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root/gclib/gclib/GBam.cpp
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# Line 32 | Line 32
32   GBamRecord::GBamRecord(const char* qname, int32_t gseq_tid,
33                   int pos, bool reverse, const char* qseq,
34                   const char* cigar, const char* quals):exons(1) {
35 <   novel=true;
35 >   //novel=true;
36     bam_header=NULL;
37     b=bam_init1();
38     b->core.tid=gseq_tid;
# Line 58 | Line 58
58               int pos, int map_qual, const char* cigar, int32_t mg_tid, int mate_pos,
59               int insert_size, const char* qseq, const char* quals,
60               GVec<char*>* aux_strings):exons(1)  {
61 <  novel=true;
61 >  //novel=true;
62    bam_header=NULL;
63    b=bam_init1();
64    b->core.tid=g_tid;
# Line 266 | Line 266
266             else if (op == BAM_CREF_SKIP) { //N
267                 //intron starts
268                 //exon ends here
269 <               exons.Add(new GSeg(exstart+1,l));
269 >               GSeg exon(exstart+1,l);
270 >               exons.Add(exon);
271                 l += cigar[i]>>4;
272                 exstart=c->pos+l;
273                 }
274          }
275 <   exons.Add(new GSeg(exstart+1, l));
275 >   GSeg exon(exstart+1,l);
276 >   exons.Add(exon);
277     end=c->pos+l;
278   }
279  
# Line 327 | Line 329
329         } //switch (tag_type)
330       if (tag[0]==key[0] && tag[1]==key[1])
331          return inc;
332 +     s+=inc;
333       }//while aux data
334     return 0;
335     }

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