4145 #define SCAN_WINDOW 49            // odd number!!!  macro
4213     vector<double> coverage_raw(mrna_len+SCAN_WINDOW);  in CChain()
4223                 coverage_raw[i+SCAN_WINDOW/2] += align.Weight();  in CChain()
4229     for(int i = 0; i < SCAN_WINDOW; ++i)  in CChain()
4230         cov += coverage_raw[i]/SCAN_WINDOW;  in CChain()
4233         cov -= coverage_raw[i]/SCAN_WINDOW;  in CChain()
4234         cov += coverage_raw[i+SCAN_WINDOW]/SCAN_WINDOW;  in CChain()
5477     if(core_lim.GetTo()-core_lim.GetFrom() < SCAN_WINDOW)      // too short  in ClipLowCoverageUTR()
5560     if(!fivep_confirmed && !(Status()&eCap) && core_lim.GetFrom() > SCAN_WINDOW/2) {  in ClipLowCoverageUTR()
5590     if(!threep_confirmed && !(Status()&ePolyA) && core_lim.GetTo() < mrna_len-1-SCAN_WINDOW/2) {  in ClipLowCoverageUTR()
5599         for(int i = right_limit-SCAN_WINDOW/2; i <= right_limit+SCAN_WINDOW/2; ++i)  in ClipLowCoverageUTR()
5692 …for( ; first_bump < soft_limit.GetFrom()-SCAN_WINDOW && m_coverage[first_bump+SCAN_WINDOW] < m_cov…  in CalculateDropLimits()
5699             if(first_drop+SCAN_WINDOW/2 < mrna_len) {  in CalculateDropLimits()
5700                 for( ; first_drop-SCAN_WINDOW/2 > 0; --first_drop) {  in CalculateDropLimits()
5701 …if(m_coverage[first_drop-SCAN_WINDOW/2] >= m_coverage[first_drop+SCAN_WINDOW/2])  // check for neg…  in CalculateDropLimits()
5703 …if(m_coverage[first_drop-SCAN_WINDOW/2]+m_coverage[first_drop+SCAN_WINDOW/2]-2*m_coverage[first_dr…  in CalculateDropLimits()
5727 …for( ; first_bump > soft_limit.GetTo()+SCAN_WINDOW && m_coverage[first_bump-SCAN_WINDOW] < m_cover…  in CalculateDropLimits()
5734             if(first_drop-SCAN_WINDOW/2 > 0) {  in CalculateDropLimits()
5735                 for( ; first_drop < mrna_len-SCAN_WINDOW/2; ++first_drop) {  in CalculateDropLimits()
5736 …if(m_coverage[first_drop+SCAN_WINDOW/2] >= m_coverage[first_drop-SCAN_WINDOW/2])  // check for neg…  in CalculateDropLimits()
5738 …if(m_coverage[first_drop-SCAN_WINDOW/2]+m_coverage[first_drop+SCAN_WINDOW/2]-2*m_coverage[first_dr…  in CalculateDropLimits()