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/*
Ray
Copyright (C) 2010, 2011, 2012 Sébastien Boisvert
http://DeNovoAssembler.SourceForge.Net/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, version 3 of the License.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You have received a copy of the GNU General Public License
along with this program (gpl-3.0.txt).
see <http://www.gnu.org/licenses/>
*/
#include "TipWatchdog.h"
bool TipWatchdog::getApproval(ExtensionData*ed,DepthFirstSearchData*dfsData,int minimumCoverage,Kmer SEEDING_currentVertex,
int w,BubbleData*bubbleData){
int id=dfsData->m_doChoice_tips_newEdges[0];
Kmer key=ed->m_enumerateChoices_outgoingEdges[id];
int readsInFavorOfThis=ed->m_EXTENSION_readPositionsForVertices[key].size();
int coverageAtTheVertexLocation=(ed->m_EXTENSION_coverages)[id];
// reads are not supportive of this.
if(readsInFavorOfThis*10<coverageAtTheVertexLocation){
// no luck..., yet.
return false;
}
return true;
if(ed->m_enumerateChoices_outgoingEdges.size()==2 &&
(int)ed->m_EXTENSION_readPositionsForVertices[ed->m_enumerateChoices_outgoingEdges[0]].size() < minimumCoverage
&& (int)ed->m_EXTENSION_readPositionsForVertices[ed->m_enumerateChoices_outgoingEdges[1]].size() < minimumCoverage){
int winner=dfsData->m_doChoice_tips_newEdges[0];
int loser=0;
if(winner==loser){
loser++;
}
int readsForWinner=ed->m_EXTENSION_readPositionsForVertices[ed->m_enumerateChoices_outgoingEdges[winner]].size();
int readsForLoser=ed->m_EXTENSION_readPositionsForVertices[ed->m_enumerateChoices_outgoingEdges[loser]].size();
int diff=readsForWinner-readsForLoser;
if(diff<0){
diff=-diff;
}
if(diff<2){
#ifdef SHOW_TIP_WATCHDOG
cout<<"Ray Oddity: The genome lacks coverage after "<<idToWord(SEEDING_currentVertex,w)<<"; Ray can't choose wisely if you don't provide enough data, be manly and rerun your sample!"<<endl;
#endif
ed->m_doChoice_tips_Detected=true;
bubbleData->m_doChoice_bubbles_Detected=false;
bubbleData->m_doChoice_bubbles_Initiated=false;
return false;
}
}
return true;
}
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