1 // ***************************************************************************
2 // bamtools_count.cpp (c) 2010 Derek Barnett, Erik Garrison
3 // Marth Lab, Department of Biology, Boston College
4 // All rights reserved.
5 // ---------------------------------------------------------------------------
6 // Last modified: 2 June 2010
7 // ---------------------------------------------------------------------------
8 // Prints alignment count for BAM file
10 // ** Expand to multiple??
12 // ***************************************************************************
19 #include "bamtools_count.h"
20 #include "bamtools_options.h"
21 #include "bamtools_utilities.h"
22 #include "BamReader.h"
25 using namespace BamTools;
27 // ---------------------------------------------
28 // CountSettings implementation
30 struct CountTool::CountSettings {
33 bool HasBamIndexFilename;
34 bool HasInputBamFilename;
38 string BamIndexFilename;
39 string InputBamFilename;
44 : HasBamIndexFilename(false)
45 , HasInputBamFilename(false)
47 , InputBamFilename(Options::StandardIn())
51 // ---------------------------------------------
52 // CountTool implementation
54 CountTool::CountTool(void)
56 , m_settings(new CountSettings)
58 // set program details
59 Options::SetProgramInfo("bamtools count", "prints alignment counts for a BAM file", "-in <filename> [-region <REGION> [-index <filename>]]");
62 OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
63 Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputBamFilename, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
64 Options::AddValueOption("-index", "BAM index filename", "the BAM index file", "", m_settings->HasBamIndexFilename, m_settings->BamIndexFilename, IO_Opts);
66 OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
67 Options::AddValueOption("-region", "REGION", "genomic region. Index file is recommended for better performance. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
70 CountTool::~CountTool(void) {
75 int CountTool::Help(void) {
76 Options::DisplayHelp();
80 int CountTool::Run(int argc, char* argv[]) {
82 // parse command line arguments
83 Options::Parse(argc, argv, 1);
87 reader.Open(m_settings->InputBamFilename);
90 int alignmentCount(0);
92 // set up error handling
93 ostringstream errorStream("");
94 bool foundError(false);
96 // if no region specified, count entire file
97 if ( !m_settings->HasRegion ) {
99 while ( reader.GetNextAlignment(al) )
103 // more complicated - region specified
107 if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
109 // has index, we can jump directly to
110 if ( m_settings->HasBamIndexFilename ) {
112 // this is kind of a hack...?
113 // re-open BamReader, this time with the index file
115 reader.Open(m_settings->InputBamFilename, m_settings->BamIndexFilename);
117 // attempt Jump(), catch error
118 // if ( !reader.Jump(region.StartChromID, region.StartPosition) ) {
119 // foundError = true;
120 // errorStream << "Could not jump to desired REGION: " << m_settings->Region << endl;
123 if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
125 errorStream << "Could not set BamReader region to REGION: " << m_settings->Region << endl;
132 // read through sequentially, until first overlapping read is found
134 bool alignmentFound(false);
135 while( reader.GetNextAlignment(al) ) {
136 if ( (al.RefID == region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) ) {
137 alignmentFound = true;
142 // if overlapping alignment found (not EOF), increment counter
143 if ( alignmentFound ) ++ alignmentCount;
146 // -----------------------------
147 // count alignments until stop hit
150 // while valid alignment AND
151 // ( either current ref is before stopRefID OR
152 // current ref stopRefID but we're before stopPos )
154 //while ( reader.GetNextAlignment(al) && ((al.RefID < region.StopChromID ) || (al.RefID == region.StopChromID && al.Position <= region.StopPosition)) )
157 while ( reader.GetNextAlignment(al) )
164 errorStream << "Could not parse REGION: " << m_settings->Region << endl;
165 errorStream << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
169 // print errors OR results
171 cerr << errorStream.str() << endl;
173 cout << alignmentCount << endl;
177 return (int)foundError;