From 3bd86d6353c7b8f13cc29994ff0c403330595678 Mon Sep 17 00:00:00 2001 From: Rayan CHIKHI Date: Sun, 5 Nov 2023 21:19:33 +0000 Subject: [PATCH] tweak to simplifications --- .../src/gatb/debruijn/impl/Simplifications.cpp | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp b/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp index 9b545862..a633bdd5 100644 --- a/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp +++ b/gatb-core/src/gatb/debruijn/impl/Simplifications.cpp @@ -133,6 +133,21 @@ void Simplifications::simplify() && _nbTipRemovalPasses < 20); } + // do one round of bubble removal, then one EC, then go on with the rest of the rounds + // that's because bubble removal gets much faster after EC + + nbBubblesRemovedPreviously = nbBubblesRemoved; + nbBubblesRemoved = removeBulges(); + if (bubbleRemoval.size() != 0) + bubbleRemoval += " + "; + bubbleRemoval += to_string(nbBubblesRemoved); + + nbECRemovedPreviously = nbECRemoved; + nbECRemoved = removeErroneousConnections(); // now we're using bulges removal, not bubbles (to follow SPAdes) + if (ECRemoval.size() != 0) + ECRemoval += " + "; + ECRemoval += to_string(nbECRemoved); + if (_doBulgeRemoval) { do