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/*
* trimflowscommand.cpp
* Mothur
*
* Created by Pat Schloss on 12/22/10.
* Copyright 2010 Schloss Lab. All rights reserved.
*
*/
#include "trimflowscommand.h"
#include "needlemanoverlap.hpp"
#include "counttable.h"
//**********************************************************************************************************************
vector<string> TrimFlowsCommand::setParameters(){
try {
CommandParameter pflow("flow", "InputTypes", "", "", "none", "none", "none","flow-file",false,true,true); parameters.push_back(pflow);
CommandParameter poligos("oligos", "InputTypes", "", "", "none", "none", "none","",false,false,true); parameters.push_back(poligos);
CommandParameter preorient("checkorient", "Boolean", "", "F", "", "", "","",false,false,true); parameters.push_back(preorient);
CommandParameter pmaxhomop("maxhomop", "Number", "", "9", "", "", "","",false,false); parameters.push_back(pmaxhomop);
CommandParameter pmaxflows("maxflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pmaxflows);
CommandParameter pminflows("minflows", "Number", "", "450", "", "", "","",false,false); parameters.push_back(pminflows);
CommandParameter ppdiffs("pdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(ppdiffs);
CommandParameter pbdiffs("bdiffs", "Number", "", "0", "", "", "","",false,false,true); parameters.push_back(pbdiffs);
CommandParameter pldiffs("ldiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pldiffs);
CommandParameter psdiffs("sdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(psdiffs);
CommandParameter ptdiffs("tdiffs", "Number", "", "0", "", "", "","",false,false); parameters.push_back(ptdiffs);
CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
CommandParameter psignal("signal", "Number", "", "0.50", "", "", "","",false,false); parameters.push_back(psignal);
CommandParameter pnoise("noise", "Number", "", "0.70", "", "", "","",false,false); parameters.push_back(pnoise);
CommandParameter pallfiles("allfiles", "Boolean", "", "t", "", "", "","",false,false); parameters.push_back(pallfiles);
CommandParameter porder("floworder", "Multiple", "A-B-I", "A", "", "", "","",false,false, true); parameters.push_back(porder);
CommandParameter pfasta("fasta", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pfasta);
CommandParameter pseed("seed", "Number", "", "0", "", "", "","",false,false); parameters.push_back(pseed);
CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
vector<string> tempOutNames;
outputTypes["flow"] = tempOutNames;
outputTypes["fasta"] = tempOutNames;
outputTypes["file"] = tempOutNames;
outputTypes["count"] = tempOutNames;
abort = false; calledHelp = false; comboStarts = 0;
vector<string> myArray;
for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
return myArray;
}
catch(exception& e) {
m->errorOut(e, "TrimFlowsCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string TrimFlowsCommand::getHelpString(){
try {
string helpString = "";
helpString += "The trim.flows command reads a flowgram file and creates .....\n";
helpString += "The oligos parameter allows you to provide an oligos file.\n";
helpString += "The maxhomop parameter allows you to set a maximum homopolymer length. \n";
helpString += "The tdiffs parameter is used to specify the total number of differences allowed in the sequence. The default is pdiffs + bdiffs + sdiffs + ldiffs.\n";
helpString += "The checkorient parameter will check look for the reverse compliment of the barcode or primer in the sequence. The default is false.\n";
helpString += "The bdiffs parameter is used to specify the number of differences allowed in the barcode. The default is 0.\n";
helpString += "The pdiffs parameter is used to specify the number of differences allowed in the primer. The default is 0.\n";
