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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.
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