1 #include "VelvetUtils.hh"
2
importSequences(const string & seqFileName,int argc,char * argv[],boolean & flagDoubleStrand,boolean & flagNoHash)3 void VelvetUtils::importSequences( const string& seqFileName, int argc, char* argv[], boolean& flagDoubleStrand, boolean& flagNoHash ){
4 parseDataAndReadFiles( VUtils::getCharFileName(seqFileName), argc - 2, &(argv[2]), &flagDoubleStrand, &flagNoHash );
5 }
6
setRoadmaps(const string & seqFileName,const string & roadmapFileName,int hashLength,boolean flagDoubleStrand,boolean noHash)7 void VelvetUtils::setRoadmaps( const string& seqFileName, const string& roadmapFileName, int hashLength, boolean flagDoubleStrand, boolean noHash ){
8 resetWordFilter( hashLength );
9 SplayTable* splayTable = newSplayTable( hashLength, (boolean)true );
10 ReadSet* allSequences = importReadSet( VUtils::getCharFileName(seqFileName) );
11 inputSequenceArrayIntoSplayTableAndArchive( allSequences, splayTable, VUtils::getCharFileName(roadmapFileName), VUtils::getCharFileName(seqFileName) );
12 destroySplayTable( splayTable );
13 }
14
constructPregraph(const string & seqFileName,const string & roadmapFileName,const string & pregraphFileName)15 void VelvetUtils::constructPregraph( const string& seqFileName, const string& roadmapFileName, const string& pregraphFileName ){
16 RoadMapArray* roadmaps = importRoadMapArray( VUtils::getCharFileName(roadmapFileName) );
17 PreGraph* preGraph = newPreGraph_pg( roadmaps, VUtils::getCharFileName(seqFileName) );
18 concatenatePreGraph_pg( preGraph );
19 clipTips_pg( preGraph );
20 exportPreGraph_pg( VUtils::getCharFileName(pregraphFileName), preGraph );
21 destroyPreGraph_pg( preGraph );
22 }
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