X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=chimerauchimecommand.cpp;h=bad4c96b8c74d645208be1158ad11cd2ef924faf;hb=01f8d2c7d982a6209211f5abbcf2a086fdf60d0a;hp=e28775f016c4e992d2d8f2d23904c93c6e3f74ef;hpb=f6b5fea6e0fcc395235dfbfb466b9b6a031b540a;p=mothur.git diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp index e28775f..bad4c96 100644 --- a/chimerauchimecommand.cpp +++ b/chimerauchimecommand.cpp @@ -19,8 +19,9 @@ vector ChimeraUchimeCommand::setParameters(){ try { CommandParameter ptemplate("reference", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(ptemplate); CommandParameter pfasta("fasta", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pfasta); - CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pname); - CommandParameter pgroup("group", "InputTypes", "", "", "none", "none", "none",false,false); parameters.push_back(pgroup); + CommandParameter pname("name", "InputTypes", "", "", "NameCount", "none", "none",false,false); parameters.push_back(pname); + CommandParameter pcount("count", "InputTypes", "", "", "NameCount-CountGroup", "none", "none",false,false); parameters.push_back(pcount); + CommandParameter pgroup("group", "InputTypes", "", "", "CountGroup", "none", "none",false,false); parameters.push_back(pgroup); CommandParameter pprocessors("processors", "Number", "", "1", "", "", "",false,false); parameters.push_back(pprocessors); CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir); CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir); @@ -58,9 +59,10 @@ string ChimeraUchimeCommand::getHelpString(){ string helpString = ""; helpString += "The chimera.uchime command reads a fastafile and referencefile and outputs potentially chimeric sequences.\n"; helpString += "This command is a wrapper for uchime written by Robert C. Edgar.\n"; - helpString += "The chimera.uchime command parameters are fasta, name, reference, processors, abskew, chimealns, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, skipgaps, skipgaps2, minlen, maxlen, ucl and queryfact.\n"; + helpString += "The chimera.uchime command parameters are fasta, name, count, reference, processors, abskew, chimealns, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, skipgaps, skipgaps2, minlen, maxlen, ucl and queryfact.\n"; helpString += "The fasta parameter allows you to enter the fasta file containing your potentially chimeric sequences, and is required, unless you have a valid current fasta file. \n"; helpString += "The name parameter allows you to provide a name file, if you are using template=self. \n"; + helpString += "The count parameter allows you to provide a count file, if you are using template=self. \n"; helpString += "You may enter multiple fasta files by separating their names with dashes. ie. fasta=abrecovery.fasta-amazon.fasta \n"; helpString += "The group parameter allows you to provide a group file. The group file can be used with a namesfile and reference=self. When checking sequences, only sequences from the same group as the query sequence will be used as the reference. \n"; helpString += "The reference parameter allows you to enter a reference file containing known non-chimeric sequences, and is required. You may also set template=self, in this case the abundant sequences will be used as potential parents. \n"; @@ -98,6 +100,28 @@ string ChimeraUchimeCommand::getHelpString(){ } } //********************************************************************************************************************** +string ChimeraUchimeCommand::getOutputFileNameTag(string type, string inputName=""){ + try { + string outputFileName = ""; + map >::iterator it; + + //is this a type this command creates + it = outputTypes.find(type); + if (it == outputTypes.end()) { m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); } + else { + if (type == "chimera") { outputFileName = "uchime.chimeras"; } + else if (type == "accnos") { outputFileName = "uchime.accnos"; } + else if (type == "alns") { outputFileName = "uchime.alns"; } + else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true; } + } + return outputFileName; + } + catch(exception& e) { + m->errorOut(e, "ChimeraUchimeCommand", "getOutputFileNameTag"); + exit(1); + } +} +//********************************************************************************************************************** ChimeraUchimeCommand::ChimeraUchimeCommand(){ try { abort = true; calledHelp = true; @@ -115,7 +139,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(){ //*************************************************************************************************************** ChimeraUchimeCommand::ChimeraUchimeCommand(string option) { try { - abort = false; calledHelp = false; + abort = false; calledHelp = false; hasName=false; hasCount=false; ReferenceDB* rdb = ReferenceDB::getInstance(); //allow user to run help @@ -225,9 +249,8 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) { //check for required parameters - bool hasName = true; namefile = validParameter.validFile(parameters, "name", false); - if (namefile == "not found") { namefile = ""; hasName = false; } + if (namefile == "not found") { namefile = ""; } else { m->splitAtDash(namefile, nameFileNames); @@ -294,12 +317,91 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) { } } } + } + + if (nameFileNames.size() != 0) { hasName = true; } + + //check for required parameters + vector countfileNames; + countfile = validParameter.validFile(parameters, "count", false); + if (countfile == "not found") { + countfile = ""; + }else { + m->splitAtDash(countfile, countfileNames); - //make sure there is at least one valid file left - if (nameFileNames.size() == 0) { m->mothurOut("[ERROR]: no valid name files."); m->mothurOutEndLine(); abort = true; } + //go through files and make sure they are good, if not, then disregard them + for (int i = 0; i < countfileNames.size(); i++) { + + bool ignore = false; + if (countfileNames[i] == "current") { + countfileNames[i] = m->getCountTableFile(); + if (nameFileNames[i] != "") { m->mothurOut("Using " + countfileNames[i] + " as input file for the count parameter where you had given current."); m->mothurOutEndLine(); } + else { + m->mothurOut("You have no current count file, ignoring current."); m->mothurOutEndLine(); ignore=true; + //erase from file list + countfileNames.erase(countfileNames.begin()+i); + i--; + } + } + + if (!ignore) { + + if (inputDir != "") { + string path = m->hasPath(countfileNames[i]); + //if the user has not given a path then, add inputdir. else leave path alone. + if (path == "") { countfileNames[i] = inputDir + countfileNames[i]; } + } + + int ableToOpen; + ifstream in; + + ableToOpen = m->openInputFile(countfileNames[i], in, "noerror"); + + //if you can't open it, try default location + if (ableToOpen == 1) { + if (m->getDefaultPath() != "") { //default path is set + string tryPath = m->getDefaultPath() + m->getSimpleName(countfileNames[i]); + m->mothurOut("Unable to open " + countfileNames[i] + ". Trying default " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + countfileNames[i] = tryPath; + } + } + + if (ableToOpen == 1) { + if (m->getOutputDir() != "") { //default path is set + string tryPath = m->getOutputDir() + m->getSimpleName(countfileNames[i]); + m->mothurOut("Unable to open " + countfileNames[i] + ". Trying output directory " + tryPath); m->mothurOutEndLine(); + ifstream in2; + ableToOpen = m->openInputFile(tryPath, in2, "noerror"); + in2.close(); + countfileNames[i] = tryPath; + } + } + + in.close(); + + if (ableToOpen == 1) { + m->mothurOut("Unable to open " + countfileNames[i] + ". It will be disregarded."); m->mothurOutEndLine(); + //erase from file list + countfileNames.erase(countfileNames.begin()+i); + i--; + }else { + m->setCountTableFile(countfileNames[i]); + } + } + } } - - if (hasName && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of namefiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; } + + if (countfileNames.size() != 0) { hasCount = true; } + + //make sure there is at least one valid file left + if (hasName && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or name."); m->mothurOutEndLine(); abort = true; } + + if (!hasName && hasCount) { nameFileNames = countfileNames; } + + if ((hasCount || hasName) && (nameFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of name or count files does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; } bool hasGroup = true; groupfile = validParameter.validFile(parameters, "group", false); @@ -377,6 +479,10 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) { if (hasGroup && (groupFileNames.size() != fastaFileNames.size())) { m->mothurOut("[ERROR]: The number of groupfiles does not match the number of fastafiles, please correct."); m->mothurOutEndLine(); abort=true; } + if (hasGroup && hasCount) { m->mothurOut("[ERROR]: You must enter ONLY ONE of the following: count or group."); m->mothurOutEndLine(); abort = true; } + //if the user changes the output directory command factory will send this info to us in the output parameter + outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } + //if the user changes the output directory command factory will send this info to us in the output parameter outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = ""; } @@ -405,6 +511,7 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) { } } }else if (hasName) { templatefile = "self"; } + else if (hasCount) { templatefile = "self"; } else { if (rdb->getSavedReference() != "") { templatefile = rdb->getSavedReference(); @@ -481,8 +588,26 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) { ifstream in; uchimeCommand = m->getFullPathName(uchimeCommand); int ableToOpen = m->openInputFile(uchimeCommand, in, "no error"); in.close(); - if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + uchimeCommand + " file does not exist. mothur requires the uchime executable."); m->mothurOutEndLine(); abort = true; } - } + if(ableToOpen == 1) { + m->mothurOut(uchimeCommand + " file does not exist. Checking path... \n"); + //check to see if uchime is in the path?? + + string uLocation = m->findProgramPath("uchime"); + + + ifstream in2; +#if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) + ableToOpen = m->openInputFile(uLocation, in2, "no error"); in2.close(); +#else + ableToOpen = m->openInputFile((uLocation + ".exe"), in2, "no error"); in2.close(); +#endif + + if(ableToOpen == 1) { m->mothurOut("[ERROR]: " + uLocation + " file does not exist. mothur requires the uchime executable."); m->mothurOutEndLine(); abort = true; } + else { m->mothurOut("Found uchime in your path, using " + uLocation + "\n");uchimeLocation = uLocation; } + }else { uchimeLocation = uchimeCommand; } + + uchimeLocation = m->getFullPathName(uchimeLocation); + } } catch(exception& e) { m->errorOut(e, "ChimeraSlayerCommand", "ChimeraSlayerCommand"); @@ -493,7 +618,8 @@ ChimeraUchimeCommand::ChimeraUchimeCommand(string option) { int ChimeraUchimeCommand::execute(){ try{ - if (abort == true) { if (calledHelp) { return 0; } return 2; } + + if (abort == true) { if (calledHelp) { return 0; } return 2; } m->mothurOut("\nuchime by Robert C. Edgar\nhttp://drive5.com/uchime\nThis code is donated to the public domain.\n\n"); @@ -504,16 +630,21 @@ int ChimeraUchimeCommand::execute(){ int start = time(NULL); string nameFile = ""; if (outputDir == "") { outputDir = m->hasPath(fastaFileNames[s]); }//if user entered a file with a path then preserve it - string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "uchime.chimera"; - string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "uchime.accnos"; - string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + "uchime.alns"; + string outputFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("chimera"); + string accnosFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("accnos"); + string alnsFileName = outputDir + m->getRootName(m->getSimpleName(fastaFileNames[s])) + getOutputFileNameTag("alns"); string newFasta = m->getRootName(fastaFileNames[s]) + "temp"; //you provided a groupfile string groupFile = ""; - if (groupFileNames.size() != 0) { groupFile = groupFileNames[s]; } + bool hasGroup = false; + if (groupFileNames.size() != 0) { groupFile = groupFileNames[s]; hasGroup = true; } + else if (hasCount) { + CountTable ct; + if (ct.testGroups(nameFileNames[s])) { hasGroup = true; } + } - if ((templatefile == "self") && (groupFile == "")) { //you want to run uchime with a reference template + if ((templatefile == "self") && (!hasGroup)) { //you want to run uchime with a template=self and no groups if (processors != 1) { m->mothurOut("When using template=self, mothur can only use 1 processor, continuing."); m->mothurOutEndLine(); processors = 1; } if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one @@ -525,7 +656,21 @@ int ChimeraUchimeCommand::execute(){ //read namefile vector nameMapCount; - int error = m->readNames(nameFile, nameMapCount, seqs); if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } + int error; + if (hasCount) { + CountTable ct; + ct.readTable(nameFile); + for(map::iterator it = seqs.begin(); it != seqs.end(); it++) { + int num = ct.getNumSeqs(it->first); + if (num == 0) { error = 1; } + else { + seqPriorityNode temp(num, it->second, it->first); + nameMapCount.push_back(temp); + } + } + }else { + error = m->readNames(nameFile, nameMapCount, seqs); if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } + } if (error == 1) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } if (seqs.size() != nameMapCount.size()) { m->mothurOut( "The number of sequences in your fastafile does not match the number of sequences in your namefile, aborting."); m->mothurOutEndLine(); for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } @@ -535,14 +680,23 @@ int ChimeraUchimeCommand::execute(){ if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } - if (groupFile != "") { + if (hasGroup) { if (nameFileNames.size() != 0) { //you provided a namefile and we don't need to create one nameFile = nameFileNames[s]; }else { nameFile = getNamesFile(fastaFileNames[s]); } //Parse sequences by group - SequenceParser parser(groupFile, fastaFileNames[s], nameFile); - vector groups = parser.getNamesOfGroups(); + vector groups; + map uniqueNames; + if (hasCount) { + cparser = new SequenceCountParser(nameFile, fastaFileNames[s]); + groups = cparser->getNamesOfGroups(); + uniqueNames = cparser->getAllSeqsMap(); + }else{ + sparser = new SequenceParser(groupFile, fastaFileNames[s], nameFile); + groups = sparser->getNamesOfGroups(); + uniqueNames = sparser->getAllSeqsMap(); + } if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } @@ -553,12 +707,14 @@ int ChimeraUchimeCommand::execute(){ if (chimealns) { m->openOutputFile(alnsFileName, out2); out2.close(); } int totalSeqs = 0; - if(processors == 1) { totalSeqs = driverGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups); } - else { totalSeqs = createProcessesGroups(parser, outputFileName, newFasta, accnosFileName, alnsFileName, groups, nameFile, groupFile, fastaFileNames[s]); } + if(processors == 1) { totalSeqs = driverGroups(outputFileName, newFasta, accnosFileName, alnsFileName, 0, groups.size(), groups); } + else { totalSeqs = createProcessesGroups(outputFileName, newFasta, accnosFileName, alnsFileName, groups, nameFile, groupFile, fastaFileNames[s]); } if (m->control_pressed) { for (int j = 0; j < outputNames.size(); j++) { m->mothurRemove(outputNames[j]); } return 0; } + if (hasCount) { delete cparser; } + else { delete sparser; } - int totalChimeras = deconvoluteResults(parser, outputFileName, accnosFileName, alnsFileName); + int totalChimeras = deconvoluteResults(uniqueNames, outputFileName, accnosFileName, alnsFileName); m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(totalSeqs) + " sequences. " + toString(totalChimeras) + " chimeras were found."); m->mothurOutEndLine(); m->mothurOut("The number of sequences checked may be larger than the number of unique sequences because some sequences are found in several samples."); m->mothurOutEndLine(); @@ -617,9 +773,8 @@ int ChimeraUchimeCommand::execute(){ } } //********************************************************************************************************************** -int ChimeraUchimeCommand::deconvoluteResults(SequenceParser& parser, string outputFileName, string accnosFileName, string alnsFileName){ +int ChimeraUchimeCommand::deconvoluteResults(map& uniqueNames, string outputFileName, string accnosFileName, string alnsFileName){ try { - map uniqueNames = parser.getAllSeqsMap(); map::iterator itUnique; int total = 0; @@ -959,7 +1114,7 @@ string ChimeraUchimeCommand::getNamesFile(string& inputFile){ } } //********************************************************************************************************************** -int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, int start, int end, vector groups){ +int ChimeraUchimeCommand::driverGroups(string outputFName, string filename, string accnos, string alns, int start, int end, vector groups){ try { int totalSeqs = 0; @@ -967,8 +1122,10 @@ int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFNam for (int i = start; i < end; i++) { int start = time(NULL); if (m->control_pressed) { return 0; } - - int error = parser.getSeqs(groups[i], filename, true); if ((error == 1) || m->control_pressed) { return 0; } + + int error; + if (hasCount) { error = cparser->getSeqs(groups[i], filename, true); if ((error == 1) || m->control_pressed) { return 0; } } + else { error = sparser->getSeqs(groups[i], filename, true); if ((error == 1) || m->control_pressed) { return 0; } } int numSeqs = driver((outputFName + groups[i]), filename, (accnos+ groups[i]), (alns+ groups[i]), numChimeras); totalSeqs += numSeqs; @@ -976,7 +1133,8 @@ int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFNam if (m->control_pressed) { return 0; } //remove file made for uchime - m->mothurRemove(filename); + if (!m->debug) { m->mothurRemove(filename); } + else { m->mothurOut("[DEBUG]: saving file: " + filename + ".