// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 31 August 2010
+// Last modified: 21 March 2011
// ---------------------------------------------------------------------------
// Merges multiple BAM files into one.
-//
-// ** Provide selectable region? eg chr2:10000..20000
-//
// ***************************************************************************
+#include "bamtools_merge.h"
+
+#include <api/BamMultiReader.h>
+#include <api/BamWriter.h>
+#include <utils/bamtools_options.h>
+#include <utils/bamtools_utilities.h>
+using namespace BamTools;
+
#include <iostream>
#include <string>
#include <vector>
-
-#include "bamtools_merge.h"
-#include "bamtools_options.h"
-#include "bamtools_utilities.h"
-#include "BamMultiReader.h"
-#include "BamWriter.h"
-
using namespace std;
-using namespace BamTools;
// ---------------------------------------------
// MergeSettings implementation
bool HasInputBamFilename;
bool HasOutputBamFilename;
bool IsForceCompression;
-// bool HasRegion;
+ bool HasRegion;
// filenames
vector<string> InputFiles;
// other parameters
string OutputFilename;
-// string Region;
+ string Region;
// constructor
MergeSettings(void)
: HasInputBamFilename(false)
, HasOutputBamFilename(false)
, IsForceCompression(false)
-// , HasRegion(false)
+ , HasRegion(false)
, OutputFilename(Options::StandardOut())
{ }
};
, m_settings(new MergeSettings)
{
// set program details
- Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one", "[-in <filename> -in <filename> ...] [-out <filename>]");
+ Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one", "[-in <filename> -in <filename> ...] [-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("-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);
-
-// OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
-// Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
+ Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
}
MergeTool::~MergeTool(void) {
int MergeTool::Help(void) {
Options::DisplayHelp();
- return 0;
+ return 0;
}
int MergeTool::Run(int argc, char* argv[]) {
Options::Parse(argc, argv, 1);
// set to default input if none provided
- if ( !m_settings->HasInputBamFilename ) m_settings->InputFiles.push_back(Options::StandardIn());
+ if ( !m_settings->HasInputBamFilename )
+ m_settings->InputFiles.push_back(Options::StandardIn());
- // opens the BAM files without checking for indexes
+ // opens the BAM files (by default without checking for indexes)
BamMultiReader reader;
- reader.Open(m_settings->InputFiles, false, true);
-
+ if ( !reader.Open(m_settings->InputFiles) ) {
+ cerr << "bamtools merge ERROR: could not open input BAM file(s)... Aborting." << endl;
+ return 1;
+ }
+
// retrieve header & reference dictionary info
std::string mergedHeader = reader.GetHeaderText();
RefVector references = reader.GetReferenceData();
- // open writer
+ // determine compression mode for BamWriter
+ bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() &&
+ !m_settings->IsForceCompression );
+ BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
+ if ( writeUncompressed ) compressionMode = BamWriter::Uncompressed;
+
+ // open BamWriter
BamWriter writer;
- bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() && !m_settings->IsForceCompression );
- writer.Open(m_settings->OutputFilename, mergedHeader, references, writeUncompressed);
+ writer.SetCompressionMode(compressionMode);
+ if ( !writer.Open(m_settings->OutputFilename, mergedHeader, references) ) {
+ cerr << "bamtools merge ERROR: could not open " << m_settings->OutputFilename << " for writing." << endl;
+ reader.Close();
+ return false;
+ }
+
+ // if no region specified, store entire contents of file(s)
+ if ( !m_settings->HasRegion ) {
+ BamAlignment al;
+ while ( reader.GetNextAlignmentCore(al) )
+ writer.SaveAlignment(al);
+ }
+
+ // otherwise attempt to use region as constraint
+ else {
+
+ // if region string parses OK
+ BamRegion region;
+ if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
+
+ // attempt to find index files
+ reader.LocateIndexes();
+
+ // if index data available for all BAM files, we can use SetRegion
+ if ( reader.HasIndexes() ) {
- // store alignments to output file
- BamAlignment bAlignment;
- while (reader.GetNextAlignmentCore(bAlignment)) {
- writer.SaveAlignment(bAlignment);
+ // attempt to use SetRegion(), if failed report error
+ if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
+ cerr << "bamtools merge ERROR: set region failed. Check that REGION describes a valid range" << endl;
+ reader.Close();
+ return 1;
+ }
+
+ // everything checks out, just iterate through specified region, storing alignments
+ BamAlignment al;
+ while ( reader.GetNextAlignmentCore(al) )
+ writer.SaveAlignment(al);
+ }
+
+ // no index data available, we have to iterate through until we
+ // find overlapping alignments
+ else {
+ BamAlignment al;
+ while ( reader.GetNextAlignmentCore(al) ) {
+ if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
+ (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
+ {
+ writer.SaveAlignment(al);
+ }
+ }
+ }
+ }
+
+ // error parsing REGION string
+ else {
+ cerr << "bamtools merge ERROR: could not parse REGION - " << m_settings->Region << endl;
+ cerr << "Check that REGION is in valid format (see documentation) and that the coordinates are valid"
+ << endl;
+ reader.Close();
+ writer.Close();
+ return 1;
+ }
}
// clean & exit
projects / bamtools.git / blobdiff