1 // ***************************************************************************
2 // bamtools_merge.cpp (c) 2010 Derek Barnett, Erik Garrison
3 // Marth Lab, Department of Biology, Boston College
4 // ---------------------------------------------------------------------------
5 // Last modified: 7 April 2011
6 // ---------------------------------------------------------------------------
7 // Merges multiple BAM files into one
8 // ***************************************************************************
10 #include "bamtools_merge.h"
12 #include <api/BamMultiReader.h>
13 #include <api/BamWriter.h>
14 #include <utils/bamtools_options.h>
15 #include <utils/bamtools_utilities.h>
16 using namespace BamTools;
23 // ---------------------------------------------
24 // MergeSettings implementation
26 struct MergeTool::MergeSettings {
29 bool HasInputBamFilename;
30 bool HasOutputBamFilename;
31 bool IsForceCompression;
35 vector<string> InputFiles;
38 string OutputFilename;
43 : HasInputBamFilename(false)
44 , HasOutputBamFilename(false)
45 , IsForceCompression(false)
47 , OutputFilename(Options::StandardOut())
51 // ---------------------------------------------
52 // MergeToolPrivate implementation
54 struct MergeTool::MergeToolPrivate {
58 MergeToolPrivate(MergeTool::MergeSettings* settings)
59 : m_settings(settings)
62 ~MergeToolPrivate(void) { }
70 MergeTool::MergeSettings* m_settings;
73 bool MergeTool::MergeToolPrivate::Run(void) {
75 // set to default input if none provided
76 if ( !m_settings->HasInputBamFilename )
77 m_settings->InputFiles.push_back(Options::StandardIn());
79 // opens the BAM files (by default without checking for indexes)
80 BamMultiReader reader;
81 if ( !reader.Open(m_settings->InputFiles) ) {
82 cerr << "bamtools merge ERROR: could not open input BAM file(s)... Aborting." << endl;
86 // retrieve header & reference dictionary info
87 std::string mergedHeader = reader.GetHeaderText();
88 RefVector references = reader.GetReferenceData();
90 // determine compression mode for BamWriter
91 bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() &&
92 !m_settings->IsForceCompression );
93 BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
94 if ( writeUncompressed ) compressionMode = BamWriter::Uncompressed;
98 writer.SetCompressionMode(compressionMode);
99 if ( !writer.Open(m_settings->OutputFilename, mergedHeader, references) ) {
100 cerr << "bamtools merge ERROR: could not open "
101 << m_settings->OutputFilename << " for writing." << endl;
106 // if no region specified, store entire contents of file(s)
107 if ( !m_settings->HasRegion ) {
109 while ( reader.GetNextAlignmentCore(al) )
110 writer.SaveAlignment(al);
113 // otherwise attempt to use region as constraint
116 // if region string parses OK
118 if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
120 // attempt to find index files
121 reader.LocateIndexes();
123 // if index data available for all BAM files, we can use SetRegion
124 if ( reader.HasIndexes() ) {
126 // attempt to use SetRegion(), if failed report error
127 if ( !reader.SetRegion(region.LeftRefID,
130 region.RightPosition) )
132 cerr << "bamtools merge ERROR: set region failed. Check that REGION describes a valid range"
138 // everything checks out, just iterate through specified region, storing alignments
140 while ( reader.GetNextAlignmentCore(al) )
141 writer.SaveAlignment(al);
144 // no index data available, we have to iterate through until we
145 // find overlapping alignments
148 while ( reader.GetNextAlignmentCore(al) ) {
149 if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
150 (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
152 writer.SaveAlignment(al);
158 // error parsing REGION string
160 cerr << "bamtools merge ERROR: could not parse REGION - " << m_settings->Region << endl;
161 cerr << "Check that REGION is in valid format (see documentation) and that the coordinates are valid"
175 // ---------------------------------------------
176 // MergeTool implementation
178 MergeTool::MergeTool(void)
180 , m_settings(new MergeSettings)
183 // set program details
184 Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one", "[-in <filename> -in <filename> ...] [-out <filename> | [-forceCompression]] [-region <REGION>]");
187 OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
188 Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts);
189 Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts);
190 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);
191 Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
194 MergeTool::~MergeTool(void) {
203 int MergeTool::Help(void) {
204 Options::DisplayHelp();
208 int MergeTool::Run(int argc, char* argv[]) {
210 // parse command line arguments
211 Options::Parse(argc, argv, 1);
213 // initialize MergeTool with settings
214 m_impl = new MergeToolPrivate(m_settings);
216 // run MergeTool, return success/fail