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    core/segment.{h,cpp}: both V and J kmers must be above DETECT_THRESHOLD to... · a8df78ec
    Mathieu Giraud authored
    core/segment.{h,cpp}: both V and J kmers must be above DETECT_THRESHOLD to flag the germline as 'detected'
    
    This reverts the idea of 41b4f071, but still uses a 'detected' flag.
    This flag tells us whether we should continue to the remaining germlines.
    In the case of incomplete rearrangements, we certainly want to continue even if we have
    many V or many J (but now both of them).
    Tests d2a0dbd5 are now passing.
    
    Note that we don't run this test when strand == 2, this should be changed.
    a8df78ec
segment.cpp 19.3 KB