From: Derek <derekwbarnett@gmail.com> Date: Mon, 7 Jun 2010 17:24:51 +0000 (-0400) Subject: Fixed typo in settings config. X-Git-Url: https://git.donarmstrong.com/?a=commitdiff_plain;h=dac30b06e53e46cfd4efb0d2d4f771b0202e09d9;p=bamtools.git Fixed typo in settings config. --- diff --git a/bamtools_convert.cpp b/bamtools_convert.cpp index 5c0ec03..bf54b03 100644 --- a/bamtools_convert.cpp +++ b/bamtools_convert.cpp @@ -13,12 +13,13 @@ #include <vector> #include "bamtools_convert.h" +#include "bamtools_format.h" #include "bamtools_options.h" #include "BamReader.h" #include "BamMultiReader.h" using namespace std; -using namespace BamTools; +using namespace BamTools; // --------------------------------------------- // ConvertSettings implementation @@ -39,8 +40,9 @@ struct ConvertTool::ConvertSettings { ConvertSettings(void) : HasInputBamFilename(false) , HasOutputBamFilename(false) + , InputFilename(Options::StandardIn()) , OutputFilename(Options::StandardOut()) - { } + { } }; // --------------------------------------------- @@ -51,7 +53,7 @@ ConvertTool::ConvertTool(void) , m_settings(new ConvertSettings) { // set program details - Options::SetProgramInfo("bamtools convert", "converts between BAM and a number of other formats)", "-in <filename> [-in <filename> ... ] -out <filename> -format FORMAT"); + Options::SetProgramInfo("bamtools convert", "converts between BAM and a number of other formats", "-in <filename> -out <filename> -format <FORMAT>"); // set up options OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output"); @@ -77,10 +79,13 @@ int ConvertTool::Run(int argc, char* argv[]) { // open files BamReader reader; - reader.Open(m_settings->InputFilename, false); + reader.Open(m_settings->InputFilename); // do conversion + + + // clean up & exit reader.Close(); return 0;