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|
//
// mergesfffilecommand.cpp
// Mothur
//
// Created by Sarah Westcott on 1/31/14.
// Copyright (c) 2014 Schloss Lab. All rights reserved.
//
#include "mergesfffilecommand.h"
#include "endiannessmacros.h"
//********************************************************************************
MergeSfffilesCommand::~MergeSfffilesCommand(){
for (int i = 0; i < commonHeaders.size(); i++) { delete commonHeaders[i]; }
commonHeaders.clear();
}
//********************************************************************************
vector<string> MergeSfffilesCommand::setParameters(){
try {
CommandParameter psff("sff", "InputTypes", "", "", "sffFile", "sffFile", "none","sff",false,false); parameters.push_back(psff);
CommandParameter pfile("file", "InputTypes", "", "", "sffFile", "sffFile", "none","sff",false,false); parameters.push_back(pfile);
CommandParameter pkeytrim("keytrim", "Boolean", "", "F", "", "", "","",false,false); parameters.push_back(pkeytrim);
CommandParameter poutput("output", "String", "", "", "", "", "","",false,true,true); parameters.push_back(poutput);
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);
abort = false; calledHelp = false;
vector<string> tempOutNames;
outputTypes["sff"] = tempOutNames;
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, "MergeSfffilesCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************
string MergeSfffilesCommand::getHelpString(){
try {
string helpString = "";
helpString += "The merge.sfffiles command reads a sff file or a file containing a list of sff files and merges the individual files into a single sff file. \n";
helpString += "The merge.sfffiles command parameters are sff, file and output. sff or file is required. \n";
helpString += "The sff parameter allows you to enter the sff list of sff files separated by -'s.\n";
helpString += "The file parameter allows you to provide a file containing a list of sff files to merge. \n";
helpString += "The keytrim parameter allows you to mergesff files with different keysequence by trimming them to the first 4 characters. Provided the first 4 match. \n";
helpString += "The output parameter allows you to provide an output filename. \n";
helpString += "Example sffinfo(sff=mySffFile.sff-mySecond.sff).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "MergeSfffilesCommand", "getHelpString");
exit(1);
}
}
//*******************************************************************************
string MergeSfffilesCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "sff") { pattern = "[filename],"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->setControl_pressed(true); }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "MergeSfffilesCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************
MergeSfffilesCommand::MergeSfffilesCommand(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;
string inputDir = validParameter.validPath(parameters, "inputdir");
if (inputDir == "not found"){ inputDir = ""; }
sffFilename = validParameter.validPath(parameters, "sff");
if (sffFilename == "not found") { sffFilename = ""; }
else {
util.splitAtDash(sffFilename, filenames);
//go through files and make sure they are good, if not, then disregard them
for (int i = 0; i < filenames.size(); i++) {
bool ignore = false;
if (filenames[i] == "current") {
filenames[i] = current->getSFFFile();
if (filenames[i] != "") { m->mothurOut("Using " + filenames[i] + " as input file for the sff parameter where you had given current.\n"); }
else {
m->mothurOut("You have no current sfffile, ignoring current.\n"); ignore=true;
//erase from file list
filenames.erase(filenames.begin()+i);
i--;
}
}
if (!ignore) {
if (inputDir != "") {
string path = util.hasPath(filenames[i]);
//if the user has not given a path then, add inputdir. else leave path alone.