helpString += "The ldiffs parameter is used to specify the number of differences allowed in the linker. The default is 0.\n";
helpString += "The sdiffs parameter is used to specify the number of differences allowed in the spacer. The default is 0.\n";
helpString += "The floworder parameter options are A, B or I. Default=A. A = TACG and B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n";
;
helpString += "For more details please check out the wiki http://www.mothur.org/wiki/Trim.flows.\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "TrimFlowsCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string TrimFlowsCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "flow") { pattern = "[filename],[tag],flow"; }
else if (type == "count") { pattern = "[filename],flow.count_table"; }
else if (type == "fasta") { pattern = "[filename],flow.fasta"; }
else if (type == "file") { pattern = "[filename],flow.files"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "TrimFlowsCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
TrimFlowsCommand::TrimFlowsCommand(string option) : Command() {
try {
if(option == "help") { help(); abort = true; calledHelp = true; }
else if(option == "citation") { citation(); abort = true; calledHelp = true;}
else if(option == "category") { abort = true; calledHelp = true; }
else {
OptionParser parser(option, setParameters());
map<string,string> parameters = parser.getParameters();
ValidParameters validParameter;
flowFileName = validParameter.validFile(parameters, "flow");
if (flowFileName == "not found") {
flowFileName = current->getFlowFile();
if (flowFileName != "") { m->mothurOut("Using " + flowFileName + " as input file for the flow parameter.\n"); }
else {
m->mothurOut("No valid current flow file. You must provide a flow file.\n");
abort = true;
}
}else if (flowFileName == "not open") { flowFileName = ""; abort = true; }
if (outputdir == ""){ outputdir += util.hasPath(flowFileName); }
string temp = validParameter.valid(parameters, "minflows"); if (temp == "not found") { temp = "450"; }
util.mothurConvert(temp, minFlows);
temp = validParameter.valid(parameters, "maxflows"); if (temp == "not found") { temp = "450"; }
util.mothurConvert(temp, maxFlows);
temp = validParameter.validFile(parameters, "oligos");
if (temp == "not found") { oligoFileName = ""; }
else if(temp == "not open") { abort = true; }
else { oligoFileName = temp; current->setOligosFile(oligoFileName); }
temp = validParameter.valid(parameters, "fasta"); if (temp == "not found"){ fasta = 0; }
else if(util.isTrue(temp)) { fasta = 1; }
temp = validParameter.valid(parameters, "maxhomop"); if (temp == "not found"){ temp = "9"; }
util.mothurConvert(temp, maxHomoP);
temp = validParameter.valid(parameters, "signal"); if (temp == "not found"){ temp = "0.50"; }
util.mothurConvert(temp, signal);
temp = validParameter.valid(parameters, "noise"); if (temp == "not found"){ temp = "0.70"; }
util.mothurConvert(temp, noise);
temp = validParameter.valid(parameters, "bdiffs"); if (temp == "not found"){ temp = "0"; }
util.mothurConvert(temp, bdiffs);
temp = validParameter.valid(parameters, "pdiffs"); if (temp == "not found"){ temp = "0"; }
util.mothurConvert(temp, pdiffs);
temp = validParameter.valid(parameters, "ldiffs"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, ldiffs);
temp = validParameter.valid(parameters, "sdiffs"); if (temp == "not found") { temp = "0"; }
util.mothurConvert(temp, sdiffs);
temp = validParameter.valid(parameters, "tdiffs"); if (temp == "not found") { int tempTotal = pdiffs + bdiffs + ldiffs + sdiffs; temp = toString(tempTotal); }
util.mothurConvert(temp, tdiffs);
if(tdiffs == 0){ tdiffs = bdiffs + pdiffs + ldiffs + sdiffs; }
temp = validParameter.valid(parameters, "processors"); if (temp == "not found"){ temp = current->getProcessors(); }
