1 // ***************************************************************************
2 // bamtools_merge.cpp (c) 2010 Derek Barnett, Erik Garrison
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 7 September 2010
7 // ---------------------------------------------------------------------------
8 // Merges multiple BAM files into one.
9 // ***************************************************************************
15 #include "bamtools_merge.h"
16 #include "bamtools_options.h"
17 #include "bamtools_utilities.h"
18 #include "BamMultiReader.h"
19 #include "BamWriter.h"
22 using namespace BamTools;
24 // ---------------------------------------------
25 // MergeSettings implementation
27 struct MergeTool::MergeSettings {
30 bool HasInputBamFilename;
31 bool HasOutputBamFilename;
32 bool IsForceCompression;
36 vector<string> InputFiles;
39 string OutputFilename;
44 : HasInputBamFilename(false)
45 , HasOutputBamFilename(false)
46 , IsForceCompression(false)
48 , OutputFilename(Options::StandardOut())
52 // ---------------------------------------------
53 // MergeTool implementation
55 MergeTool::MergeTool(void)
57 , m_settings(new MergeSettings)
59 // set program details
60 Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one", "[-in <filename> -in <filename> ...] [-out <filename>]");
63 OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
64 Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts);
65 Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts);
66 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);
68 OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
69 Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
72 MergeTool::~MergeTool(void) {
77 int MergeTool::Help(void) {
78 Options::DisplayHelp();
82 int MergeTool::Run(int argc, char* argv[]) {
84 // parse command line arguments
85 Options::Parse(argc, argv, 1);
87 // set to default input if none provided
88 if ( !m_settings->HasInputBamFilename )
89 m_settings->InputFiles.push_back(Options::StandardIn());
91 // opens the BAM files (by default without checking for indexes)
92 BamMultiReader reader;
93 if ( !reader.Open(m_settings->InputFiles, false, true) ) {
94 cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
98 // retrieve header & reference dictionary info
99 std::string mergedHeader = reader.GetHeaderText();
100 RefVector references = reader.GetReferenceData();
104 bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() && !m_settings->IsForceCompression );
105 if ( !writer.Open(m_settings->OutputFilename, mergedHeader, references, writeUncompressed) ) {
106 cerr << "ERROR: Could not open BAM file " << m_settings->OutputFilename << " for writing... Aborting." << endl;
111 // if no region specified, store entire contents of file(s)
112 if ( !m_settings->HasRegion ) {
114 while ( reader.GetNextAlignmentCore(al) )
115 writer.SaveAlignment(al);
118 // otherwise attempt to use region as constraint
121 // if region string parses OK
123 if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
125 // attempt to re-open reader with index files
127 bool openedOK = reader.Open(m_settings->InputFiles, true, true );
131 cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
135 // if index data available, we can use SetRegion
136 if ( reader.IsIndexLoaded() ) {
138 // attempt to use SetRegion(), if failed report error
139 if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
140 cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
145 // everything checks out, just iterate through specified region, storing alignments
147 while ( reader.GetNextAlignmentCore(al) )
148 writer.SaveAlignment(al);
151 // no index data available, we have to iterate through until we
152 // find overlapping alignments
155 while ( reader.GetNextAlignmentCore(al) ) {
156 if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
157 (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
159 writer.SaveAlignment(al);
165 // error parsing REGION string
167 cerr << "ERROR: Could not parse REGION - " << m_settings->Region << endl;
168 cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;