#include "bamtools_convert.h"
#include "bamtools_options.h"
+#include "bamtools_utilities.h"
#include "BGZF.h"
#include "BamReader.h"
#include "BamMultiReader.h"
bool HasRegion;
// options
- vector<string> InputFilenames;
+ vector<string> InputFiles;
string OutputFilename;
string Format;
string Region;
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
- Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilenames, m_settings->InputFiles, IO_Opts, Options::StandardIn());
- Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
+ Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputFilenames, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputFilename, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
Options::AddValueOption("-format", "FORMAT", "the output file format - see README for recognized formats", "", m_settings->HasFormat, m_settings->Format, IO_Opts);
OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
// initialize conversion input/output
// set to default input if none provided
- if ( !m_settings->HasInputBamFilename )
+ if ( !m_settings->HasInputFilenames )
m_settings->InputFiles.push_back(Options::StandardIn());
// open files
BamMultiReader reader;
reader.Open(m_settings->InputFiles);
- references = reader.GetReferenceData();
+ m_references = reader.GetReferenceData();
BamRegion region;
if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {