2 * removelineagecommand.cpp
5 * Created by westcott on 9/24/10.
6 * Copyright 2010 Schloss Lab. All rights reserved.
10 #include "removelineagecommand.h"
11 #include "sequence.hpp"
12 #include "listvector.hpp"
14 //**********************************************************************************************************************
15 vector<string> RemoveLineageCommand::setParameters(){
17 CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pfasta);
18 CommandParameter pname("name", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pname);
19 CommandParameter pgroup("group", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(pgroup);
20 CommandParameter plist("list", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(plist);
21 CommandParameter ptaxonomy("taxonomy", "InputTypes", "", "", "none", "FNGLT", "none",false,true); parameters.push_back(ptaxonomy);
22 CommandParameter palignreport("alignreport", "InputTypes", "", "", "none", "FNGLT", "none",false,false); parameters.push_back(palignreport);
23 CommandParameter ptaxon("taxon", "String", "", "", "", "", "",false,true); parameters.push_back(ptaxon);
24 CommandParameter pdups("dups", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pdups);
25 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
26 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
28 vector<string> myArray;
29 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
33 m->errorOut(e, "RemoveLineageCommand", "setParameters");
37 //**********************************************************************************************************************
38 string RemoveLineageCommand::getHelpString(){
40 string helpString = "";
41 helpString += "The remove.lineage command reads a taxonomy file and any of the following file types: fasta, name, group, list or alignreport file.\n";
42 helpString += "It outputs a file containing only the sequences from the taxonomy file that are not from the taxon you requested to be removed.\n";
43 helpString += "The remove.lineage command parameters are taxon, fasta, name, group, list, taxonomy, alignreport and dups. You must provide taxonomy unless you have a valid current taxonomy file.\n";
44 helpString += "The dups parameter allows you to add the entire line from a name file if you add any name from the line. default=false. \n";
45 helpString += "The taxon parameter allows you to select the taxons you would like to remove, and is required.\n";
46 helpString += "You may enter your taxons with confidence scores, doing so will remove only those sequences that belong to the taxonomy and whose cofidence scores fall below the scores you give.\n";
47 helpString += "If they belong to the taxonomy and have confidences above those you provide the sequence will not be removed.\n";
48 helpString += "The remove.lineage command should be in the following format: remove.lineage(taxonomy=yourTaxonomyFile, taxon=yourTaxons).\n";
49 helpString += "Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon=Bacteria;Firmicutes;Bacilli;Lactobacillales;).\n";
50 helpString += "Note: If you are running mothur in script mode you must wrap the taxon in ' characters so mothur will ignore the ; in the taxon.\n";
51 helpString += "Example remove.lineage(taxonomy=amazon.silva.taxonomy, taxon='Bacteria;Firmicutes;Bacilli;Lactobacillales;').\n";
52 helpString += "Note: No spaces between parameter labels (i.e. fasta), '=' and parameters (i.e.yourFasta).\n";
56 m->errorOut(e, "RemoveLineageCommand", "getHelpString");
62 //**********************************************************************************************************************
63 RemoveLineageCommand::RemoveLineageCommand(){
65 abort = true; calledHelp = true;
67 vector<string> tempOutNames;
68 outputTypes["fasta"] = tempOutNames;
69 outputTypes["taxonomy"] = tempOutNames;
70 outputTypes["name"] = tempOutNames;
71 outputTypes["group"] = tempOutNames;
72 outputTypes["alignreport"] = tempOutNames;
73 outputTypes["list"] = tempOutNames;
76 m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
80 //**********************************************************************************************************************
81 RemoveLineageCommand::RemoveLineageCommand(string option) {
83 abort = false; calledHelp = false;
85 //allow user to run help
86 if(option == "help") { help(); abort = true; calledHelp = true; }
89 vector<string> myArray = setParameters();
91 OptionParser parser(option);
92 map<string,string> parameters = parser.getParameters();
94 ValidParameters validParameter;
95 map<string,string>::iterator it;
97 //check to make sure all parameters are valid for command
98 for (it = parameters.begin(); it != parameters.end(); it++) {
99 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
102 //initialize outputTypes
103 vector<string> tempOutNames;
104 outputTypes["fasta"] = tempOutNames;
105 outputTypes["taxonomy"] = tempOutNames;
106 outputTypes["name"] = tempOutNames;
107 outputTypes["group"] = tempOutNames;
108 outputTypes["alignreport"] = tempOutNames;
109 outputTypes["list"] = tempOutNames;
111 //if the user changes the output directory command factory will send this info to us in the output parameter
112 outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; }
114 //if the user changes the input directory command factory will send this info to us in the output parameter
115 string inputDir = validParameter.validFile(parameters, "inputdir", false);
116 if (inputDir == "not found"){ inputDir = ""; }
119 it = parameters.find("alignreport");
120 //user has given a template file
121 if(it != parameters.end()){
122 path = m->hasPath(it->second);
123 //if the user has not given a path then, add inputdir. else leave path alone.
