From c9c7a14ad8e6b22fd760741b76f4e687a9ced458 Mon Sep 17 00:00:00 2001 From: Pat Schloss Date: Tue, 10 Apr 2012 17:45:35 -0400 Subject: [PATCH] fixed shhh.flows outputdir bug --- calculator.h | 2 +- shhhercommand.cpp | 4 ++-- trimflowscommand.cpp | 3 +-- trimflowscommand.h | 4 +--- 4 files changed, 5 insertions(+), 8 deletions(-) diff --git a/calculator.h b/calculator.h index 2c41329..6791d83 100644 --- a/calculator.h +++ b/calculator.h @@ -100,7 +100,7 @@ class BrokenStick void doBStick(vector); }; -/**************************************************************************************************/ +//**************************************************************************************************/ /*This Class calculates the geometric series distribution for the data. It prints the D-Statistic and the critical values for the Kolmogorov-Smirnov 1-sample test at the 95% confidence interval.*/ diff --git a/shhhercommand.cpp b/shhhercommand.cpp index 32891c3..d00ead8 100644 --- a/shhhercommand.cpp +++ b/shhhercommand.cpp @@ -1734,7 +1734,7 @@ void ShhherCommand::writeSequences(vector otuCounts){ outputNames.push_back(fastaFileName); if(compositeFASTAFileName != ""){ - m->appendFiles(fastaFileName, compositeFASTAFileName); + m->appendFiles(fastaFileName, thisOutputDir + compositeFASTAFileName); } } catch(exception& e) { @@ -1772,7 +1772,7 @@ void ShhherCommand::writeNames(vector otuCounts){ if(compositeNamesFileName != ""){ - m->appendFiles(nameFileName, compositeNamesFileName); + m->appendFiles(nameFileName, thisOutputDir + compositeNamesFileName); } } catch(exception& e) { diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp index 86de668..0557c71 100644 --- a/trimflowscommand.cpp +++ b/trimflowscommand.cpp @@ -392,8 +392,7 @@ int TrimFlowsCommand::driverCreateTrim(string flowFileName, string trimFlowFileN TrimOligos trimOligos(pdiffs, bdiffs, ldiffs, sdiffs, primers, barcodes, revPrimer, linker, spacer); while(moreSeqs) { - //cout << "driver " << count << endl; - + if (m->control_pressed) { break; } int success = 1; diff --git a/trimflowscommand.h b/trimflowscommand.h index 27bafd5..414c73c 100644 --- a/trimflowscommand.h +++ b/trimflowscommand.h @@ -59,9 +59,7 @@ private: bool allFiles; int processors; int numFPrimers, numRPrimers; - int numLinkers, numSpacers; - - int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs; + int maxFlows, minFlows, minLength, maxLength, maxHomoP, tdiffs, bdiffs, pdiffs, sdiffs, ldiffs, numLinkers, numSpacers; int numFlows; float signal, noise; bool fasta; -- 2.39.2