if (path == "") { filenames[i] = inputDir + filenames[i]; }
}
bool ableToOpen = util.checkLocations(filenames[i], current->getLocations());
if (!ableToOpen) {
m->mothurOut("Unable to open " + filenames[i] + ". It will be disregarded.\n");
filenames.erase(filenames.begin()+i); //erase from file list
i--;
}else { current->setSFFFile(filenames[i]); }
}
}
}
file = validParameter.validFile(parameters, "file");
if (file == "not open") { abort = true; }
else if (file == "not found") { file = ""; }
if ((file == "") && (filenames.size() == 0)) { m->mothurOut("[ERROR]: no valid files.\n"); abort = true; }
if ((file != "") && (filenames.size() != 0)) { //both are given
m->mothurOut("[ERROR]: cannot use file option and sff option at the same time, choose one.\n"); abort = true;
}
outputFile = validParameter.validPath(parameters, "output");
if (outputFile == "not found") { m->mothurOut("you must enter an output file name\n"); abort=true; }
if (outputdir != "") { outputFile = outputdir + util.getSimpleName(outputFile); }
string temp = validParameter.valid(parameters, "keytrim"); if (temp == "not found") { temp = "F"; }
keyTrim = util.isTrue(temp);
}
}
catch(exception& e) {
m->errorOut(e, "MergeSfffilesCommand", "MergeSfffilesCommand");
exit(1);
}
}
//*****************************************************************************
int MergeSfffilesCommand::execute(){
try {
if (abort) { if (calledHelp) { return 0; } return 2; }
if (file != "") {
readFile();
if (outputdir == "") { outputdir = util.hasPath(file); }
}
ofstream out;
map<string, string> variables;
string thisOutputDir = outputdir;
if (outputdir == "") { thisOutputDir += util.hasPath(outputFile); }
variables["[filename]"] = thisOutputDir + util.getSimpleName(outputFile);
outputFile = getOutputFileName("sff",variables);
util.openOutputFileBinary(outputFile, out);
outputNames.push_back(outputFile); outputTypes["sff"].push_back(outputFile);
outputFileHeader = outputFile + ".headers";
numTotalReads = 0;
for (int s = 0; s < filenames.size(); s++) {
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
long start = time(nullptr);
filenames[s] = util.getFullPathName(filenames[s]);
m->mothurOut("\nMerging info from " + filenames[s] + " ..." ); m->mothurOutEndLine();
int numReads = mergeSffInfo(filenames[s], out);
m->mothurOut("It took " + toString(time(nullptr) - start) + " secs to merge " + toString(numReads) + ".\n");
}
out.close();
//create new common header and add to merged file
adjustCommonHeader();
if (m->getControl_pressed()) { for (int i = 0; i < outputNames.size(); i++) { util.mothurRemove(outputNames[i]); } return 0; }
//set sff file as new current sff file
string currentName = "";
itTypes = outputTypes.find("sff");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { currentName = (itTypes->second)[0]; current->setSFFFile(currentName); }
}
//report output filenames
m->mothurOut("\nOutput File Names: \n");
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i] +"\n"); } m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "MergeSfffilesCommand", "execute");
exit(1);
}
}
//*****************************************************************************
int MergeSfffilesCommand::mergeSffInfo(string input, ofstream& out){
try {
currentFileName = input;
ifstream in; util.openInputFileBinary(input, in);
SffCommonHeader* header = new SffCommonHeader();
bool goodHeader = header->read(in);
if (!goodHeader) { return 0; }
commonHeaders.push_back(header); //save for adjustHeader sanity check
//read through the sff file
int count = 0; int numFlows = header->getNumFlows();
while (!in.eof()) {
//read data
SffRead* read = new SffRead(numFlows);
bool okay = read->readSff(in);
if (!okay) { break; }
read->printSff(out); numTotalReads++; count++;
delete read;
//report progress
if((count+1) % 10000 == 0){ m->mothurOut(toString(count+1)); m->mothurOutEndLine(); }
if (m->getControl_pressed()) { count = 0; break; }
if (count >= header->getNumReads()) { break; }
}
//report progress
if (!m->getControl_pressed()) { if((count) % 10000 != 0){ m->mothurOut(toString(count)); m->mothurOutEndLine(); } }
in.close();
return count;
}
catch(exception& e) {
m->errorOut(e, "MergeSfffilesCommand", "mergeSffInfo");
exit(1);
}
}
//****************************************************************************
void MergeSfffilesCommand::adjustCommonHeader(){
try {
//sanity check
bool okayMagic = true;
bool okayVersion = true;
bool okayHeader = true;
bool okayKeyLength = true;
bool okayNumFlows = true;
bool okayformatCode = true;
bool okayflowChar = true;
bool okayKeySequence = true;
if (commonHeaders.size() != 0) {
unsigned int magicN = commonHeaders[0]->getMagicNumber();
string version = commonHeaders[0]->getVersion();
unsigned short headerLength = commonHeaders[0]->getHeaderLength();
unsigned short keyLength = commonHeaders[0]->getKeyLength();
unsigned short numFlows = commonHeaders[0]->getNumFlows();
