// 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);