124 if (path == "") { parameters["alignreport"] = inputDir + it->second; }
127 it = parameters.find("fasta");
128 //user has given a template file
129 if(it != parameters.end()){
130 path = m->hasPath(it->second);
131 //if the user has not given a path then, add inputdir. else leave path alone.
132 if (path == "") { parameters["fasta"] = inputDir + it->second; }
135 it = parameters.find("list");
136 //user has given a template file
137 if(it != parameters.end()){
138 path = m->hasPath(it->second);
139 //if the user has not given a path then, add inputdir. else leave path alone.
140 if (path == "") { parameters["list"] = inputDir + it->second; }
143 it = parameters.find("name");
144 //user has given a template file
145 if(it != parameters.end()){
146 path = m->hasPath(it->second);
147 //if the user has not given a path then, add inputdir. else leave path alone.
148 if (path == "") { parameters["name"] = inputDir + it->second; }
151 it = parameters.find("group");
152 //user has given a template file
153 if(it != parameters.end()){
154 path = m->hasPath(it->second);
155 //if the user has not given a path then, add inputdir. else leave path alone.
156 if (path == "") { parameters["group"] = inputDir + it->second; }
159 it = parameters.find("taxonomy");
160 //user has given a template file
161 if(it != parameters.end()){
162 path = m->hasPath(it->second);
163 //if the user has not given a path then, add inputdir. else leave path alone.
164 if (path == "") { parameters["taxonomy"] = inputDir + it->second; }
169 //check for required parameters
170 fastafile = validParameter.validFile(parameters, "fasta", true);
171 if (fastafile == "not open") { abort = true; }
172 else if (fastafile == "not found") { fastafile = ""; }
174 namefile = validParameter.validFile(parameters, "name", true);
175 if (namefile == "not open") { abort = true; }
176 else if (namefile == "not found") { namefile = ""; }
178 groupfile = validParameter.validFile(parameters, "group", true);
179 if (groupfile == "not open") { abort = true; }
180 else if (groupfile == "not found") { groupfile = ""; }
182 alignfile = validParameter.validFile(parameters, "alignreport", true);
183 if (alignfile == "not open") { abort = true; }
184 else if (alignfile == "not found") { alignfile = ""; }
186 listfile = validParameter.validFile(parameters, "list", true);
187 if (listfile == "not open") { abort = true; }
188 else if (listfile == "not found") { listfile = ""; }
190 taxfile = validParameter.validFile(parameters, "taxonomy", true);
191 if (taxfile == "not open") { abort = true; }
192 else if (taxfile == "not found") {
193 taxfile = m->getTaxonomyFile();
194 if (taxfile != "") { m->mothurOut("Using " + taxfile + " as input file for the taxonomy parameter."); m->mothurOutEndLine(); }
195 else { m->mothurOut("You have no current taxonomy file and the taxonomy parameter is required."); m->mothurOutEndLine(); abort = true; }
198 string usedDups = "true";
199 string temp = validParameter.validFile(parameters, "dups", false);
200 if (temp == "not found") {
201 if (namefile != "") { temp = "true"; }
202 else { temp = "false"; usedDups = ""; }
204 dups = m->isTrue(temp);
206 taxons = validParameter.validFile(parameters, "taxon", false);
207 if (taxons == "not found") { taxons = ""; m->mothurOut("No taxons given, please correct."); m->mothurOutEndLine(); abort = true; }
210 if (taxons[0] == '\'') { taxons = taxons.substr(1); }
211 if (taxons[(taxons.length()-1)] == '\'') { taxons = taxons.substr(0, (taxons.length()-1)); }
215 if ((fastafile == "") && (namefile == "") && (groupfile == "") && (alignfile == "") && (listfile == "") && (taxfile == "")) { m->mothurOut("You must provide one of the following: fasta, name, group, alignreport, taxonomy or listfile."); m->mothurOutEndLine(); abort = true; }
217 if ((usedDups != "") && (namefile == "")) { m->mothurOut("You may only use dups with the name option."); m->mothurOutEndLine(); abort = true; }
222 catch(exception& e) {
223 m->errorOut(e, "RemoveLineageCommand", "RemoveLineageCommand");
227 //**********************************************************************************************************************
229 int RemoveLineageCommand::execute(){
232 if (abort == true) { if (calledHelp) { return 0; } return 2; }
234 if (m->control_pressed) { return 0; }
236 //read through the correct file and output lines you want to keep
237 if (taxfile != "") { readTax(); } //fills the set of names to remove
238 if (namefile != "") { readName(); }
239 if (fastafile != "") { readFasta(); }
240 if (groupfile != "") { readGroup(); }
241 if (alignfile != "") { readAlign(); }
242 if (listfile != "") { readList(); }
245 if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) { remove(outputNames[i].c_str()); } return 0; }
247 if (outputNames.size() != 0) {
248 m->mothurOutEndLine();
249 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
250 for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
