string temp = validParameter.validFile(parameters, "processors", false); if (temp == "not found"){ temp = m->getProcessors(); }
m->setProcessors(temp);
- convert(temp, processors);
+ m->mothurConvert(temp, processors);
temp = validParameter.validFile(parameters, "save", false); if (temp == "not found"){ temp = "f"; }
save = m->isTrue(temp);
temp = validParameter.validFile(parameters, "ksize", false); if (temp == "not found") { temp = "7"; }
- convert(temp, ksize);
+ m->mothurConvert(temp, ksize);
temp = validParameter.validFile(parameters, "window", false); if (temp == "not found") { temp = "50"; }
- convert(temp, window);
+ m->mothurConvert(temp, window);
temp = validParameter.validFile(parameters, "match", false); if (temp == "not found") { temp = "5"; }
- convert(temp, match);
+ m->mothurConvert(temp, match);
temp = validParameter.validFile(parameters, "mismatch", false); if (temp == "not found") { temp = "-4"; }
- convert(temp, mismatch);
+ m->mothurConvert(temp, mismatch);
temp = validParameter.validFile(parameters, "divergence", false); if (temp == "not found") { temp = "1.007"; }
- convert(temp, divR);
+ m->mothurConvert(temp, divR);
temp = validParameter.validFile(parameters, "minsim", false); if (temp == "not found") { temp = "90"; }
- convert(temp, minSimilarity);
+ m->mothurConvert(temp, minSimilarity);
temp = validParameter.validFile(parameters, "mincov", false); if (temp == "not found") { temp = "70"; }
- convert(temp, minCoverage);
+ m->mothurConvert(temp, minCoverage);
temp = validParameter.validFile(parameters, "minbs", false); if (temp == "not found") { temp = "90"; }
- convert(temp, minBS);
+ m->mothurConvert(temp, minBS);
temp = validParameter.validFile(parameters, "minsnp", false); if (temp == "not found") { temp = "10"; }
- convert(temp, minSNP);
+ m->mothurConvert(temp, minSNP);
temp = validParameter.validFile(parameters, "parents", false); if (temp == "not found") { temp = "3"; }
- convert(temp, parents);
+ m->mothurConvert(temp, parents);
temp = validParameter.validFile(parameters, "realign", false); if (temp == "not found") { temp = "t"; }
realign = m->isTrue(temp);
search = validParameter.validFile(parameters, "search", false); if (search == "not found") { search = "blast"; }
temp = validParameter.validFile(parameters, "iters", false); if (temp == "not found") { temp = "1000"; }
- convert(temp, iters);
+ m->mothurConvert(temp, iters);
temp = validParameter.validFile(parameters, "increment", false); if (temp == "not found") { temp = "5"; }
- convert(temp, increment);
+ m->mothurConvert(temp, increment);
temp = validParameter.validFile(parameters, "numwanted", false); if (temp == "not found") { temp = "15"; }
- convert(temp, numwanted);
+ m->mothurConvert(temp, numwanted);
blastlocation = validParameter.validFile(parameters, "blastlocation", false);
if (blastlocation == "not found") { blastlocation = ""; }
else {
//add / to name if needed
string lastChar = blastlocation.substr(blastlocation.length()-1);
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
if (lastChar != "/") { blastlocation += "/"; }
#else
if (lastChar != "\\") { blastlocation += "\\"; }
#endif
blastlocation = m->getFullPathName(blastlocation);
string formatdbCommand = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
formatdbCommand = blastlocation + "formatdb";
#else
formatdbCommand = blastlocation + "formatdb.exe";
if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + formatdbCommand + " file does not exist. mothur requires formatdb.exe to run chimera.slayer."); m->mothurOutEndLine(); abort = true; }
string blastCommand = "";
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
blastCommand = blastlocation + "megablast";
#else
blastCommand = blastlocation + "megablast.exe";
if (hasGroup && (templatefile != "self")) { m->mothurOut("You have provided a group file and the reference parameter is not set to self. I am not sure what reference you are trying to use, aborting."); m->mothurOutEndLine(); abort=true; }
//until we resolve the issue 10-18-11
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
#else
//processors=1;
#endif
#else
//break up file
vector<unsigned long long> positions;
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
positions = m->divideFile(thisFastaName, processors);
for (int i = 0; i < (positions.size()-1); i++) { lines.push_back(linePair(positions[i], positions[(i+1)])); }
#else
if (processors == 1) { lines.push_back(linePair(0, 1000)); }
else {
positions = m->setFilePosFasta(thisFastaName, numSeqs);
+ if (positions.size() < processors) { processors = positions.size(); }
//figure out how many sequences you have to process
int numSeqsPerProcessor = numSeqs / processors;
map<string, string> uniqueNames = parser->getAllSeqsMap();
map<string, string>::iterator itUnique;
int total = 0;
+
+ if (trimera) { //add in more potential uniqueNames
+ map<string, string> newUniqueNames = uniqueNames;
+ for (map<string, string>::iterator it = uniqueNames.begin(); it != uniqueNames.end(); it++) {
+ newUniqueNames[(it->first)+"_LEFT"] = (it->first)+"_LEFT";
+ newUniqueNames[(it->first)+"_RIGHT"] = (it->first)+"_RIGHT";
+ }
+ uniqueNames = newUniqueNames;
+ newUniqueNames.clear();
+ }
//edit accnos file
ifstream in2;
m->mothurOutEndLine(); m->mothurOut("Checking sequences from group: " + fileGroup[thisFastaName] + "."); m->mothurOutEndLine();
lines.clear();
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
int proc = 1;
vector<unsigned long long> positions = m->divideFile(thisFastaName, proc);
lines.push_back(linePair(positions[0], positions[1]));
breakUp.push_back(thisFileToPriority);
}
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();
count++;
}
- #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
int num = 0;
processIDS.clear();
-#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
+#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
//loop through and create all the processes you want
while (process != processors) {
int pid = fork();