// bamtools_convert.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 11 November 2012
+// Last modified: 10 December 2012
// ---------------------------------------------------------------------------
// Converts between BAM and a number of other formats
// ***************************************************************************
// flag
bool HasInput;
+ bool HasInputFilelist;
bool HasOutput;
bool HasFormat;
bool HasRegion;
// options
vector<string> InputFiles;
+ string InputFilelist;
string OutputFilename;
string Format;
string Region;
// constructor
ConvertSettings(void)
: HasInput(false)
+ , HasInputFilelist(false)
, HasOutput(false)
, HasFormat(false)
, HasRegion(false)
// initialize conversion input/output
// set to default input if none provided
- if ( !m_settings->HasInput )
+ if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
m_settings->InputFiles.push_back(Options::StandardIn());
+ // add files in the filelist to the input file list
+ if ( m_settings->HasInputFilelist ) {
+
+ ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
+ if ( !filelist.is_open() ) {
+ cerr << "bamtools convert ERROR: could not open input BAM file list... Aborting." << endl;
+ return false;
+ }
+
+ string line;
+ while ( getline(filelist, line) )
+ m_settings->InputFiles.push_back(line);
+ }
+
// open input files
BamMultiReader reader;
if ( !reader.Open(m_settings->InputFiles) ) {
, m_impl(0)
{
// set program details
- Options::SetProgramInfo("bamtools convert", "converts BAM to a number of other formats", "-format <FORMAT> [-in <filename> -in <filename> ...] [-out <filename>] [-region <REGION>] [format-specific options]");
+ Options::SetProgramInfo("bamtools convert", "converts BAM to a number of other formats",
+ "-format <FORMAT> [-in <filename> -in <filename> ... | -list <filelist>] [-out <filename>] [-region <REGION>] [format-specific options]");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-list", "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutput, 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);
Options::AddValueOption("-region", "REGION", "genomic region. Index file is recommended for better performance, and is used automatically if it exists. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
// bamtools_count.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 April 2011
+// Last modified: 10 December 2012
// ---------------------------------------------------------------------------
// Prints alignment count for BAM file(s)
// ***************************************************************************
#include <utils/bamtools_utilities.h>
using namespace BamTools;
+#include <fstream>
#include <iostream>
#include <string>
#include <vector>
// flags
bool HasInput;
+ bool HasInputFilelist;
bool HasRegion;
// filenames
vector<string> InputFiles;
+ string InputFilelist;
string Region;
// constructor
CountSettings(void)
: HasInput(false)
+ , HasInputFilelist(false)
, HasRegion(false)
{ }
};
bool CountTool::CountToolPrivate::Run(void) {
- // if no '-in' args supplied, default to stdin
- if ( !m_settings->HasInput )
+ // set to default input if none provided
+ if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
m_settings->InputFiles.push_back(Options::StandardIn());
+ // add files in the filelist to the input file list
+ if ( m_settings->HasInputFilelist ) {
+
+ ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
+ if ( !filelist.is_open() ) {
+ cerr << "bamtools count ERROR: could not open input BAM file list... Aborting." << endl;
+ return false;
+ }
+
+ string line;
+ while ( getline(filelist, line) )
+ m_settings->InputFiles.push_back(line);
+ }
+
// open reader without index
BamMultiReader reader;
if ( !reader.Open(m_settings->InputFiles) ) {
, m_impl(0)
{
// set program details
- Options::SetProgramInfo("bamtools count", "prints number of alignments in BAM file(s)", "[-in <filename> -in <filename> ...] [-region <REGION>]");
+ Options::SetProgramInfo("bamtools count", "prints number of alignments in BAM file(s)",
+ "[-in <filename> -in <filename> ... | -list <filelist>] [-region <REGION>]");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
- Options::AddValueOption("-region", "REGION", "genomic region. Index file is recommended for better performance, and is used automatically if it exists. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
+ Options::AddValueOption("-list", "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
+ Options::AddValueOption("-region", "REGION",
+ "genomic region. Index file is recommended for better performance, and is used automatically if it exists. See \'bamtools help index\' for more details on creating one",
+ "", m_settings->HasRegion, m_settings->Region, IO_Opts);
}
CountTool::~CountTool(void) {
// bamtools_filter.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 14 October 2011
+// Last modified: 10 December 2012
// ---------------------------------------------------------------------------
// Filters BAM file(s) according to some user-specified criteria
// ***************************************************************************
using namespace Json;
#include <cstdio>
+#include <fstream>