int flowCode = commonHeaders[0]->getFlowgramFormat();
string flowChars = commonHeaders[0]->getFlows();
string keySeq = commonHeaders[0]->getKeySequence();
for (int i = 1; i < commonHeaders.size(); i++) {
if (commonHeaders[i]->getMagicNumber() != magicN) { okayMagic = false; m->mothurOut("[ERROR]: merge issue with common headers. Magic numbers do not match. " + filenames[0] + " magic number is " + toString(magicN) + ", but " + filenames[i] + " magic number is " + toString(commonHeaders[i]->getMagicNumber()) + ".\n"); }
if (commonHeaders[i]->getVersion() != version) { okayVersion = false; m->mothurOut("[ERROR]: merge issue with common headers. Versions do not match. " + filenames[0] + " version is " + version + ", but " + filenames[i] + " version is " + commonHeaders[i]->getVersion() + ".\n"); }
if (commonHeaders[i]->getHeaderLength() != headerLength) { okayHeader = false; m->mothurOut("[ERROR]: merge issue with common headers. Header lengths do not match. " + filenames[0] + " header length is " + toString(headerLength) + ", but " + filenames[i] + " header length is " + toString(commonHeaders[i]->getHeaderLength()) + ".\n"); }
if (commonHeaders[i]->getKeyLength() != keyLength) { okayKeyLength = false; m->mothurOut("[ERROR]: merge issue with common headers. Key Lengths do not match. " + filenames[0] + " Key length is " + toString(keyLength) + ", but " + filenames[i] + " key length is " + toString(commonHeaders[i]->getKeyLength()) + ".\n"); }
if (commonHeaders[i]->getNumFlows() != numFlows) { okayNumFlows = false; m->mothurOut("[ERROR]: merge issue with common headers. Number of flows per read do not match. " + filenames[0] + " number of flows is " + toString(numFlows) + ", but " + filenames[i] + " number of flows is " + toString(commonHeaders[i]->getNumFlows()) + ".\n"); }
if (commonHeaders[i]->getFlowgramFormat() != flowCode) { okayformatCode = false; m->mothurOut("[ERROR]: merge issue with common headers. Flow format codes do not match. " + filenames[0] + " Flow format code is " + toString(flowCode) + ", but " + filenames[i] + " flow format code is " + toString(commonHeaders[i]->getFlowgramFormat()) + ".\n"); }
if (commonHeaders[i]->getFlows() != flowChars) { okayflowChar = false; m->mothurOut("[ERROR]: merge issue with common headers. Flow characters do not match. " + filenames[0] + " Flow characters are " + flowChars + ", but " + filenames[i] + " flow characters are " + commonHeaders[i]->getFlows() + ".\n"); }
if (commonHeaders[i]->getKeySequence() != keySeq) { okayKeySequence = false;
if (keyTrim) {
m->mothurOut("[WARNING]: merge issue with common headers. Key sequences do not match. " + filenames[0] + " Key sequence is " + keySeq + ", but " + filenames[i] + " key sequence is " + commonHeaders[i]->getKeySequence() + ". We will attempt to trim them.\n");
}else { m->mothurOut("[ERROR]: merge issue with common headers. Key sequences do not match. " + filenames[0] + " Key sequence is " + keySeq + ", but " + filenames[i] + " key sequence is " + commonHeaders[i]->getKeySequence() + ".\n");
}
}
}
}else { m->setControl_pressed(true); return; } //should never get here
bool modify = false;
if (!okayMagic || !okayVersion || !okayHeader || !okayKeyLength || !okayNumFlows || !okayformatCode || !okayflowChar) { m->setControl_pressed(true); return; }
if (!okayKeySequence) {
bool okayKeySequence2 = true;
string keySeq = commonHeaders[0]->getKeySequence().substr(0,4);
for (int i = 1; i < commonHeaders.size(); i++) {
if ((commonHeaders[i]->getKeySequence().substr(0,4)) != keySeq) { okayKeySequence2 = false; }
}
if (okayKeySequence2 && keyTrim) { modify = true;
m->mothurOut("We are able to trim the key sequences. Merged key seqeunce will be " + keySeq + ".\n");
}
}
ofstream out;
util.openOutputFileBinaryAppend(outputFileHeader, out);
commonHeaders[0]->printSampleCommonHeader(out, numTotalReads);
out.close();
util.appendSFFFiles(outputFile, outputFileHeader);
util.renameFile(outputFileHeader, outputFile);
util.mothurRemove(outputFileHeader);
}
catch(exception& e) {
m->errorOut(e, "MergeSfffilesCommand", "adjustCommonHeader");
exit(1);
}
}
//*************************************************************************************
void MergeSfffilesCommand::readFile(){
try {
ifstream in; util.openInputFile(file, in);
string filename;
while(!in.eof()) {
if (m->getControl_pressed()) { return; }
in >> filename; gobble(in);
if (m->getDebug()) { m->mothurOut("[DEBUG]: filename = " + filename + ".\n"); }
bool ableToOpen = util.checkLocations(filename, current->getLocations());
if (!ableToOpen) { //can't find it
m->mothurOut("[WARNING]: can't find " + filename + ", ignoring.\n");
}else{ filenames.push_back(filename); }
}
in.close();
}
catch(exception& e) {
m->errorOut(e, "MergeSfffilesCommand", "readFile");
exit(1);
}
}
//******************************************************************************************
|
