• Mathieu Giraud's avatar
    core/segment.{cpp,h}: computes only half of the DP matrix for VJ segments · 513a047b
    Mathieu Giraud authored
    Starting from the full read, we can not limit the DP computations
    to a k-band around the diagonal without first knowing where is exactly the junction.
    Nevertheless, we can avoid computing about one half of the DP matrix,
    as the end of the V / the start of the J (minus some deletions) must be matched.
    The BOTTOM_TRIANGLE_SHIFT is now set to 20, and this should be large enough
    to handle V/J deletions until ~30 bp (see comment in segment.h).
    (The current tests were even passing with BOTTOM_TRIANGLE_SHIFT set to 10.)
    Now the FineSegmenter (as launched by 'make shouldvdj_with_rc_merged') is about 35% faster.
segment.cpp 30.7 KB