     return qcls[q];
1041     }
1042     };
1043    
1044     class GXConsensus:public GSeg {
1045     public:
1046     static int count;
1047     int id; //XConsensus ID
1048     int tss_id; //group id for those xconsensi with shared first exon
1049     int p_id; //group id for those xconsensi with "similar" protein
1050     GffObj* tcons; //longest transcript to represent the combined "consensus" structure
1051     GffObj* ref; //overlapping reference transcript
1052     char refcode; // the code for ref relationship (like in the tracking file)
1053     char* aa;
1054     int aalen;
1055     GXConsensus* contained; //if contained into another GXConsensus
1056     //list of ichain-matching query (cufflinks) transcripts that contributed to this consensus
1057     GList<GffObj> qchain;
1058     GXConsensus(GffObj* c, CEqList* qlst, GffObj* r=NULL, char rcode=0)
1059     :qchain(false,false,false) {
1060     ref=r;
1061     refcode=rcode;
1062     tcons=c;
1063     if (qlst!=NULL) qchain.Add(*((GList<GffObj>*)qlst));
1064     else qchain.Add(c);
1065     count++;
1066     tss_id=0;
1067     p_id=0;
1068     aalen=0;
1069     id=count;
1070     aa=NULL;
1071     start=tcons->start;
1072     end=tcons->end;
1073     contained=NULL;
1074     }
1075     ~GXConsensus() {
1076     if (aa!=NULL) GFREE(aa);
1077     }
1078     };
1079    
1080     class GXLocus:public GSeg {
1081     public:
1082     int id;
1083     int num_mtcons; //number of multi-exon "consensus" transcripts in this locus
1084     char strand;
1085     GList<GLocus> rloci; //list of ref loci overlapping any of the mexons
1086     GList<GLocus> qloci; //loci from all qry datasets that have overlapping exons with this region
1087     GArray<GSeg> mexons; //list of merged exonic regions for this locus
1088     GList<GXConsensus> tcons;
1089     GXLocus(GLocus* lfirst=NULL):GSeg(0,0),
1090     rloci((GCompareProc*)cmpByPtr, (GFreeProc*)NULL, true),
1091     qloci((GCompareProc*)cmpByPtr, (GFreeProc*)NULL, true),
1092     mexons(true,true), tcons(true,true,false) {
1093     strand='.';
1094     num_mtcons=0;
1095     if (lfirst!=NULL) {
1096     add_Locus(lfirst);
1097     }
1098     id=0;
1099     }
1100    
1101     bool add_Locus(GLocus* loc) {
1102     if (mexons.Count()>0 && (end<loc->start || start > loc->end))
1103     return false; //no chance for overlapping exons
1104     if (mexons.Count()==0) {
1105     mexons.Add(loc->mexons);
1106     start=loc->start;
1107     end=loc->end;
1108     if (loc->qfidx<0) rloci.Add(loc);
1109     else qloci.Add(loc);
1110     strand=loc->mrna_maxcov->strand;
1111     loc->xlocus=this;
1112     return true;
1113     }
1114     int f=0;
1115     if (loc->qfidx<0) {
1116     if (rloci.Found(loc,f)) return false;
1117     }
1118     else if (qloci.Found(loc,f)) return false;
1119    
1120     // -- merge mexons
1121     GArray<int> ovlexons(true,true); //list of locus.mexons indexes overlapping existing mexons
1122     int i=0; //index of first mexons with a merge
1123     int j=0; //index current mrna exon
1124     while (i<mexons.Count() && j<loc->mexons.Count()) {
1125     uint istart=mexons[i].start;
1126     uint iend=mexons[i].end;
1127     uint jstart=loc->mexons[j].start;
1128     uint jend=loc->mexons[j].end;
1129     if (iend<jstart) { i++; continue; }
1130     if (jend<istart) { j++; continue; }
1131     //if (mexons[i].overlap(jstart, jend)) {
1132     //exon overlap was found :
1133     ovlexons.Add(j);
1134     //extend mexons[i] as needed
1135     if (jstart<istart) mexons[i].start=jstart;
1136     if (jend>iend) { //mexons[i] end extend
1137     mexons[i].end=jend;
1138     //now this could overlap the next mexon(s), so we have to merge them all
1139     while (i<mexons.Count()-1 && mexons[i].end>mexons[i+1].start) {
1140     uint nextend=mexons[i+1].end;
1141     mexons.Delete(i+1);
1142     if (nextend>mexons[i].end) {
1143     mexons[i].end=nextend;
1144     break; //no need to check next mexons
1145     }
1146     } //while next mexons merge
1147     } // mexons[i] end extend
1148     // } //exon overlap
1149     j++; //check the next locus.mexon
1150     }//while mexons
1151     if (ovlexons.Count()==0) return false;
1152     if (strand=='.' && loc->mrna_maxcov->strand!='.')
1153     strand=loc->mrna_maxcov->strand;
1154     //have exon overlap:
1155     //-- add the rest of the non-overlapping mexons:
1156     GSeg seg;
1157     for (int i=0;i<loc->mexons.Count();i++) {
1158     seg.start=loc->mexons[i].start;
1159     seg.end=loc->mexons[i].end;
1160     if (!ovlexons.Exists(i)) mexons.Add(seg);
1161     }
1162     // -- adjust start/end as needed
1163     if (start>loc->start) start=loc->start;
1164     if (end<loc->end) end=loc->end;
1165     loc->xlocus=this;
1166     if (loc->qfidx<0) rloci.Add(loc);
1167     else qloci.Add(loc);
1168     return true;
1169     }
1170    
1171     void addMerge(GXLocus& oxloc) {
1172     GArray<int> ovlexons(true,true); //list of oxloc.mexons indexes overlapping existing mexons
1173     int i=0; //index of first mexons with a merge
1174     int j=0; //index current mrna exon
1175     while (i<mexons.Count() && j<oxloc.mexons.Count()) {
1176     uint istart=mexons[i].start;
1177     uint iend=mexons[i].end;
1178     uint jstart=oxloc.mexons[j].start;
1179     uint jend=oxloc.mexons[j].end;
1180     if (iend<jstart) { i++; continue; }
1181     if (jend<istart) { j++; continue; }
1182     //if (mexons[i].overlap(jstart, jend)) {
1183     //exon overlap was found :
1184     ovlexons.Add(j);
1185     //extend mexons[i] as needed
1186     if (jstart<istart) mexons[i].start=jstart;
1187     if (jend>iend) { //mexons[i] end extend
1188     mexons[i].end=jend;
1189     //now this could overlap the next mexon(s), so we have to merge them all
1190     while (i<mexons.Count()-1 && mexons[i].end>mexons[i+1].start) {
1191     uint nextend=mexons[i+1].end;
1192     mexons.Delete(i+1);
1193     if (nextend>mexons[i].end) {
1194     mexons[i].end=nextend;
1195     break; //no need to check next mexons
1196     }
1197     } //while next mexons merge
1198     } // mexons[i] end extend
1199     // } //exon overlap
1200     j++; //check the next oxloc.mexon
1201     }
1202     if (ovlexons.Count()==0) {
1203     GError("Error: attempt to merge GXLoci with non-overlapping exons!\n");
1204     }
1205     //-- add the rest of the non-overlapping mexons:
1206     GSeg seg;
1207     for (int i=0;i<oxloc.mexons.Count();i++) {
1208     seg.start=oxloc.mexons[i].start;
1209     seg.end=oxloc.mexons[i].end;
1210     if (!ovlexons.Exists(i)) mexons.Add(seg);
1211     }
1212     if (start>oxloc.start) start=oxloc.start;
1213     if (end<oxloc.end) end=oxloc.end;
1214     if (strand=='.') strand=oxloc.strand;
1215     //-- steal all qloci and rloci
1216     for (int i=0;i<oxloc.qloci.Count();i++) {
1217     if (oxloc.qloci[i]->xlocus==this) continue;
1218     qloci.Add(oxloc.qloci[i]);
1219     oxloc.qloci[i]->xlocus=this;
1220     }
1221     for (int i=0;i<oxloc.rloci.Count();i++) {
1222     if (oxloc.rloci[i]->xlocus==this) continue;
1223     rloci.Add(oxloc.rloci[i]);
1224     oxloc.rloci[i]->xlocus=this;
1225     }
1226     } //::addMerge()
1227    
1228    
1229     void checkContainment() {
1230     //checking containment
1231     for (int j=0;j<tcons.Count()-1;j++) {
1232     GXConsensus* t=tcons[j];
1233     for (int i=j+1;i<tcons.Count();i++) {
1234     if (tcons[i]->contained!=NULL && t->tcons->exons.Count()>1) continue; //will check the container later anyway