processors = current->setProcessors(temp);
temp = validParameter.valid(parameters, "floworder"); if (temp == "not found"){ temp = "A"; }
if (temp.length() > 1) { m->mothurOut("[ERROR]: " + temp + " is not a valid option for floworder. floworder options are A, B, or I. A = TACG, B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC, and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n"); abort=true;
}
else {
if (toupper(temp[0]) == 'A') { flowOrder = "TACG"; }
else if(toupper(temp[0]) == 'B'){
flowOrder = "TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC"; }
else if(toupper(temp[0]) == 'I'){
flowOrder = "TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC"; }
else {
m->mothurOut("[ERROR]: " + temp + " is not a valid option for order. order options are A, B, or I. A = TACG, B = TACGTACGTACGATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATAGATCGCATGACGATCGCATATCGTCAGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGTAGTCGAGCATCATCTGACGCAGTACGTGCATGATCTCAGTCAGCAGCTATGTCAGTGCATGCATAGATCGCATGACGATCGCATATCGTCAGTGCAGTGACTGATCGTCATCAGCTAGCATCGACTGCATGATCTCAGTCAGCAGC, and I = TACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGCTACGTACGTCTGAGCATCGATCGATGTACAGC.\n"); abort=true;
}
}
if(oligoFileName == "") { allFiles = 0; }
else { allFiles = 1; }
temp = validParameter.valid(parameters, "checkorient"); if (temp == "not found") { temp = "F"; }
reorient = util.isTrue(temp);
numBarcodes = 0;
numFPrimers = 0;
numRPrimers = 0;
numLinkers = 0;
numSpacers = 0;
}
}
catch(exception& e) {
m->errorOut(e, "TrimFlowsCommand", "TrimFlowsCommand");
exit(1);
}
}
//***************************************************************************************************************
int TrimFlowsCommand::execute(){
try{
if (abort) { if (calledHelp) { return 0; } return 2; }
map<string, string> variables;
variables["[filename]"] = outputdir + util.getRootName(util.getSimpleName(flowFileName));
string fastaFileName = getOutputFileName("fasta",variables);
if(fasta){ outputNames.push_back(fastaFileName); outputTypes["fasta"].push_back(fastaFileName); }
variables["[tag]"] = "trim";
string trimFlowFileName = getOutputFileName("flow",variables);
outputNames.push_back(trimFlowFileName); outputTypes["flow"].push_back(trimFlowFileName);
variables["[tag]"] = "scrap";
string scrapFlowFileName = getOutputFileName("flow",variables);
outputNames.push_back(scrapFlowFileName); outputTypes["flow"].push_back(scrapFlowFileName);
createGroup = false;
if(oligoFileName != ""){ getOligos(); }
createProcessesCreateTrim(flowFileName, trimFlowFileName, scrapFlowFileName, fastaFileName);
if (m->getControl_pressed()) { return 0; }
string flowFilesFileName = getOutputFileName("file",variables);
outputTypes["file"].push_back(flowFilesFileName);
outputNames.push_back(flowFilesFileName);
if((allFiles) && (groupMap.size() != 0)) {
//print count file
string countFileName = getOutputFileName("count",variables);
CountTable ct; ct.createTable(groupMap);
ct.printCompressedTable(countFileName);
outputNames.push_back(countFileName); outputTypes["count"].push_back(countFileName);
//run split.groups command
string inputString = "flow=" + trimFlowFileName + ", count=" + countFileName;
m->mothurOut("\n/******************************************/\n");
m->mothurOut("Generating flow files for each sample...\n\nRunning command: split.groups(" + inputString + ")\n");
current->setMothurCalling(true);
SplitGroupCommand* splitCommand = new SplitGroupCommand(inputString);
splitCommand->execute();
map<string, vector<string> > filenames = splitCommand->getOutputFiles();
delete splitCommand;
current->setMothurCalling(false);
m->mothurOut("/******************************************/\n");
//print file file
map<string, vector<string> >::iterator itFiles = filenames.find("flow");