#include <iostream>
#include <sstream>
#include <string>
// IO opts
// flags
- bool HasInputBamFilename;
- bool HasOutputBamFilename;
+ bool HasInput;
+ bool HasInputFilelist;
+ bool HasOutput;
bool HasRegion;
- bool HasScriptFilename;
+ bool HasScript;
bool IsForceCompression;
// filenames
vector<string> InputFiles;
+ string InputFilelist;
string OutputFilename;
string Region;
string ScriptFilename;
// constructor
FilterSettings(void)
- : HasInputBamFilename(false)
- , HasOutputBamFilename(false)
+ : HasInput(false)
+ , HasInputFilelist(false)
+ , HasOutput(false)
, HasRegion(false)
- , HasScriptFilename(false)
+ , HasScript(false)
, IsForceCompression(false)
, OutputFilename(Options::StandardOut())
, HasAlignmentFlagFilter(false)
m_filterEngine.setProperty(filterName, propertyName, stringValue, type);
}
- else if ( propertyName == TAG_PROPERTY ) {
- // this will be stored directly as the TAG:VALUE token
- // (VALUE may contain compare ops, will be parsed out later)
- m_filterEngine.setProperty(filterName, propertyName, token, PropertyFilterValue::EXACT);
- }
+ else if ( propertyName == TAG_PROPERTY ) {
+ // this will be stored directly as the TAG:VALUE token
+ // (VALUE may contain compare ops, will be parsed out later)
+ m_filterEngine.setProperty(filterName, propertyName, token, PropertyFilterValue::EXACT);
+ }
// else unknown property
else {
// peek ahead, make sure there is data available
char ch = fgetc(inFile);
ungetc(ch, inFile);
- if( feof(inFile) ) break;
+ if( feof(inFile) )
+ break;
// read next block of data
if ( fgets(buffer, 1024, inFile) == 0 ) {
bool FilterTool::FilterToolPrivate::Run(void) {
// set to default input if none provided
- if ( !m_settings->HasInputBamFilename )
+ if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
m_settings->InputFiles.push_back(Options::StandardIn());
+ // add files in the filelist to the input file list
+ if ( m_settings->HasInputFilelist ) {
+
+ ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
+ if ( !filelist.is_open() ) {
+ cerr << "bamtools filter ERROR: could not open input BAM file list... Aborting." << endl;
+ return false;
+ }
+
+ string line;
+ while ( getline(filelist, line) )
+ m_settings->InputFiles.push_back(line);
+ }
+
// initialize defined properties & user-specified filters
// quit if failed
- if ( !SetupFilters() ) return false;
+ if ( !SetupFilters() )
+ return false;
// open reader without index
BamMultiReader reader;
InitProperties();
// parse script for filter rules, if given
- if ( m_settings->HasScriptFilename )
+ if ( m_settings->HasScript )
return ParseScript();
// otherwise check command line for filters
// ----------------------------------
// set program details
- const string usage = "[-in <filename> -in <filename> ...] "
+ const string usage = "[-in <filename> -in <filename> ... | -list <filelist>] "
"[-out <filename> | [-forceCompression]] [-region <REGION>] "
"[ [-script <filename] | [filterOptions] ]";
+
Options::SetProgramInfo("bamtools filter", "filters BAM file(s)", usage );
// ----------------------------------
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
const string inDesc = "the input BAM file(s)";
+ const string listDesc = "the input BAM file list, one line per file";
const string outDesc = "the output BAM file";
const string regionDesc = "only read data from this genomic region (see documentation for more details)";
const string scriptDesc = "the filter script file (see documentation for more details)";
"default behavior is to leave output uncompressed. Use this flag to "
"override and force compression";
- Options::AddValueOption("-in", "BAM filename", inDesc, "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts, Options::StandardIn());
- Options::AddValueOption("-out", "BAM filename", outDesc, "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
- Options::AddValueOption("-region", "REGION", regionDesc, "", m_settings->HasRegion, m_settings->Region, IO_Opts);
- Options::AddValueOption("-script", "filename", scriptDesc, "", m_settings->HasScriptFilename, m_settings->ScriptFilename, IO_Opts);
+ Options::AddValueOption("-in", "BAM filename", inDesc, "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-list", "filename", listDesc, "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
+ Options::AddValueOption("-out", "BAM filename", outDesc, "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
+ Options::AddValueOption("-region", "REGION", regionDesc, "", m_settings->HasRegion, m_settings->Region, IO_Opts);
+ Options::AddValueOption("-script", "filename", scriptDesc, "", m_settings->HasScript, m_settings->ScriptFilename, IO_Opts);
Options::AddOption("-forceCompression",forceDesc, m_settings->IsForceCompression, IO_Opts);
// ----------------------------------
// bamtools_header.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 April 2011
+// Last modified: 10 December 2012
// ---------------------------------------------------------------------------
// Prints the SAM-style header from a single BAM file ( or merged header from
// multiple BAM files) to stdout
#include <utils/bamtools_options.h>
using namespace BamTools;
+#include <fstream>
