1 // ***************************************************************************
2 // bamtools_merge.cpp (c) 2010 Derek Barnett, Erik Garrison
3 // Marth Lab, Department of Biology, Boston College
4 // ---------------------------------------------------------------------------
5 // Last modified: 10 December 2012
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;
24 // ---------------------------------------------
25 // MergeSettings implementation
27 struct MergeTool::MergeSettings {
31 bool HasInputFilelist;
33 bool IsForceCompression;
37 vector<string> InputFiles;
41 string OutputFilename;
47 , HasInputFilelist(false)
49 , IsForceCompression(false)
51 , OutputFilename(Options::StandardOut())
55 // ---------------------------------------------
56 // MergeToolPrivate implementation
58 struct MergeTool::MergeToolPrivate {
62 MergeToolPrivate(MergeTool::MergeSettings* settings)
63 : m_settings(settings)
66 ~MergeToolPrivate(void) { }
74 MergeTool::MergeSettings* m_settings;
77 bool MergeTool::MergeToolPrivate::Run(void) {
79 // set to default input if none provided
80 if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
81 m_settings->InputFiles.push_back(Options::StandardIn());
83 // add files in the filelist to the input file list
84 if ( m_settings->HasInputFilelist ) {
86 ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
87 if ( !filelist.is_open() ) {
88 cerr << "bamtools merge ERROR: could not open input BAM file list... Aborting." << endl;
93 while ( getline(filelist, line) )
94 m_settings->InputFiles.push_back(line);
97 // opens the BAM files (by default without checking for indexes)
98 BamMultiReader reader;
99 if ( !reader.Open(m_settings->InputFiles) ) {
100 cerr << "bamtools merge ERROR: could not open input BAM file(s)... Aborting." << endl;
104 // retrieve header & reference dictionary info
105 std::string mergedHeader = reader.GetHeaderText();
106 RefVector references = reader.GetReferenceData();
108 // determine compression mode for BamWriter
109 bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() &&
110 !m_settings->IsForceCompression );
111 BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
112 if ( writeUncompressed ) compressionMode = BamWriter::Uncompressed;
116 writer.SetCompressionMode(compressionMode);
117 if ( !writer.Open(m_settings->OutputFilename, mergedHeader, references) ) {
118 cerr << "bamtools merge ERROR: could not open "
119 << m_settings->OutputFilename << " for writing." << endl;
124 // if no region specified, store entire contents of file(s)
125 if ( !m_settings->HasRegion ) {
127 while ( reader.GetNextAlignmentCore(al) )
128 writer.SaveAlignment(al);
131 // otherwise attempt to use region as constraint
134 // if region string parses OK
136 if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
138 // attempt to find index files
139 reader.LocateIndexes();
141 // if index data available for all BAM files, we can use SetRegion
142 if ( reader.HasIndexes() ) {
144 // attempt to use SetRegion(), if failed report error
145 if ( !reader.SetRegion(region.LeftRefID,
148 region.RightPosition) )
150 cerr << "bamtools merge ERROR: set region failed. Check that REGION describes a valid range"
156 // everything checks out, just iterate through specified region, storing alignments
158 while ( reader.GetNextAlignmentCore(al) )
159 writer.SaveAlignment(al);
162 // no index data available, we have to iterate through until we
163 // find overlapping alignments
166 while ( reader.GetNextAlignmentCore(al) ) {
167 if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
168 (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
170 writer.SaveAlignment(al);
176 // error parsing REGION string
178 cerr << "bamtools merge ERROR: could not parse REGION - " << m_settings->Region << endl;
179 cerr << "Check that REGION is in valid format (see documentation) and that the coordinates are valid"
193 // ---------------------------------------------
194 // MergeTool implementation
196 MergeTool::MergeTool(void)
198 , m_settings(new MergeSettings)
201 // set program details
202 Options::SetProgramInfo("bamtools merge", "merges multiple BAM files into one",
203 "[-in <filename> -in <filename> ... | -list <filelist>] [-out <filename> | [-forceCompression]] [-region <REGION>]");
206 OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
207 Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts);
208 Options::AddValueOption("-list", "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
209 Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts);
210 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);
211 Options::AddValueOption("-region", "REGION", "genomic region. See README for more details", "", m_settings->HasRegion, m_settings->Region, IO_Opts);
214 MergeTool::~MergeTool(void) {
223 int MergeTool::Help(void) {
224 Options::DisplayHelp();
228 int MergeTool::Run(int argc, char* argv[]) {
230 // parse command line arguments
231 Options::Parse(argc, argv, 1);
233 // initialize MergeTool with settings
234 m_impl = new MergeToolPrivate(m_settings);
236 // run MergeTool, return success/fail