if (itFiles != filenames.end()) {
ofstream output; util.openOutputFile(flowFilesFileName, output);
for (int i = 0; i < (itFiles->second).size(); i++) {
output << (itFiles->second)[i] << endl;
outputNames.push_back((itFiles->second)[i]);
}
output.close();
}else {
ofstream output; util.openOutputFile(flowFilesFileName, output);
output << util.getFullPathName(trimFlowFileName) << endl; output.close();
}
}else{
ofstream output; util.openOutputFile(flowFilesFileName, output);
output << util.getFullPathName(trimFlowFileName) << endl; output.close();
}
current->setFileFile(flowFilesFileName);
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
//set group file as new current groupfile
string currentName = "";
itTypes = outputTypes.find("count");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setCountFile(currentName); }
}
itTypes = outputTypes.find("file");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setFileFile(currentName); }
}
return 0;
}
catch(exception& e) {
m->errorOut(e, "TrimFlowsCommand", "execute");
exit(1);
}
}
/**************************************************************************************************/
struct trimFlowData {
MothurOut* m;
string flowFileName, flowOrder;
OutputWriter* trimFile;
OutputWriter* scrapFile;
OutputWriter* fastaFile;
set<string> badNames;
unsigned long long lineStart, lineEnd;
bool pairedOligos, reorient, fasta, createGroup;
int tdiffs, bdiffs, pdiffs, ldiffs, sdiffs, numFlows, maxHomoP, maxFlows, minFlows;
float signal, noise;
long long count;
vector<string> revPrimer;
map<string, int> barcodes;
map<string, int> primers;
vector<string> linker;
vector<string> spacer;
vector<string> primerNameVector;
vector<string> barcodeNameVector;
map<int, oligosPair> pairedBarcodes;
map<int, oligosPair> pairedPrimers;
map<string, string> groupMap;
Utils util;
trimFlowData(){}
~trimFlowData() { }
trimFlowData(string fn, OutputWriter* tn, OutputWriter* sn, OutputWriter* ffn, bool useFasta, unsigned long long lstart, unsigned long long lend) {
fasta = useFasta;
fastaFile = ffn;
flowFileName = fn;
trimFile = tn;
scrapFile = sn;
lineStart = lstart;
lineEnd = lend;
m = MothurOut::getInstance();
}
void setOligosOptions(bool cg, int pd, int bd, int ld, int sd, int td, map<string, int> pri, map<string, int> bar, vector<string> revP, vector<string> li, vector<string> spa, map<int, oligosPair> pbr, map<int, oligosPair> ppr, bool po, vector<string> priNameVector, vector<string> barNameVector, bool reo, float sg, float nos, int mhom, string flo, int mxflo, int mnflo, int nmf) {
createGroup = cg;
pdiffs = pd;
bdiffs = bd;
ldiffs = ld;
sdiffs = sd;
tdiffs = td;
barcodes = bar;
pairedPrimers = ppr;
pairedBarcodes = pbr;
pairedOligos = po;
primers = pri;
revPrimer = revP;
linker = li;
spacer = spa;
primerNameVector = priNameVector;
barcodeNameVector = barNameVector;
reorient = reo;
signal = sg;
noise = nos;
maxHomoP = mhom;
flowOrder = flo;
maxFlows = mxflo;
minFlows = mnflo;
numFlows = nmf;
count = 0;
}
};
//***************************************************************************************************************
void driverCreateTrim(trimFlowData* params){
try {
ifstream flowFile; params->util.openInputFile(params->flowFileName, flowFile);
flowFile.seekg(params->lineStart);
if(params->lineStart == 0){ int temp; flowFile >> temp; gobble(flowFile); }
FlowData flowData(params->numFlows, params->signal, params->noise, params->maxHomoP, params->flowOrder);
params->count = 0;
int numBarcodes = 0;
int numLinkers = params->linker.size();
int numSpacers = params->spacer.size();
int numFPrimers = 0;
int numRPrimers = 0;
TrimOligos* trimOligos = nullptr;
if (params->pairedOligos) { trimOligos = new TrimOligos(params->pdiffs, params->bdiffs, 0, 0, params->pairedPrimers, params->pairedBarcodes, false); numBarcodes = params->pairedBarcodes.size(); numFPrimers = params->pairedPrimers.size(); }
