1 // ***************************************************************************
2 // bamtools_revert.cpp (c) 2010 Derek Barnett, Alistair Ward
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 7 April 2011
7 // ---------------------------------------------------------------------------
8 // Removes duplicate marks and restores original base qualities
9 // ***************************************************************************
11 #include "bamtools_revert.h"
13 #include <api/BamReader.h>
14 #include <api/BamWriter.h>
15 #include <utils/bamtools_options.h>
16 #include <utils/bamtools_utilities.h>
17 using namespace BamTools;
25 static const string OQ_TAG = "OQ";
27 } // namespace BamTools;
29 // ---------------------------------------------
30 // RevertSettings implementation
32 struct RevertTool::RevertSettings {
37 bool IsForceCompression;
38 bool IsKeepDuplicateFlag;
43 string OutputFilename;
49 , IsForceCompression(false)
50 , IsKeepDuplicateFlag(false)
51 , IsKeepQualities(false)
52 , InputFilename(Options::StandardIn())
53 , OutputFilename(Options::StandardOut())
57 // ---------------------------------------------
58 // RevertToolPrivate implementation
60 struct RevertTool::RevertToolPrivate {
64 RevertToolPrivate(RevertTool::RevertSettings* settings)
65 : m_settings(settings)
67 ~RevertToolPrivate(void) { }
75 void RevertAlignment(BamAlignment& al);
79 RevertTool::RevertSettings* m_settings;
82 // 'reverts' a BAM alignment
83 // default behavior (for now) is:
84 // 1 - replace Qualities with OQ contents
85 // 2 - clear IsDuplicate flag
86 // can override default behavior using command line options
87 void RevertTool::RevertToolPrivate::RevertAlignment(BamAlignment& al) {
89 // replace Qualities with OQ contents, if requested
90 if ( !m_settings->IsKeepQualities ) {
91 string originalQualities;
92 if ( al.GetTag(OQ_TAG, originalQualities) ) {
93 al.Qualities = originalQualities;
98 // clear duplicate flag, if requested
99 if ( !m_settings->IsKeepDuplicateFlag )
100 al.SetIsDuplicate(false);
103 bool RevertTool::RevertToolPrivate::Run(void) {
105 // opens the BAM file without checking for indexes
107 if ( !reader.Open(m_settings->InputFilename) ) {
108 cerr << "bamtools revert ERROR: could not open " << m_settings->InputFilename
109 << " for reading... Aborting." << endl;
113 // get BAM file metadata
114 const string& headerText = reader.GetHeaderText();
115 const RefVector& references = reader.GetReferenceData();
117 // determine compression mode for BamWriter
118 bool writeUncompressed = ( m_settings->OutputFilename == Options::StandardOut() &&
119 !m_settings->IsForceCompression );
120 BamWriter::CompressionMode compressionMode = BamWriter::Compressed;
121 if ( writeUncompressed ) compressionMode = BamWriter::Uncompressed;
125 writer.SetCompressionMode(compressionMode);
126 if ( !writer.Open(m_settings->OutputFilename, headerText, references) ) {
127 cerr << "bamtools revert ERROR: could not open " << m_settings->OutputFilename
128 << " for writing... Aborting." << endl;
133 // plow through file, reverting alignments
135 while ( reader.GetNextAlignment(al) ) {
137 writer.SaveAlignment(al);
146 // ---------------------------------------------
147 // RevertTool implementation
149 RevertTool::RevertTool(void)
151 , m_settings(new RevertSettings)
154 // set program details
155 Options::SetProgramInfo("bamtools revert", "removes duplicate marks and restores original (non-recalibrated) base qualities", "[-in <filename> -in <filename> ...] [-out <filename> | [-forceCompression]] [revertOptions]");
158 OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
159 Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInput, m_settings->InputFilename, IO_Opts, Options::StandardIn());
160 Options::AddValueOption("-out", "BAM filename", "the output BAM file", "", m_settings->HasOutput, m_settings->OutputFilename, IO_Opts, Options::StandardOut());
161 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);
163 OptionGroup* RevertOpts = Options::CreateOptionGroup("Revert Options");
164 Options::AddOption("-keepDuplicate", "keep duplicates marked", m_settings->IsKeepDuplicateFlag, RevertOpts);
165 Options::AddOption("-keepQualities", "keep base qualities (do not replace with OQ contents)", m_settings->IsKeepQualities, RevertOpts);
168 RevertTool::~RevertTool(void) {
177 int RevertTool::Help(void) {
178 Options::DisplayHelp();
182 int RevertTool::Run(int argc, char* argv[]) {
184 // parse command line arguments
185 Options::Parse(argc, argv, 1);
187 // intialize RevertTool with settings
188 m_impl = new RevertToolPrivate(m_settings);
190 // run RevertTool, return success/fail