@@ -72,72 +72,75 @@ void write_record(Cluster const & cluster,
7272
7373 if (mate1.seq_name == mate2.seq_name )
7474 {
75- size_t const insert_size = cluster.get_average_inserted_sequence_size ();
76- int const distance = mate2.position - mate1.position - 1 ;
77- int sv_length{};
78- int sv_length_iGenVar{};
79- std::string sv_type;
80-
81- // Tandem Duplication
82- // In case of a small deletion inside of a duplication, the distance is a small positive value
83- if (cluster.get_common_tandem_dup_count () > 0 && static_cast <uint64_t >(distance) <= args.max_tol_deleted_length )
75+ if (mate1.orientation == strand::forward)
8476 {
85- record.alt () = {" <DUP:TANDEM>"
86- // Increment end by 1 because VCF is 1-based
87- record.info ().push_back ({.id = " END" value = mate2.position + 1 });
88- sv_length = distance + 2 ;
89- sv_length_iGenVar = insert_size;
90- sv_type = " DUP"
91- }
92- // Deletion OR Inversion
93- else if (distance > 0 )
94- {
95- // Inversion
96- // An Inversion consists of 2 Breakpoints, thus it looks like a deletion with an inserted sequence
97- if (insert_size >= args.min_var_length )
77+ size_t const insert_size = cluster.get_average_inserted_sequence_size ();
78+ int const distance = mate2.position - mate1.position - 1 ;
79+ int sv_length{};
80+ int sv_length_iGenVar{};
81+ std::string sv_type;
82+
83+ // Tandem Duplication
84+ // In case of a small deletion inside of a duplication, the distance is a small positive value
85+ if (cluster.get_common_tandem_dup_count () > 0 && static_cast <uint64_t >(distance) <= args.max_tol_deleted_length )
9886 {
99- // Increment position by 1 because INV mate1 points on its last element
100- record.pos () += 1 ;
101- record.alt () = {" <INV>"
87+ record.alt () = {" <DUP:TANDEM>"
10288 // Increment end by 1 because VCF is 1-based
103- // Increment end by 1 because inversion ends one base before mate2 begins
10489 record.info ().push_back ({.id = " END" value = mate2.position + 1 });
105- sv_length = distance;
106- sv_length_iGenVar = sv_length ;
107- sv_type = " INV "
90+ sv_length = distance + 2 ;
91+ sv_length_iGenVar = insert_size ;
92+ sv_type = " DUP "
10893 }
109- // Deletion
110- // In case of a small insertion inside of an deletion, the insert_size is a small positive value.
111- else if (insert_size <= args.max_tol_inserted_length )
94+ // Deletion OR Inversion
95+ else if (distance > 0 )
11296 {
113- record.alt () = {" <DEL>"
97+ // Inversion
98+ // An Inversion consists of 2 Breakpoints, thus it looks like a deletion with an inserted sequence
99+ if (insert_size >= args.min_var_length )
100+ {
101+ // Increment position by 1 because INV mate1 points on its last element
102+ record.pos () += 1 ;
103+ record.alt () = {" <INV>"
104+ // Increment end by 1 because VCF is 1-based
105+ // Increment end by 1 because inversion ends one base before mate2 begins
106+ record.info ().push_back ({.id = " END" value = mate2.position + 1 });
107+ sv_length = distance;
108+ sv_length_iGenVar = sv_length;
109+ sv_type = " INV"
110+ }
111+ // Deletion
112+ // In case of a small insertion inside of a deletion, the insert_size is a small positive value.
113+ else if (insert_size <= args.max_tol_inserted_length )
114+ {
115+ record.alt () = {" <DEL>"
116+ // Increment end by 1 because VCF is 1-based
117+ // Decrement end by 1 because deletion ends one base before mate2 begins
118+ record.info ().push_back ({.id = " END" value = mate2.position });
119+ sv_length = -distance;
120+ sv_length_iGenVar = sv_length;
121+ sv_type = " DEL"
122+ }
123+ }
124+ // Insertion (sv_length is positive)
125+ // In case of a small deletion inside of an insertion, the distance is a small positive value
126+ else if (insert_size > 0 && static_cast <uint64_t >(distance) <= args.max_tol_deleted_length )
127+ {
128+ record.alt () = {" <INS>"
114129 // Increment end by 1 because VCF is 1-based
115- // Decrement end by 1 because deletion ends one base before mate2 begins
116- record.info ().push_back ({.id = " END" value = mate2.position });
117- sv_length = -distance;
130+ record.info ().push_back ({.id = " END" value = mate1.position + 1 });
131+ sv_length = insert_size;
118132 sv_length_iGenVar = sv_length;
119- sv_type = " DEL"
133+ sv_type = " INS"
134+ }
135+ // The SVLEN is neither too short nor too long than specified by the user.
136+ if (std::abs (sv_length) >= args.min_var_length &&
137+ std::abs (sv_length) <= args.max_var_length )
138+ {
139+ record.info ().push_back ({.id = " SVLEN" value = sv_length});
140+ record.info ().push_back ({.id = " iGenVar_SVLEN" value = sv_length_iGenVar});
141+ record.info ().push_back ({.id = " SVTYPE" value = sv_type});
142+ found_SV = true ;
120143 }
121- }
122- // Insertion (sv_length is positive)
123- // In case of a small deletion inside of an insertion, the distance is a small positive value
124- else if (insert_size > 0 && static_cast <uint64_t >(distance) <= args.max_tol_deleted_length )
125- {
126- record.alt () = {" <INS>"
127- // Increment end by 1 because VCF is 1-based
128- record.info ().push_back ({.id = " END" value = mate1.position + 1 });
129- sv_length = insert_size;
130- sv_length_iGenVar = sv_length;
131- sv_type = " INS"
132- }
133- // The SVLEN is neither too short nor too long than specified by the user.
134- if (std::abs (sv_length) >= args.min_var_length &&
135- std::abs (sv_length) <= args.max_var_length )
136- {
137- record.info ().push_back ({.id = " SVLEN" value = sv_length});
138- record.info ().push_back ({.id = " iGenVar_SVLEN" value = sv_length_iGenVar});
139- record.info ().push_back ({.id = " SVTYPE" value = sv_type});
140- found_SV = true ;
141144 }
142145 }
143146}
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