else { trimOligos = new TrimOligos(params->pdiffs, params->bdiffs, params->ldiffs, params->sdiffs, params->primers, params->barcodes, params->revPrimer, params->linker, params->spacer); numBarcodes = params->barcodes.size(); numFPrimers = params->primers.size(); numRPrimers = params->revPrimer.size(); }
TrimOligos* rtrimOligos = nullptr;
if (params->reorient) {
//create reoriented primer and barcode pairs
map<int, oligosPair> rpairedPrimers, rpairedBarcodes;
for (map<int, oligosPair>::iterator it = params->pairedPrimers.begin(); it != params->pairedPrimers.end(); it++) {
oligosPair tempPair(params->util.reverseOligo((it->second).reverse), (params->util.reverseOligo((it->second).forward))); //reversePrimer, rc ForwardPrimer
rpairedPrimers[it->first] = tempPair;
}
for (map<int, oligosPair>::iterator it = params->pairedBarcodes.begin(); it != params->pairedBarcodes.end(); it++) {
oligosPair tempPair(params->util.reverseOligo((it->second).reverse), (params->util.reverseOligo((it->second).forward))); //reverseBarcode, rc ForwardBarcode
rpairedBarcodes[it->first] = tempPair;
}
int index = rpairedBarcodes.size();
for (map<string, int>::iterator it = params->barcodes.begin(); it != params->barcodes.end(); it++) {
oligosPair tempPair("", params->util.reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode
rpairedBarcodes[index] = tempPair; index++;
}
index = rpairedPrimers.size();
for (map<string, int>::iterator it = params->primers.begin(); it != params->primers.end(); it++) {
oligosPair tempPair("", params->util.reverseOligo((it->first))); //reverseBarcode, rc ForwardBarcode
rpairedPrimers[index] = tempPair; index++;
}
rtrimOligos = new TrimOligos(params->pdiffs, params->bdiffs, 0, 0, rpairedPrimers, rpairedBarcodes, false); numBarcodes = rpairedBarcodes.size();
}
bool moreSeqs = 1;
while(moreSeqs) {
if (params->m->getControl_pressed()) { break; }
int success = 1;
int currentSeqDiffs = 0;
string trashCode = "";
string commentString = "";
flowData.getNext(flowFile);
flowData.capFlows(params->maxFlows);
Sequence currSeq = flowData.getSequence();
//for reorient
Sequence savedSeq(currSeq.getName(), currSeq.getAligned());
if(!flowData.hasMinFlows(params->minFlows)){ //screen to see if sequence is of a minimum number of flows
success = 0;
trashCode += 'l';
}
if(!flowData.hasGoodHomoP()){ //screen to see if sequence meets the maximum homopolymer limit
success = 0;
trashCode += 'h';
}
int primerIndex = 0;
int barcodeIndex = 0;
if(numLinkers != 0){
success = trimOligos->stripLinker(currSeq);
if(success > params->ldiffs) { trashCode += 'k'; }
else{ currentSeqDiffs += success; }
}
if (params->m->getDebug()) { params->m->mothurOut("[DEBUG]: " + currSeq.getName() + " " + currSeq.getUnaligned() + "\n"); }
if(numBarcodes != 0){
vector<int> results = trimOligos->stripBarcode(currSeq, barcodeIndex);
if (params->pairedOligos) {
success = results[0] + results[2];
commentString += "fbdiffs=" + toString(results[0]) + "(" + trimOligos->getCodeValue(results[1], params->bdiffs) + "), rbdiffs=" + toString(results[2]) + "(" + trimOligos->getCodeValue(results[3], params->bdiffs) + ") ";
}
else {
success = results[0];
commentString += "bdiffs=" + toString(results[0]) + "(" + trimOligos->getCodeValue(results[1], params->bdiffs) + ") ";
}
if(success > params->bdiffs) { trashCode += 'b'; }
else{ currentSeqDiffs += success; }
}
if(numSpacers != 0){
success = trimOligos->stripSpacer(currSeq);
if(success > params->sdiffs) { trashCode += 's'; }
else{ currentSeqDiffs += success; }
}
if(numFPrimers != 0){
vector<int> results = trimOligos->stripForward(currSeq, primerIndex);
if (params->pairedOligos) {
success = results[0] + results[2];
