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: 13 October 2010
7 // ---------------------------------------------------------------------------
8 // Merges multiple BAM files into one.
9 // ***************************************************************************
14 #include "bamtools_merge.h"
15 #include "bamtools_options.h"
16 #include "bamtools_utilities.h"
17 #include "BamMultiReader.h"
18 #include "BamWriter.h"
20 using namespace BamTools;
22 // ---------------------------------------------
23 // MergeSettings implementation
25 struct MergeTool::MergeSettings {
28 bool HasInputBamFilename;
29 bool HasOutputBamFilename;
30 bool IsForceCompression;
34 vector<string> InputFiles;
37 string OutputFilename;
42 : HasInputBamFilename(false)
43 , HasOutputBamFilename(false)
44 , IsForceCompression(false)
46 , OutputFilename(Options::StandardOut())
50 // ---------------------------------------------
51 // MergeTool implementation
53 MergeTool::MergeTool(void)
55 , m_settings(new MergeSettings)
57 // set program details
58 Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one", "[-in <filename> -in <filename> ...] [-out <filename> | [-forceCompression]] [-region <REGION>]");
61 OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
62 Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInputBamFilename, m_settings->InputFiles, IO_Opts);
63 Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutputBamFilename, m_settings->OutputFilename, IO_Opts);
64 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);
65 Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
68 MergeTool::~MergeTool(void) {
73 int MergeTool::Help(void) {
74 Options::DisplayHelp();
78 int MergeTool::Run(int argc, char* argv[]) {
80 // parse command line arguments
81 Options::Parse(argc, argv, 1);
83 // set to default input if none provided
84 if ( !m_settings->HasInputBamFilename )
85 m_settings->InputFiles.push_back(Options::StandardIn());
87 // opens the BAM files (by default without checking for indexes)
88 BamMultiReader reader;
89 if ( !reader.Open(m_settings->InputFiles, false, true) ) {
90 cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
94 // retrieve header & reference dictionary info
95 std::string mergedHeader = reader.GetHeaderText();
96 RefVector references = reader.GetReferenceData();
100 bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() && !m_settings->IsForceCompression );
101 if ( !writer.Open(m_settings->OutputFilename, mergedHeader, references, writeUncompressed) ) {
102 cerr << "ERROR: Could not open BAM file " << m_settings->OutputFilename << " for writing... Aborting." << endl;
107 // if no region specified, store entire contents of file(s)
108 if ( !m_settings->HasRegion ) {
110 while ( reader.GetNextAlignmentCore(al) )
111 writer.SaveAlignment(al);
114 // otherwise attempt to use region as constraint
117 // if region string parses OK
119 if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
121 // attempt to re-open reader with index files
123 bool openedOK = reader.Open(m_settings->InputFiles, true, true );
127 cerr << "ERROR: Could not open input BAM file(s)... Aborting." << endl;
131 // if index data available, we can use SetRegion
132 if ( reader.IsIndexLoaded() ) {
134 // attempt to use SetRegion(), if failed report error
135 if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
136 cerr << "ERROR: Region requested, but could not set BamReader region to REGION: " << m_settings->Region << " Aborting." << endl;
141 // everything checks out, just iterate through specified region, storing alignments
143 while ( reader.GetNextAlignmentCore(al) )
144 writer.SaveAlignment(al);
147 // no index data available, we have to iterate through until we
148 // find overlapping alignments
151 while ( reader.GetNextAlignmentCore(al) ) {
152 if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
153 (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
155 writer.SaveAlignment(al);
161 // error parsing REGION string
163 cerr << "ERROR: Could not parse REGION - " << m_settings->Region << endl;
164 cerr << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;