251 m->mothurOutEndLine();
253 //set fasta file as new current fastafile
255 itTypes = outputTypes.find("fasta");
256 if (itTypes != outputTypes.end()) {
257 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setFastaFile(current); }
260 itTypes = outputTypes.find("name");
261 if (itTypes != outputTypes.end()) {
262 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setNameFile(current); }
265 itTypes = outputTypes.find("group");
266 if (itTypes != outputTypes.end()) {
267 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setGroupFile(current); }
270 itTypes = outputTypes.find("list");
271 if (itTypes != outputTypes.end()) {
272 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setListFile(current); }
275 itTypes = outputTypes.find("taxonomy");
276 if (itTypes != outputTypes.end()) {
277 if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTaxonomyFile(current); }
284 catch(exception& e) {
285 m->errorOut(e, "RemoveLineageCommand", "execute");
290 //**********************************************************************************************************************
291 int RemoveLineageCommand::readFasta(){
293 string thisOutputDir = outputDir;
294 if (outputDir == "") { thisOutputDir += m->hasPath(fastafile); }
295 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(fastafile)) + "pick" + m->getExtension(fastafile);
298 m->openOutputFile(outputFileName, out);
301 m->openInputFile(fastafile, in);
304 bool wroteSomething = false;
307 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
309 Sequence currSeq(in);
310 name = currSeq.getName();
313 //if this name is in the accnos file
314 if (names.count(name) == 0) {
315 wroteSomething = true;
317 currSeq.printSequence(out);
325 if (wroteSomething == false) { m->mothurOut("Your fasta file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
326 outputNames.push_back(outputFileName); outputTypes["fasta"].push_back(outputFileName);
331 catch(exception& e) {
332 m->errorOut(e, "RemoveLineageCommand", "readFasta");
336 //**********************************************************************************************************************
337 int RemoveLineageCommand::readList(){
339 string thisOutputDir = outputDir;
340 if (outputDir == "") { thisOutputDir += m->hasPath(listfile); }
341 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(listfile)) + "pick" + m->getExtension(listfile);
344 m->openOutputFile(outputFileName, out);
347 m->openInputFile(listfile, in);
349 bool wroteSomething = false;
352 //read in list vector
355 //make a new list vector
357 newList.setLabel(list.getLabel());
360 for (int i = 0; i < list.getNumBins(); i++) {
361 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
363 //parse out names that are in accnos file
364 string binnames = list.get(i);
366 string newNames = "";
367 while (binnames.find_first_of(',') != -1) {
368 string name = binnames.substr(0,binnames.find_first_of(','));
369 binnames = binnames.substr(binnames.find_first_of(',')+1, binnames.length());
371 //if that name is in the .accnos file, add it
372 if (names.count(name) == 0) { newNames += name + ","; }
376 if (names.count(binnames) == 0) { newNames += binnames + ","; }
378 //if there are names in this bin add to new list
379 if (newNames != "") {
380 newNames = newNames.substr(0, newNames.length()-1); //rip off extra comma
381 newList.push_back(newNames);
385 //print new listvector
386 if (newList.getNumBins() != 0) {
387 wroteSomething = true;
396 if (wroteSomething == false) { m->mothurOut("Your list file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
397 outputNames.push_back(outputFileName); outputTypes["list"].push_back(outputFileName);
402 catch(exception& e) {
403 m->errorOut(e, "RemoveLineageCommand", "readList");
407 //**********************************************************************************************************************
408 int RemoveLineageCommand::readName(){
410 string thisOutputDir = outputDir;
411 if (outputDir == "") { thisOutputDir += m->hasPath(namefile); }
412 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(namefile)) + "pick" + m->getExtension(namefile);
415 m->openOutputFile(outputFileName, out);
418 m->openInputFile(namefile, in);
419 string name, firstCol, secondCol;
421 bool wroteSomething = false;
424 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
429 vector<string> parsedNames;
430 m->splitAtComma(secondCol, parsedNames);
432 vector<string> validSecond; validSecond.clear();
433 for (int i = 0; i < parsedNames.size(); i++) {
434 if (names.count(parsedNames[i]) == 0) {
435 validSecond.push_back(parsedNames[i]);
439 if ((dups) && (validSecond.size() != parsedNames.size())) { //if dups is true and we want to get rid of anyone, get rid of everyone
440 for (int i = 0; i < parsedNames.size(); i++) { names.insert(parsedNames[i]); }
442 //if the name in the first column is in the set then print it and any other names in second column also in set