commentString += "fpdiffs=" + toString(results[0]) + "(" + trimOligos->getCodeValue(results[1], params->pdiffs) + "), rpdiffs=" + toString(results[2]) + "(" + trimOligos->getCodeValue(results[3], params->pdiffs) + ") ";
}
else {
success = results[0];
commentString += "fpdiffs=" + toString(results[0]) + "(" + trimOligos->getCodeValue(results[1], params->pdiffs) + ") ";
}
if(success > params->pdiffs) { trashCode += 'f'; }
else{ currentSeqDiffs += success; }
}
if(numRPrimers != 0){
vector<int> results = trimOligos->stripReverse(currSeq);
success = results[0];
commentString += "rpdiffs=" + toString(results[0]) + "(" + trimOligos->getCodeValue(results[1], params->pdiffs) + ") ";
if(success > params->pdiffs) { trashCode += 'r'; }
else{ currentSeqDiffs += success; }
}
if (currentSeqDiffs > params->tdiffs) { trashCode += 't'; }
if (params->reorient && (trashCode != "")) { //if you failed and want to check the reverse
int thisSuccess = 0;
string thisTrashCode = "";
int thisCurrentSeqsDiffs = 0;
string thiscommentString = "";
int thisBarcodeIndex = 0;
int thisPrimerIndex = 0;
if(numBarcodes != 0){
vector<int> results = rtrimOligos->stripBarcode(savedSeq, thisBarcodeIndex);
if (params->pairedOligos) {
thisSuccess = results[0] + results[2];
thiscommentString += "fbdiffs=" + toString(results[0]) + "(" + rtrimOligos->getCodeValue(results[1], params->bdiffs) + "), rbdiffs=" + toString(results[2]) + "(" + rtrimOligos->getCodeValue(results[3], params->bdiffs) + ") ";
}
else {
thisSuccess = results[0];
thiscommentString += "bdiffs=" + toString(results[0]) + "(" + rtrimOligos->getCodeValue(results[1], params->bdiffs) + ") ";
}
if(thisSuccess > params->bdiffs) { thisTrashCode += "b"; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
if(numFPrimers != 0){
vector<int> results = rtrimOligos->stripForward(savedSeq, thisPrimerIndex);
if (params->pairedOligos) {
thisSuccess = results[0] + results[2];
thiscommentString += "fpdiffs=" + toString(results[0]) + "(" + rtrimOligos->getCodeValue(results[1], params->pdiffs) + "), rpdiffs=" + toString(results[2]) + "(" + rtrimOligos->getCodeValue(results[3], params->pdiffs) + ") ";
}
else {
thisSuccess = results[0];
thiscommentString += "pdiffs=" + toString(results[0]) + "(" + rtrimOligos->getCodeValue(results[1], params->pdiffs) + ") ";
}
if(thisSuccess > params->pdiffs) { thisTrashCode += "f"; }
else{ thisCurrentSeqsDiffs += thisSuccess; }
}
if (thisCurrentSeqsDiffs > params->tdiffs) { thisTrashCode += 't'; }
if (thisTrashCode == "") {
trashCode = thisTrashCode;
success = thisSuccess;
currentSeqDiffs = thisCurrentSeqsDiffs;
commentString = thiscommentString;
barcodeIndex = thisBarcodeIndex;
primerIndex = thisPrimerIndex;
savedSeq.reverseComplement();
currSeq.setAligned(savedSeq.getAligned());
}else { trashCode += "(" + thisTrashCode + ")"; }
}
currSeq.setComment(commentString);
if(trashCode.length() == 0){
string thisGroup = "";
if (params->createGroup) {
if(numBarcodes != 0){
thisGroup = params->barcodeNameVector[barcodeIndex];
if (numFPrimers != 0) {
if (params->primerNameVector[primerIndex] != "") {
if(thisGroup != "") { thisGroup += "." + params->primerNameVector[primerIndex]; }
else { thisGroup = params->primerNameVector[primerIndex]; }
}
}
}
}
int pos = thisGroup.find("ignore");
if (pos == string::npos) {
flowData.printFlows(params->trimFile);
if(params->fasta) { currSeq.printSequence(params->fastaFile); }
if (thisGroup != "") { params->groupMap[currSeq.getName()] = thisGroup; }
}
}else{
params->badNames.insert(currSeq.getName());
flowData.printFlows(params->scrapFile, trashCode);
}
params->count++;
if((params->count) % 10000 == 0){ params->m->mothurOut(toString(params->count)+"\n"); }
#if defined NON_WINDOWS
unsigned long long pos = flowFile.tellg();
if ((pos == -1) || (pos >= params->lineEnd)) { break; }
#else
if ((params->count == params->lineEnd) || (flowFile.eof())) { break; }