\n"); } //append files m->appendFiles((outputFName+groups[i]), outputFName); m->mothurRemove((outputFName+groups[i])); @@ -985,7 +1143,6 @@ int ChimeraUchimeCommand::driverGroups(SequenceParser& parser, string outputFNam m->mothurOutEndLine(); m->mothurOut("It took " + toString(time(NULL) - start) + " secs to check " + toString(numSeqs) + " sequences from group " + groups[i] + "."); m->mothurOutEndLine(); } - return totalSeqs; } @@ -1010,16 +1167,10 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc vector cPara; - string path = m->argv; - string tempPath = path; - for (int i = 0; i < path.length(); i++) { tempPath[i] = tolower(path[i]); } - path = path.substr(0, (tempPath.find_last_of('m'))); - - string uchimeCommand = path; + string uchimeCommand = uchimeLocation; #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix) - uchimeCommand += "uchime "; + uchimeCommand += " "; #else - uchimeCommand += "uchime"; uchimeCommand = "\"" + uchimeCommand + "\""; #endif @@ -1258,6 +1409,7 @@ int ChimeraUchimeCommand::driver(string outputFName, string filename, string acc #else commandString = "\"" + commandString + "\""; #endif + if (m->debug) { m->mothurOut("[DEBUG]: uchime command = " + commandString + ".\n"); } system(commandString.c_str()); //free memory @@ -1430,7 +1582,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename // Allocate memory for thread data. string extension = toString(i) + ".temp"; - uchimeData* tempUchime = new uchimeData(outputFileName+extension, templatefile, files[i], "", "", "", accnos+extension, alns+extension, dummy, m, 0, 0, i); + uchimeData* tempUchime = new uchimeData(outputFileName+extension, uchimeLocation, templatefile, files[i], "", "", "", accnos+extension, alns+extension, dummy, m, 0, 0, i); tempUchime->setBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract); tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract); @@ -1483,7 +1635,7 @@ int ChimeraUchimeCommand::createProcesses(string outputFileName, string filename } /**************************************************************************************************/ -int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string outputFName, string filename, string accnos, string alns, vector groups, string nameFile, string groupFile, string fastaFile) { +int ChimeraUchimeCommand::createProcessesGroups(string outputFName, string filename, string accnos, string alns, vector groups, string nameFile, string groupFile, string fastaFile) { try { processIDS.clear(); @@ -1513,7 +1665,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o processIDS.push_back(pid); //create map from line number to pid so you can append files in correct order later process++; }else if (pid == 0){ - num = driverGroups(parser, outputFName + toString(getpid()) + ".temp", filename + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", alns + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups); + num = driverGroups(outputFName + toString(getpid()) + ".temp", filename + toString(getpid()) + ".temp", accnos + toString(getpid()) + ".temp", alns + toString(getpid()) + ".temp", lines[process].start, lines[process].end, groups); //pass numSeqs to parent ofstream out; @@ -1531,7 +1683,7 @@ int ChimeraUchimeCommand::createProcessesGroups(SequenceParser& parser, string o } //do my part - num = driverGroups(parser, outputFName, filename, accnos, alns, lines[0].start, lines[0].end, groups); + num = driverGroups(outputFName, filename, accnos, alns, lines[0].start, lines[0].end, groups); //force parent to wait until all the processes are done for (int i=0;isetBooleans(useAbskew, chimealns, useMinH, useMindiv, useXn, useDn, useXa, useChunks, useMinchunk, useIdsmoothwindow, useMinsmoothid, useMaxp, skipgaps, skipgaps2, useMinlen, useMaxlen, ucl, useQueryfract); tempUchime->setVariables(abskew, minh, mindiv, xn, dn, xa, chunks, minchunk, idsmoothwindow, minsmoothid, maxp, minlen, maxlen, queryfract);