#include <iostream>
#include <string>
#include <vector>
struct HeaderTool::HeaderSettings {
// flags
- bool HasInputBamFilename;
+ bool HasInput;
+ bool HasInputFilelist;
// filenames
vector<string> InputFiles;
+ string InputFilelist;
// constructor
HeaderSettings(void)
- : HasInputBamFilename(false)
+ : HasInput(false)
+ , HasInputFilelist(false)
{ }
};
bool HeaderTool::HeaderToolPrivate::Run(void) {
// set to default input if none provided
- if ( !m_settings->HasInputBamFilename )
+ if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
m_settings->InputFiles.push_back(Options::StandardIn());
+ // add files in the filelist to the input file list
+ if ( m_settings->HasInputFilelist ) {
+
+ ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
+ if ( !filelist.is_open() ) {
+ cerr << "bamtools header ERROR: could not open input BAM file list... Aborting." << endl;
+ return false;
+ }
+
+ string line;
+ while ( getline(filelist, line) )
+ m_settings->InputFiles.push_back(line);
+ }
+
// attemp to open BAM files
BamMultiReader reader;
if ( !reader.Open(m_settings->InputFiles) ) {
, m_impl(0)
{
// set program details
- Options::SetProgramInfo("bamtools header", "prints header from BAM file(s)", "[-in <filename> -in <filename> ...] ");
+ Options::SetProgramInfo("bamtools header", "prints header from BAM file(s)", "[-in <filename> -in <filename> ... | -list <filelist>]");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
- Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-list", "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
}
HeaderTool::~HeaderTool(void) {
// bamtools_merge.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 April 2011
+// Last modified: 10 December 2012
// ---------------------------------------------------------------------------
// Merges multiple BAM files into one
// ***************************************************************************
#include <utils/bamtools_utilities.h>
using namespace BamTools;
+#include <fstream>
#include <iostream>
#include <string>
#include <vector>
struct MergeTool::MergeSettings {
// flags
- bool HasInputBamFilename;
- bool HasInputBamFilelist;
- bool HasOutputBamFilename;
+ bool HasInput;
+ bool HasInputFilelist;
+ bool HasOutput;
bool IsForceCompression;
bool HasRegion;
// constructor
MergeSettings(void)
- : HasInputBamFilename(false)
- , HasInputBamFilelist(false)
- , HasOutputBamFilename(false)
+ : HasInput(false)
+ , HasInputFilelist(false)
+ , HasOutput(false)
, IsForceCompression(false)
, HasRegion(false)
, OutputFilename(Options::StandardOut())
bool MergeTool::MergeToolPrivate::Run(void) {
// set to default input if none provided
- if ( !m_settings->HasInputBamFilename && !m_settings->HasInputBamFilelist )
+ if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
m_settings->InputFiles.push_back(Options::StandardIn());
// add files in the filelist to the input file list
- if ( m_settings->HasInputBamFilelist ) {
- ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
- if ( !filelist.is_open() ) {
- cerr << "bamtools merge ERROR: could not open input BAM file list... Aborting." << endl;
- return false;
- }
- string line;
- while ( getline(filelist, line) ) {
- m_settings->InputFiles.push_back(line);
- }
+ if ( m_settings->HasInputFilelist ) {
+
+ ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
+ if ( !filelist.is_open() ) {
+ cerr << "bamtools merge ERROR: could not open input BAM file list... Aborting." << endl;
+ return false;
+ }
+
+ string line;
+ while ( getline(filelist, line) )
+ m_settings->InputFiles.push_back(line);
}
// opens the BAM files (by default without checking for indexes)
, m_impl(0)
{
// set program details
- Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one", "[ [-in <filename> -in <filename> ...] | [-list <filelist>] ] [-out <filename> | [-forceCompression]] [-region <REGION>]");
+ Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one",
+ "[-in <filename> -in <filename> ... | -list <filelist>] [-out <filename> | [-forceCompression]] [-region <REGION>]");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
- Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts);
- Options::AddValueOption("-list", "BAM filename", "the input BAM file list, one line per file", "", m_settings->HasInputBamFilelist, m_settings->InputFilelist, IO_Opts);
- Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts);
+ Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts);
+ Options::AddValueOption("-list", "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
+ Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts);
Options::AddOption("-forceCompression", "if results are sent to stdout (like when piping to another tool), default behavior is to leave output uncompressed. Use this flag to override and force compression", m_settings->IsForceCompression, IO_Opts);
Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
}
// bamtools_random.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 April 2011 (DB)
+// Last modified: 10 December 2012 (DB)
// ---------------------------------------------------------------------------
// Grab a random subset of alignments (testing tool)