#endif
}
//report progress
if((params->count) % 10000 != 0){ params->m->mothurOut(toString(params->count)+"\n"); }
flowFile.close();
delete trimOligos;
if (params->reorient) { delete rtrimOligos; }
}
catch(exception& e) {
params->m->errorOut(e, "TrimSeqsCommand", "driverCreateTrim");
exit(1);
}
}
//***************************************************************************************************************
int TrimFlowsCommand::getOligos(){
try {
bool allBlank = false;
Oligos oligos; oligos.read(oligoFileName);
if (m->getControl_pressed()) { return 0; } //error in reading oligos
if (oligos.hasPairedBarcodes()) {
pairedOligos = true;
pairedPrimers = oligos.getPairedPrimers(); numFPrimers = pairedPrimers.size();
pairedBarcodes = oligos.getPairedBarcodes(); numBarcodes = pairedBarcodes.size();
}else {
pairedOligos = false;
primers = oligos.getPrimers(); numFPrimers = primers.size();
barcodes = oligos.getBarcodes(); numBarcodes = barcodes.size();
}
barcodeNameVector = oligos.getBarcodeNames();
primerNameVector = oligos.getPrimerNames();
linker = oligos.getLinkers(); numLinkers = linker.size();
spacer = oligos.getSpacers(); numSpacers = spacer.size();
revPrimer = oligos.getReversePrimers(); numRPrimers = revPrimer.size();
vector<string> groupNames = oligos.getGroupNames();
if (groupNames.size() == 0) { allFiles = 0; allBlank = true; }
else { createGroup = true; }
return 0;
}
catch(exception& e) {
m->errorOut(e, "TrimFlowsCommand", "getOligos");
exit(1);
}
}
/**************************************************************************************************/
vector<double> TrimFlowsCommand::getFlowFileBreaks() {
try{
vector<double> filePos;
filePos.push_back(0);
FILE * pFile;
double size = 0.0;
//get num bytes in file
flowFileName = util.getFullPathName(flowFileName);
pFile = fopen (flowFileName.c_str(),"rb");
if (pFile==nullptr) perror ("Error opening file");
else{
fseek (pFile, 0, SEEK_END);
size=ftell (pFile);
fclose (pFile);
}
//estimate file breaks
double chunkSize = 0;
chunkSize = size / processors;
//file too small to divide by processors
if (chunkSize == 0) { processors = 1; filePos.push_back(size); return filePos; }
//for each process seekg to closest file break and search for next '>' char. make that the filebreak
for (int i = 0; i < processors; i++) {
double spot = (i+1) * chunkSize;
ifstream in; util.openInputFile(flowFileName, in);
in.seekg(spot);
string dummy = util.getline(in);
//there was not another sequence before the end of the file
double sanityPos = in.tellg();
// if (sanityPos == -1) { break; }
// else { filePos.push_back(newSpot); }
if (sanityPos == -1) { break; }
else { filePos.push_back(sanityPos); }
in.close();
}
//save end pos
filePos.push_back(size);
//sanity check filePos
for (int i = 0; i < (filePos.size()-1); i++) {
if (filePos[(i+1)] <= filePos[i]) { filePos.erase(filePos.begin()+(i+1)); i--; }
}
ifstream in; util.openInputFile(flowFileName, in);
in >> numFlows;
gobble(in);
in.close();
processors = (filePos.size() - 1);
return filePos;
}
catch(exception& e) {
m->errorOut(e, "TrimSeqsCommand", "getFlowFileBreaks");
exit(1);
}
}
/**************************************************************************************************/
int TrimFlowsCommand::createProcessesCreateTrim(string flowFileName, string trimFlowFileName, string scrapFlowFileName, string fastaFileName){
try {
time_t start = time(nullptr);
ifstream in; util.openInputFile(flowFileName, in); in >> numFlows; in.close();
vector<linePair> lines;
#if defined NON_WINDOWS
vector<double> flowFilePos = getFlowFileBreaks();
for (int i = 0; i < (flowFilePos.size()-1); i++) { lines.push_back(linePair(flowFilePos[i], flowFilePos[(i+1)])); }
#else
if (processors == 1) { lines.push_back(linePair(0, -1)); }
else {