443 if (names.count(firstCol) == 0) {
445 wroteSomething = true;
447 out << firstCol << '\t';
449 //you know you have at least one valid second since first column is valid
450 for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
451 out << validSecond[validSecond.size()-1] << endl;
453 //make first name in set you come to first column and then add the remaining names to second column
456 //you want part of this row
457 if (validSecond.size() != 0) {
459 wroteSomething = true;
461 out << validSecond[0] << '\t';
463 //you know you have at least one valid second since first column is valid
464 for (int i = 0; i < validSecond.size()-1; i++) { out << validSecond[i] << ','; }
465 out << validSecond[validSecond.size()-1] << endl;
474 if (wroteSomething == false) { m->mothurOut("Your name file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
475 outputNames.push_back(outputFileName); outputTypes["name"].push_back(outputFileName);
479 catch(exception& e) {
480 m->errorOut(e, "RemoveLineageCommand", "readName");
485 //**********************************************************************************************************************
486 int RemoveLineageCommand::readGroup(){
488 string thisOutputDir = outputDir;
489 if (outputDir == "") { thisOutputDir += m->hasPath(groupfile); }
490 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(groupfile)) + "pick" + m->getExtension(groupfile);
493 m->openOutputFile(outputFileName, out);
496 m->openInputFile(groupfile, in);
499 bool wroteSomething = false;
502 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
504 in >> name; //read from first column
505 in >> group; //read from second column
507 //if this name is in the accnos file
508 if (names.count(name) == 0) {
509 wroteSomething = true;
510 out << name << '\t' << group << endl;
518 if (wroteSomething == false) { m->mothurOut("Your group file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
519 outputNames.push_back(outputFileName); outputTypes["group"].push_back(outputFileName);
523 catch(exception& e) {
524 m->errorOut(e, "RemoveLineageCommand", "readGroup");
528 //**********************************************************************************************************************
529 int RemoveLineageCommand::readTax(){
531 string thisOutputDir = outputDir;
532 if (outputDir == "") { thisOutputDir += m->hasPath(taxfile); }
533 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(taxfile)) + "pick" + m->getExtension(taxfile);
535 m->openOutputFile(outputFileName, out);
538 m->openInputFile(taxfile, in);
541 bool wroteSomething = false;
543 bool taxonsHasConfidence = false;
544 vector< map<string, float> > searchTaxons;
545 string noConfidenceTaxons = taxons;
546 int hasConPos = taxons.find_first_of('(');
547 if (hasConPos != string::npos) {
548 taxonsHasConfidence = true;
549 searchTaxons = getTaxons(taxons);
550 noConfidenceTaxons = removeConfidences(taxons);
556 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
558 in >> name; //read from first column
559 in >> tax; //read from second column
563 //if the users file contains confidence scores we want to ignore them when searching for the taxons, unless the taxon has them
564 if (!taxonsHasConfidence) {
566 int hasConfidences = tax.find_first_of('(');
567 if (hasConfidences != string::npos) {
568 newtax = removeConfidences(tax);
571 int pos = newtax.find(taxons);
573 if (pos == string::npos) {
574 wroteSomething = true;
575 out << name << '\t' << tax << endl;
576 }else{ //this sequence contains the taxon the user wants to remove
580 }else{//if taxons has them and you don't them remove taxons
581 int hasConfidences = tax.find_first_of('(');
582 if (hasConfidences == string::npos) {
584 int pos = newtax.find(noConfidenceTaxons);
586 if (pos == string::npos) {
587 wroteSomething = true;
588 out << name << '\t' << tax << endl;
589 }else{ //this sequence contains the taxon the user wants to remove
592 }else { //both have confidences so we want to make sure the users confidences are greater then or equal to the taxons
593 //first remove confidences from both and see if the taxonomy exists
595 string noNewTax = tax;
596 int hasConfidences = tax.find_first_of('(');
597 if (hasConfidences != string::npos) {
598 noNewTax = removeConfidences(tax);
601 int pos = noNewTax.find(noConfidenceTaxons);
603 if (pos != string::npos) { //if yes, then are the confidences okay
606 vector< map<string, float> > usersTaxon = getTaxons(newtax);
608 //the usersTaxon is most likely longer than the searchTaxons, and searchTaxon[0] may relate to userTaxon[4]
609 //we want to "line them up", so we will find the the index where the searchstring starts
611 for (int i = 0; i < usersTaxon.size(); i++) {
613 if (usersTaxon[i].begin()->first == searchTaxons[0].begin()->first) {
616 bool goodspot = true;
617 //is this really the start, or are we dealing with a taxon of the same name?
