From 81ad9ebabe7f951eb2d1c922b1342e9d6e521c4e Mon Sep 17 00:00:00 2001 From: Pat Schloss Date: Tue, 12 Mar 2013 08:22:30 -0400 Subject: [PATCH] fine tuning to make.contigs parameters --- makecontigscommand.cpp | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/makecontigscommand.cpp b/makecontigscommand.cpp index c486637..0b9e084 100644 --- a/makecontigscommand.cpp +++ b/makecontigscommand.cpp @@ -32,7 +32,7 @@ vector MakeContigsCommand::setParameters(){ CommandParameter pmismatch("mismatch", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pmismatch); CommandParameter pgapopen("gapopen", "Number", "", "-2.0", "", "", "","",false,false); parameters.push_back(pgapopen); CommandParameter pgapextend("gapextend", "Number", "", "-1.0", "", "", "","",false,false); parameters.push_back(pgapextend); - CommandParameter pthreshold("insert", "Number", "", "25", "", "", "","",false,false); parameters.push_back(pthreshold); + CommandParameter pthreshold("insert", "Number", "", "20", "", "", "","",false,false); parameters.push_back(pthreshold); CommandParameter pdeltaq("deltaq", "Number", "", "6", "", "", "","",false,false); parameters.push_back(pdeltaq); CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors); CommandParameter pformat("format", "Multiple", "sanger-illumina-solexa-illumina1.8+", "illumina1.8+", "", "", "","",false,false,true); parameters.push_back(pformat); @@ -72,7 +72,7 @@ string MakeContigsCommand::getHelpString(){ helpString += "The deltaq parameter allows you to specify the delta allowed between quality scores of a mismatched base. For example in the overlap, if deltaq=5 and in the alignment seqA, pos 200 has a quality score of 30 and the same position in seqB has a quality score of 20, you take the base from seqA (30-20 >= 5). If the quality score in seqB is 28 then the base in the consensus will be an N (30-28<5) The default is 6.\n"; helpString += "The gapopen parameter allows you to specify the penalty for opening a gap in an alignment. The default is -2.0.\n"; helpString += "The gapextend parameter allows you to specify the penalty for extending a gap in an alignment. The default is -1.0.\n"; - helpString += "The insert parameter allows you to set a quality scores threshold. In the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score below the threshold we eliminate it. Default=25.\n"; + helpString += "The insert parameter allows you to set a quality scores threshold. In the case where we are trying to decide whether to keep a base or remove it because the base is compared to a gap in the other fragment, if the base has a quality score equal to or below the threshold we eliminate it. Default=20.\n"; helpString += "The processors parameter allows you to specify how many processors you would like to use. The default is 1. \n"; helpString += "The allfiles parameter will create separate group and fasta file for each grouping. The default is F.\n"; helpString += "The trimoverlap parameter allows you to trim the sequences to only the overlapping section. The default is F.\n"; @@ -288,7 +288,7 @@ MakeContigsCommand::MakeContigsCommand(string option) { m->mothurConvert(temp, gapExtend); if (gapExtend > 0) { m->mothurOut("[ERROR]: gapextend must be negative.\n"); abort=true; } - temp = validParameter.validFile(parameters, "insert", false); if (temp == "not found"){ temp = "25"; } + temp = validParameter.validFile(parameters, "insert", false); if (temp == "not found"){ temp = "20"; } m->mothurConvert(temp, insert); if ((insert < 0) || (insert > 40)) { m->mothurOut("[ERROR]: insert must be between 0 and 40.\n"); abort=true; } @@ -944,12 +944,12 @@ int MakeContigsCommand::driver(vector files, string outputFasta, string contig += seq1[i]; }else if (((seq1[i] == '.') || (seq1[i] == '-')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //seq1 is a gap and seq2 is a base, choose seq2, unless quality score for base is below insert. In that case eliminate base if (thisfqualfile != "") { - if (scores2[BBaseMap[i]] < insert) { } // + if (scores2[BBaseMap[i]] <= insert) { } // else { contig += seq2[i]; } }else { contig += seq2[i]; } //with no quality info, then we keep it? }else if (((seq2[i] == '.') || (seq2[i] == '-')) && ((seq1[i] != '-') && (seq1[i] != '.'))) { //seq2 is a gap and seq1 is a base, choose seq1, unless quality score for base is below insert. In that case eliminate base if (thisfqualfile != "") { - if (scores1[ABaseMap[i]] < insert) { } // + if (scores1[ABaseMap[i]] <= insert) { } // else { contig += seq1[i]; } }else { contig += seq1[i]; } //with no quality info, then we keep it? }else if (((seq1[i] != '-') && (seq1[i] != '.')) && ((seq2[i] != '-') && (seq2[i] != '.'))) { //both bases choose one with better quality -- 2.39.2