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root/gclib/tophat_cpp/align_status.cpp

#	Line 30 | Line 30
30		_indelFreeAlignment = false;
31		_unannotatedSpliceFreeAlignment = false;
32		_edit_dist = 0xFF;
33	+	_fusionFreeAlignment = 0;
34		}
35
36		/**
37		* Parse the cigar string of a BowtieHit in order to determine the alignment status.
38		*/
39	<	AlignStatus::AlignStatus(const BowtieHit& bh, const JunctionSet& gtf_junctions)
39	<	{
39	>	AlignStatus::AlignStatus(const BowtieHit& bh, const JunctionSet& gtf_junctions){
40		const vector<CigarOp>& cigar = bh.cigar();
41		_aligned = cigar.size() > 0;
42		_indelFreeAlignment = true;
43	+	_fusionFreeAlignment = true;
44		_unannotatedSpliceFreeAlignment = true;
45		_edit_dist = bh.edit_dist();
46		int j = bh.left();
#	Line 68 | Line 69
69		case INS:
70		_indelFreeAlignment = false;
71		break;
72	+	case FUSION_FF:
73	+	case FUSION_FR:
74	+	case FUSION_RF:
75	+	case FUSION_RR:
76	+	_fusionFreeAlignment = false;
77	+	break;
78		default:
79		break;
80		}
#	Line 88 | Line 95
95		if (rhs._aligned != _aligned) return rhs._aligned;
96		if (rhs._edit_dist!=_edit_dist)
97		return rhs._edit_dist < _edit_dist;
98	<	//int lhs_value = _aligned ? 1 : 0;
99	<	int lhs_value = _indelFreeAlignment ? 4 : 0;
100	<	lhs_value += _unannotatedSpliceFreeAlignment ? 2 : 0;
101	<
102	<	//int rhs_value = rhs._aligned ? 1 : 0;
103	<	int rhs_value = rhs._indelFreeAlignment ? 4 : 0;
104	<	rhs_value += rhs._unannotatedSpliceFreeAlignment ? 2 : 0;
105	<	return lhs_value < rhs_value;
98	>
99	>	// int lhs_value = _aligned ? 1 : 0;
100	>	int lhs_value = _fusionFreeAlignment ? 4 : 0;
101	>	lhs_value += _indelFreeAlignment ? 4 : 0;
102	>	lhs_value += _unannotatedSpliceFreeAlignment ? 2 : 0;
103	>
104	>	// int rhs_value = rhs._aligned ? 1 : 0;
105	>	int rhs_value = rhs._fusionFreeAlignment ? 4 : 0;
106	>	rhs_value += rhs._indelFreeAlignment ? 4 : 0;
107	>	rhs_value += rhs._unannotatedSpliceFreeAlignment ? 2 : 0;
108	>
109	>	return lhs_value < rhs_value;
110		}
111
112		/**
#	Line 105 | Line 116
116		{
117		return ((_aligned == rhs._aligned) && (rhs._edit_dist ==_edit_dist) &&
118		(_indelFreeAlignment == rhs._indelFreeAlignment) &&
119	<	(_unannotatedSpliceFreeAlignment == rhs._unannotatedSpliceFreeAlignment));
119	>	(_unannotatedSpliceFreeAlignment == rhs._unannotatedSpliceFreeAlignment) &&
120	>	(_fusionFreeAlignment == rhs._fusionFreeAlignment));
121		}
122
123		bool AlignStatus::operator!=(const AlignStatus& rhs) const
124		{
125		return !((*this) == rhs);
126		}
115	–
116	–
117	–

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