#include "chimera.h"
#include "chimeraslayer.h"
#include "sequenceparser.h"
+#include "sequencecountparser.h"
/***********************************************************/
int divideInHalf(Sequence, string&, string&);
map<string, int> sortFastaFile(string, string);
map<string, int> sortFastaFile(vector<Sequence>&, map<string, string>&, string newFile);
+ int sortFastaFile(vector<Sequence>&, map<string, int>&, string newFile);
string getNamesFile(string&);
//int setupChimera(string,);
int MPIExecute(string, string, string, string, map<string, int>&);
- int deconvoluteResults(SequenceParser*, string, string, string);
+ int deconvoluteResults(map<string, string>&, string, string, string);
map<string, int> priority;
int setUpForSelfReference(SequenceParser*&, map<string, string>&, map<string, map<string, int> >&, int);
+ int setUpForSelfReference(SequenceCountParser*&, map<string, string>&, map<string, map<string, int> >&, int);
int driverGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
int createProcessesGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
int MPIExecuteGroups(string, string, string, map<string, map<string, int> >&, map<string, string>&);
int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long long>&, string, map<string, int>&, bool);
#endif
- bool abort, realign, trim, trimera, save;
- string fastafile, groupfile, templatefile, outputDir, search, namefile, blastlocation;
+ bool abort, realign, trim, trimera, save, hasName, hasCount;
+ string fastafile, groupfile, templatefile, outputDir, search, namefile, countfile, blastlocation;
int processors, window, iters, increment, numwanted, ksize, match, mismatch, parents, minSimilarity, minCoverage, minBS, minSNP, numSeqs, templateSeqsLength;
float divR;