1235     int c_status=checkXConsContain(t->tcons, tcons[i]->tcons);
1236     if (c_status==0) continue; //no containment relationship between t and tcons[i]
1237     if (c_status>0) { //t is a container for tcons[i]
1238     tcons[i]->contained=t;
1239     }
1240     else { //contained into exising XCons
1241     t->contained=tcons[i];
1242     break;
1243     }
1244     }
1245     }
1246     }
1247    
1248     int checkXConsContain(GffObj* a, GffObj* b) {
1249     // returns 1 if a is the container of b
1250     // -1 if a is contained in b
1251     // 0 if no
1252     if (a->end<b->start || b->end<a->start) return 0;
1253     if (a->exons.Count()==b->exons.Count()) {
1254     if (a->exons.Count()>1) return 0; //same number of exons - no containment possible
1255     //because equivalence was already tested
1256     else { //single exon containment testing
1257     //this is fuzzy and messy (end result may vary depending on the testing order)
1258     int ovlen=a->exons[0]->overlapLen(b->exons[0]);
1259     int minlen=GMIN(a->covlen, b->covlen);
1260     if (ovlen>=minlen*0.8) { //if at least 80% of the shorter one is covered, it is contained
1261     return ((a->covlen>b->covlen) ? 1 : -1);
1262     }
1263     else return 0;
1264     //if (a->start<=b->start+10 && a->end+10>=b->end) return 1;
1265     // else { if (b->start<=a->start+10 && b->end+10>=a->end) return -1;
1266     // else return 0;
1267     //}
1268     }
1269     }
1270     //different number of exons:
1271     if (a->exons.Count()>b->exons.Count()) return t_contains(*a, *b) ? 1:0;
1272     else return t_contains(*b, *a) ? -1 : 0;
1273     }
1274    
1275     void addXCons(GXConsensus* t) {
1276     tcons.Add(t);
1277     }
1278    
1279     }; //GXLocus
1280    
1281    
1282    
1283     int parse_mRNAs(GfList& mrnas,
1284     GList<GSeqData>& glstdata,
1285     bool is_ref_set=true,
1286     bool check_for_dups=false,
1287     int qfidx=-1, bool only_multiexon=false);
1288    
1289     //reading a mRNAs from a gff file and grouping them into loci
1290     void read_mRNAs(FILE* f, GList<GSeqData>& seqdata, GList<GSeqData>* ref_data=NULL,
1291     bool check_for_dups=false, int qfidx=-1, const char* fname=NULL,
1292     bool only_multiexon=false);
1293    
1294     void read_transcripts(FILE* f, GList<GSeqData>& seqdata, bool keepAttrs=true);
1295     void sort_GSeqs_byName(GList<GSeqData>& seqdata);
1296    
1297    
1298 gpertea 54 bool tMatch(GffObj& a, GffObj& b, int& ovlen, bool fuzzunspl=false, bool contain_only=false);
1299 gpertea 20
1300     //use qsearch to "position" a given coordinate x within a list of transcripts sorted
1301     //by their start (lowest) coordinate; the returned int is the list index of the
1302     //closest GffObj starting just *ABOVE* coordinate x
1303     //Convention: returns -1 if there is no such GffObj (i.e. last GffObj start <= x)
1304     int qsearch_mrnas(uint x, GList<GffObj>& mrnas);
1305     int qsearch_loci(uint x, GList<GLocus>& segs); // same as above, but for GSeg lists
1306    
1307     GSeqData* getRefData(int gid, GList<GSeqData>& ref_data); //returns reference GSeqData for a specific genomic sequence
1308    
1309     #endif

Properties

Name Value
svn:executable *