void ResetVcfRecordFromBam( VcfRecord & vcf_rec, RefStats & rstats, vector<RefSeq*> & REF_SEQ, string & chr, int center, SamFile & samIn, SamFileHeader & samHeader ) { vector<int> raw_counts; // read-type count vector raw_counts.resize(18, 0); setReadCountInSection( raw_counts, chr, center, samIn, samHeader, REF_SEQ ); // set from bam // set gl & if 1/1 or 1/0, set breakpoint vector<MergeCell> new_vec; new_vec.resize(1); MergeCellPtr merge_ptr = new_vec.begin(); merge_ptr->dups = 1; merge_ptr->counts = raw_counts; raw_counts.clear(); merge_ptr->GL.resize(3,0); rstats.SetRecordGL( merge_ptr ); vcf_rec.SetChrName( chr ); vcf_rec.SetPosition( center ); vcf_rec.UpdateFromMergeCellPtr( merge_ptr ); // if need to refine break point && exist MEI, do refine if (REFINE_BREAK_POINT && vcf_rec.GetDosage() > 0) vcf_rec.SetBreakPointAndCIFromBam( samIn, samHeader ); }