Commit 85d97a23 authored by Mathieu Giraud's avatar Mathieu Giraud

core/segment.cpp: AlignBox::addToOutput, output also V->start and J->end when relevant

parent 7242628e
......@@ -86,13 +86,13 @@ void AlignBox::addToOutput(CloneOutput *clone, int alternative_genes) {
json j;
j["name"] = ref_label;
if (key != "3") // no end information for J
if (key != "3" || end < seq_length - 1) // end information for J
{
j["stop"] = end + 1;
j["delRight"] = del_right;
}
if (key != "5") // no start information for V
if (key != "5" || start > 0) // start information for V
{
j["start"] = start + 1;
j["delLeft"] = del_left;
......
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