#include "aligncommand.h"
#include "referencedb.h"
-//test comment
+
//**********************************************************************************************************************
vector<string> AlignCommand::setParameters(){
try {
#else
vector<unsigned long long> positions;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(candidateFileNames[s], processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(new linePair(positions[i], positions[(i+1)])); }
#else
lines.push_back(new linePair(0, 1000));
}else {
positions = m->setFilePosFasta(candidateFileNames[s], numFastaSeqs);
-
+ if (positions.size() < processors) { processors = positions.size(); }
+
//figure out how many sequences you have to process
int numSeqsPerProcessor = numFastaSeqs / processors;
for (int i = 0; i < processors; i++) {
}
delete candidateSeq;
- #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+ #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
unsigned long long pos = inFASTA.tellg();
if ((pos == -1) || (pos >= filePos->end)) { break; }
#else
try {
int num = 0;
processIDS.resize(0);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int process = 1;
//loop through and create all the processes you want