long long numFlowLines;
vector<double> flowFilePos = util.setFilePosEachLine(flowFileName, numFlowLines);
//figure out how many sequences you have to process
int numSeqsPerProcessor = numFlowLines / processors;
for (int i = 0; i < processors; i++) {
int startIndex = i * numSeqsPerProcessor;
if(i == (processors - 1)){ numSeqsPerProcessor = numFlowLines - i * numSeqsPerProcessor; }
lines.push_back(linePair(flowFilePos[startIndex], numSeqsPerProcessor));
}
}
#endif
//create array of worker threads
vector<std::thread*> workerThreads;
vector<trimFlowData*> data;
ofstream outTrim, outScrap;
util.openOutputFile(trimFlowFileName, outTrim); outTrim << maxFlows << endl; outTrim.close();
util.openOutputFile(scrapFlowFileName, outScrap); outScrap << numFlows << endl; outScrap.close();
auto synchronizedOutputTrimFile = std::make_shared<SynchronizedOutputFile>(trimFlowFileName, true); //append
auto synchronizedOutputScrapFile = std::make_shared<SynchronizedOutputFile>(scrapFlowFileName, true); //append
auto synchronizedOutputFastaFile = std::make_shared<SynchronizedOutputFile>(fastaFileName);
//Lauch worker threads
for (int i = 0; i < processors-1; i++) {
OutputWriter* threadTrimWriter = new OutputWriter(synchronizedOutputTrimFile);
OutputWriter* threadScrapWriter = new OutputWriter(synchronizedOutputScrapFile);
OutputWriter* threadFastaWriter = nullptr;
if (fasta) { threadFastaWriter = new OutputWriter(synchronizedOutputFastaFile); }
trimFlowData* dataBundle = new trimFlowData(flowFileName, threadTrimWriter, threadScrapWriter, threadFastaWriter, fasta, lines[i+1].start, lines[i+1].end);
dataBundle->setOligosOptions(createGroup, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, revPrimer, linker, spacer, pairedBarcodes, pairedPrimers, pairedOligos,
primerNameVector, barcodeNameVector, reorient, signal, noise, maxHomoP, flowOrder, maxFlows, minFlows, numFlows);
data.push_back(dataBundle);
workerThreads.push_back(new std::thread(driverCreateTrim, dataBundle));
}
OutputWriter* threadTrimWriter = new OutputWriter(synchronizedOutputTrimFile);
OutputWriter* threadScrapWriter = new OutputWriter(synchronizedOutputScrapFile);
OutputWriter* threadFastaWriter = nullptr;
if (fasta) { threadFastaWriter = new OutputWriter(synchronizedOutputFastaFile); }
trimFlowData* dataBundle = new trimFlowData(flowFileName, threadTrimWriter, threadScrapWriter, threadFastaWriter, fasta, lines[0].start, lines[0].end);
dataBundle->setOligosOptions(createGroup, pdiffs, bdiffs, ldiffs, sdiffs, tdiffs, primers, barcodes, revPrimer, linker, spacer, pairedBarcodes, pairedPrimers, pairedOligos,
primerNameVector, barcodeNameVector, reorient, signal, noise, maxHomoP, flowOrder, maxFlows, minFlows, numFlows);
driverCreateTrim(dataBundle);
long long num = dataBundle->count;
set<string> badNames = dataBundle->badNames;
groupMap = dataBundle->groupMap;
for (int i = 0; i < processors-1; i++) {
workerThreads[i]->join();
num += data[i]->count;
delete data[i]->trimFile;
delete data[i]->scrapFile;
if (fasta) { delete data[i]->fastaFile; }
badNames.insert(data[i]->badNames.begin(), data[i]->badNames.end());
groupMap.insert(data[i]->groupMap.begin(), data[i]->groupMap.end());
delete data[i];
delete workerThreads[i];
}
delete threadTrimWriter;
delete threadScrapWriter;
if (fasta) { delete threadFastaWriter; }
delete dataBundle;
m->mothurOut("It took " + toString(time(nullptr) - start) + " secs to trim " + toString(num) + " sequences."); if (m->getDebug()) { m->mothurOut("Scrapped " + toString(badNames.size()) + ".\n"); }
return num;
}
catch(exception& e) {
m->errorOut(e, "TrimFlowsCommand", "createProcessesCreateTrim");
exit(1);
}
}
//***************************************************************************************************************
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