// flags
bool HasInputBamFilename;
+ bool HasInputBamFilelist;
bool HasOutputBamFilename;
bool IsForceCompression;
bool HasRegion;
// filenames
vector<string> InputFiles;
+ string InputFilelist;
// other parameters
string OutputFilename;
// constructor
MergeSettings(void)
: HasInputBamFilename(false)
+ , HasInputBamFilelist(false)
, HasOutputBamFilename(false)
, IsForceCompression(false)
, HasRegion(false)
bool MergeTool::MergeToolPrivate::Run(void) {
// set to default input if none provided
- if ( !m_settings->HasInputBamFilename )
+ if ( !m_settings->HasInputBamFilename && !m_settings->HasInputBamFilelist )
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);
+ }
+ }
+
// opens the BAM files (by default without checking for indexes)
BamMultiReader reader;
if ( !reader.Open(m_settings->InputFiles) ) {
, m_impl(0)
{
// set program details
- Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one", "[-in <filename> -in <filename> ...] [-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::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);