From f2408a11ad53c148e3a3329018ca7d04b567f11d Mon Sep 17 00:00:00 2001 From: westcott Date: Fri, 17 Jun 2011 14:36:52 +0000 Subject: [PATCH] 1.20.0 --- Mothur.xcodeproj/project.pbxproj | 4 ++-- chimerauchimecommand.cpp | 2 +- countseqscommand.cpp | 4 ++-- pcacommand.cpp | 3 +-- 4 files changed, 6 insertions(+), 7 deletions(-) diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj index 9699584..d3030bb 100644 --- a/Mothur.xcodeproj/project.pbxproj +++ b/Mothur.xcodeproj/project.pbxproj @@ -2153,8 +2153,8 @@ GCC_OPTIMIZATION_LEVEL = 0; GCC_PREPROCESSOR_DEFINITIONS = ( "MOTHUR_FILES=\"\\\"../release\\\"\"", - "VERSION=\"\\\"1.19.0\\\"\"", - "RELEASE_DATE=\"\\\"5/9/2011\\\"\"", + "VERSION=\"\\\"1.20.0\\\"\"", + "RELEASE_DATE=\"\\\"6/20/2011\\\"\"", ); GCC_WARN_ABOUT_MISSING_NEWLINE = YES; GCC_WARN_ABOUT_RETURN_TYPE = YES; diff --git a/chimerauchimecommand.cpp b/chimerauchimecommand.cpp index 375964c..af427d8 100644 --- a/chimerauchimecommand.cpp +++ b/chimerauchimecommand.cpp @@ -65,7 +65,7 @@ string ChimeraUchimeCommand::getHelpString(){ helpString += "The abskew parameter can only be used with template=self. Minimum abundance skew. Default 1.9. Abundance skew is: min [ abund(parent1), abund(parent2) ] / abund(query).\n"; helpString += "The chimealns parameter allows you to indicate you would like a file containing multiple alignments of query sequences to parents in human readable format. Alignments show columns with differences that support or contradict a chimeric model.\n"; helpString += "The minh parameter - mininum score to report chimera. Default 0.3. Values from 0.1 to 5 might be reasonable. Lower values increase sensitivity but may report more false positives. If you decrease xn you may need to increase minh, and vice versa.\n"; - helpString += "The mindiv parameter - minimum divergence ratio, default 0.5. Div ratio is 100%% - %%identity between query sequence and the closest candidate for being a parent. If you don't care about very close chimeras, then you could increase mindiv to, say, 1.0 or 2.0, and also decrease --min h, say to 0.1, to increase sensitivity. How well this works will depend on your data. Best is to tune parameters on a good benchmark.\n"; + helpString += "The mindiv parameter - minimum divergence ratio, default 0.5. Div ratio is 100%% - %%identity between query sequence and the closest candidate for being a parent. If you don't care about very close chimeras, then you could increase mindiv to, say, 1.0 or 2.0, and also decrease minh, say to 0.1, to increase sensitivity. How well this works will depend on your data. Best is to tune parameters on a good benchmark.\n"; helpString += "The xn parameter - weight of a no vote. Default 8.0. Decreasing this weight to around 3 or 4 may give better performance on denoised data.\n"; helpString += "The dn parameter - pseudo-count prior on number of no votes. Default 1.4. Probably no good reason to change this unless you can retune to a good benchmark for your data. Reasonable values are probably in the range from 0.2 to 2.\n"; helpString += "The xa parameter - weight of an abstain vote. Default 1. So far, results do not seem to be very sensitive to this parameter, but if you have a good training set might be worth trying. Reasonable values might range from 0.1 to 2.\n"; diff --git a/countseqscommand.cpp b/countseqscommand.cpp index a9bffc6..a7890b8 100644 --- a/countseqscommand.cpp +++ b/countseqscommand.cpp @@ -147,9 +147,9 @@ int CountSeqsCommand::execute(){ if (abort == true) { if (calledHelp) { return 0; } return 2; } ofstream out; - string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + ".seq.count"; + string outputFileName = outputDir + m->getRootName(m->getSimpleName(namefile)) + "seq.count"; m->openOutputFile(outputFileName, out); outputTypes["summary"].push_back(outputFileName); - out << "Representative Sequence\t total\t"; + out << "Representative_Sequence\ttotal\t"; GroupMap* groupMap; if (groupfile != "") { diff --git a/pcacommand.cpp b/pcacommand.cpp index 5eed456..8dee743 100644 --- a/pcacommand.cpp +++ b/pcacommand.cpp @@ -319,7 +319,6 @@ int PCACommand::process(vector& lookupFloat){ vector< vector > matrix(numSamples); vector colMeans(numOTUs); - //fill matrix with shared relative abundances, re-center for (int i = 0; i < lookupFloat.size(); i++) { matrix[i].resize(numOTUs, 0); @@ -427,7 +426,7 @@ void PCACommand::output(string fnameRoot, vector name_list, vector