618 while ((spot < searchTaxons.size()) && ((i+spot) < usersTaxon.size())) {
619 if (usersTaxon[i+spot].begin()->first != searchTaxons[spot].begin()->first) { goodspot = false; break; }
623 if (goodspot) { break; }
627 for (int i = 0; i < searchTaxons.size(); i++) {
629 if ((i+index) < usersTaxon.size()) { //just in case, should never be false
630 if (usersTaxon[i+index].begin()->second < searchTaxons[i].begin()->second) { //is the users cutoff less than the search taxons
640 //passed the test so remove you
644 wroteSomething = true;
645 out << name << '\t' << tax << endl;
648 wroteSomething = true;
649 out << name << '\t' << tax << endl;
662 if (!wroteSomething) { m->mothurOut("Your taxonomy file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
663 outputNames.push_back(outputFileName); outputTypes["taxonomy"].push_back(outputFileName);
668 catch(exception& e) {
669 m->errorOut(e, "RemoveLineageCommand", "readTax");
673 /**************************************************************************************************/
674 vector< map<string, float> > RemoveLineageCommand::getTaxons(string tax) {
677 vector< map<string, float> > t;
679 int taxLength = tax.length();
680 for(int i=0;i<taxLength;i++){
683 int openParen = taxon.find_first_of('(');
684 int closeParen = taxon.find_last_of(')');
686 string newtaxon, confidence;
687 if ((openParen != string::npos) && (closeParen != string::npos)) {
688 newtaxon = taxon.substr(0, openParen); //rip off confidence
689 confidence = taxon.substr((openParen+1), (closeParen-openParen-1));
695 convert(confidence, con);
697 map<string, float> temp;
698 temp[newtaxon] = con;
710 catch(exception& e) {
711 m->errorOut(e, "RemoveLineageCommand", "getTaxons");
715 /**************************************************************************************************/
716 string RemoveLineageCommand::removeConfidences(string tax) {
720 int taxLength = tax.length();
721 for(int i=0;i<taxLength;i++){
723 taxon = taxon.substr(0, taxon.find_first_of('(')); //rip off confidence
733 catch(exception& e) {
734 m->errorOut(e, "RemoveLineageCommand", "removeConfidences");
738 //**********************************************************************************************************************
739 //alignreport file has a column header line then all other lines contain 16 columns. we just want the first column since that contains the name
740 int RemoveLineageCommand::readAlign(){
742 string thisOutputDir = outputDir;
743 if (outputDir == "") { thisOutputDir += m->hasPath(alignfile); }
744 string outputFileName = thisOutputDir + m->getRootName(m->getSimpleName(alignfile)) + "pick.align.report";
747 m->openOutputFile(outputFileName, out);
750 m->openInputFile(alignfile, in);
753 bool wroteSomething = false;
755 //read column headers
756 for (int i = 0; i < 16; i++) {
757 if (!in.eof()) { in >> junk; out << junk << '\t'; }
763 if (m->control_pressed) { in.close(); out.close(); remove(outputFileName.c_str()); return 0; }
765 in >> name; //read from first column
767 //if this name is in the accnos file
768 if (names.count(name) == 0) {
769 wroteSomething = true;
774 for (int i = 0; i < 15; i++) {
775 if (!in.eof()) { in >> junk; out << junk << '\t'; }
780 }else {//still read just don't do anything with it
783 for (int i = 0; i < 15; i++) {
784 if (!in.eof()) { in >> junk; }
794 if (wroteSomething == false) { m->mothurOut("Your align file contains only sequences from " + taxons + "."); m->mothurOutEndLine(); }
795 outputNames.push_back(outputFileName); outputTypes["alignreport"].push_back(outputFileName);
800 catch(exception& e) {
801 m->errorOut(e, "RemoveLineageCommand", "readAlign");
805 //**********************************************************************************************************************