// ***************************************************************************
#include <ctime>
#include <cstdlib>
+#include <fstream>
#include <iostream>
#include <string>
#include <vector>
// flags
bool HasAlignmentCount;
bool HasInput;
+ bool HasInputFilelist;
bool HasOutput;
bool HasRegion;
bool IsForceCompression;
// parameters
unsigned int AlignmentCount;
vector<string> InputFiles;
+ string InputFilelist;
string OutputFilename;
string Region;
RandomSettings(void)
: HasAlignmentCount(false)
, HasInput(false)
+ , HasInputFilelist(false)
, HasOutput(false)
, HasRegion(false)
, IsForceCompression(false)
bool RandomTool::RandomToolPrivate::Run(void) {
// set to default stdin if no input files provided
- if ( !m_settings->HasInput )
+ if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
m_settings->InputFiles.push_back(Options::StandardIn());
+ // add files in the filelist to the input file list
+ if ( m_settings->HasInputFilelist ) {
+
+ ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
+ if ( !filelist.is_open() ) {
+ cerr << "bamtools random ERROR: could not open input BAM file list... Aborting." << endl;
+ return false;
+ }
+
+ string line;
+ while ( getline(filelist, line) )
+ m_settings->InputFiles.push_back(line);
+ }
+
// open our reader
BamMultiReader reader;
if ( !reader.Open(m_settings->InputFiles) ) {
, m_impl(0)
{
// set program details
- Options::SetProgramInfo("bamtools random", "grab a random subset of alignments", "[-in <filename> -in <filename> ...] [-out <filename>] [-forceCompression] [-n] [-region <REGION>]");
+ Options::SetProgramInfo("bamtools random", "grab a random subset of alignments",
+ "[-in <filename> -in <filename> ... | -list <filelist>] [-out <filename>] [-forceCompression] [-n] [-region <REGION>]");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-list", "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
Options::AddOption("-forceCompression", "if results are sent to stdout (like when piping to another tool), default behavior is to leave output uncompressed. Use this flag to override and force compression", m_settings->IsForceCompression, IO_Opts);
Options::AddValueOption("-region", "REGION", "only pull random alignments from within this genomic region. Index file is recommended for better performance, and is used automatically if it exists. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
// bamtools_cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
// ---------------------------------------------------------------------------
-// Last modified: 7 April 2011
+// Last modified: 10 December 2012
// ---------------------------------------------------------------------------
// Prints general alignment statistics for BAM file(s).
// ***************************************************************************
#include <cmath>
#include <algorithm>
+#include <fstream>
#include <functional>
#include <iostream>
#include <numeric>
// flags
bool HasInput;
+ bool HasInputFilelist;
bool IsShowingInsertSizeSummary;
// filenames
vector<string> InputFiles;
+ string InputFilelist;
// constructor
StatsSettings(void)
: HasInput(false)
+ , HasInputFilelist(false)
, IsShowingInsertSizeSummary(false)
{ }
};
bool StatsTool::StatsToolPrivate::CalculateMedian(vector<int>& data, double& median) {
// skip if data empty
- if ( data.empty() ) return false;
+ if ( data.empty() )
+ return false;
// find middle element
size_t middleIndex = data.size() / 2;
}
// check for explicit proper pair flag
- if ( al.IsProperPair() ) ++m_numProperPair;
+ if ( al.IsProperPair() )
+ ++m_numProperPair;
// store insert size for first mate
if ( m_settings->IsShowingInsertSizeSummary && al.IsFirstMate() && (al.InsertSize != 0) ) {
bool StatsTool::StatsToolPrivate::Run() {
// set to default input if none provided
- if ( !m_settings->HasInput )
+ if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
m_settings->InputFiles.push_back(Options::StandardIn());
+ // add files in the filelist to the input file list
+ if ( m_settings->HasInputFilelist ) {
+
+ ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
+ if ( !filelist.is_open() ) {
+ cerr << "bamtools stats ERROR: could not open input BAM file list... Aborting." << endl;
+ return false;
+ }
+
+ string line;
+ while ( getline(filelist, line) )
+ m_settings->InputFiles.push_back(line);
+ }
+
// open the BAM files
BamMultiReader reader;
if ( !reader.Open(m_settings->InputFiles) ) {
, m_impl(0)
{
// set program details
- Options::SetProgramInfo("bamtools stats", "prints general alignment statistics", "[-in <filename> -in <filename> ...] [statsOptions]");
+ Options::SetProgramInfo("bamtools stats", "prints general alignment statistics", "[-in <filename> -in <filename> ... | -list <filelist>] [statsOptions]");
// set up options
OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts, Options::StandardIn());
+ Options::AddValueOption("-list", "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
OptionGroup* AdditionalOpts = Options::CreateOptionGroup("Additional Stats");
Options::AddOption("-insert", "summarize insert size data", m_settings->IsShowingInsertSizeSummary, AdditionalOpts);
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