8 * Created by Sarah Westcott on 5/15/09.
9 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
14 #include "command.hpp"
15 #include "database.hpp"
16 #include "alignment.hpp"
17 #include "alignmentdb.h"
19 class AlignCommand : public Command {
25 vector<string> getRequiredParameters();
26 vector<string> getValidParameters();
27 vector<string> getRequiredFiles();
28 map<string, vector<string> > getOutputFiles() { return outputTypes; }
34 unsigned long int start;
35 unsigned long int end;
36 linePair(unsigned long int i, unsigned long int j) : start(i), end(j) {}
38 vector<int> processIDS; //processid
39 vector<linePair*> lines;
41 map<string, vector<string> > outputTypes;
43 AlignmentDB* templateDB;
46 int driver(linePair*, string, string, string, string);
47 int createProcesses(string, string, string, string);
48 void appendAlignFiles(string, string);
49 void appendReportFiles(string, string);
52 int driverMPI(int, int, MPI_File&, MPI_File&, MPI_File&, MPI_File&, vector<unsigned long int>&);
55 string candidateFileName, templateFileName, distanceFileName, search, align, outputDir;
56 float match, misMatch, gapOpen, gapExtend, threshold;
57 int processors, kmerSize;
58 vector<string> candidateFileNames;
59 vector<string> outputNames;
61 bool abort, flip, calledHelp;