--- /dev/null
+// ***************************************************************************
+// bamtools_count.cpp (c) 2010 Derek Barnett, Erik Garrison
+// Marth Lab, Department of Biology, Boston College
+// All rights reserved.
+// ---------------------------------------------------------------------------
+// Last modified: 2 June 2010
+// ---------------------------------------------------------------------------
+// Prints alignment count for BAM file
+//
+// ** Expand to multiple??
+//
+// ***************************************************************************
+
+#include <iostream>
+#include <sstream>
+#include <string>
+#include <vector>
+
+#include "bamtools_count.h"
+#include "bamtools_options.h"
+#include "bamtools_utilities.h"
+#include "BamReader.h"
+#include "BamMultiReader.h"
+
+using namespace std;
+using namespace BamTools;
+
+// ---------------------------------------------
+// CountSettings implementation
+
+struct CountTool::CountSettings {
+
+ // flags
+ bool HasInput;
+ bool HasRegion;
+
+ // filenames
+ vector<string> InputFiles;
+ string Region;
+
+ // constructor
+ CountSettings(void)
+ : HasInput(false)
+ , HasRegion(false)
+ { }
+};
+
+// ---------------------------------------------
+// CountTool implementation
+
+CountTool::CountTool(void)
+ : AbstractTool()
+ , m_settings(new CountSettings)
+{
+ // set program details
+ Options::SetProgramInfo("bamtools count", "prints alignment counts for a BAM file", "-in <filename> [-region <REGION>]");
+
+ // set up options
+ OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
+ Options::AddValueOption("-in", "BAM filename", "the input BAM file(s)", "", m_settings->HasInput, m_settings->InputFiles, IO_Opts);
+ //Options::AddValueOption("-index", "BAM index filename", "the BAM index file", "", m_settings->HasBamIndexFilename, m_settings->BamIndexFilename, IO_Opts);
+
+ OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
+ Options::AddValueOption("-region", "REGION", "genomic region. Index file is recommended for better performance, and is read automatically if it exists as <filename>.bai or <filename>.bti. See \'bamtools help index\' for more details on creating one", "", m_settings->HasRegion, m_settings->Region, FilterOpts);
+}
+
+CountTool::~CountTool(void) {
+ delete m_settings;
+ m_settings = 0;
+}
+
+int CountTool::Help(void) {
+ Options::DisplayHelp();
+ return 0;
+}
+
+int CountTool::Run(int argc, char* argv[]) {
+
+ // parse command line arguments
+ Options::Parse(argc, argv, 1);
+
+ if ( !m_settings->HasInput )
+ m_settings->InputFiles.push_back(Options::StandardIn());
+
+ BamMultiReader reader;
+ reader.Open(m_settings->InputFiles, false, true);
+
+ // alignment counter
+ int alignmentCount(0);
+
+ // set up error handling
+ ostringstream errorStream("");
+ bool foundError(false);
+
+ // if no region specified, count entire file
+ if ( !m_settings->HasRegion ) {
+ BamAlignment al;
+ while ( reader.GetNextAlignmentCore(al) )
+ ++alignmentCount;
+ }
+
+ // more complicated - region specified
+ else {
+
+ BamRegion region;
+ if ( Utilities::ParseRegionString(m_settings->Region, reader, region) ) {
+
+ // check if there are index files *.bai/*.bti corresponding to the input files
+ bool hasDefaultIndex = false;
+ bool hasBamtoolsIndex = false;
+ bool hasNoIndex = false;
+ int defaultIndexCount = 0;
+ int bamtoolsIndexCount = 0;
+ for (vector<string>::const_iterator f = m_settings->InputFiles.begin(); f != m_settings->InputFiles.end(); ++f) {
+
+ if ( Utilities::FileExists(*f + ".bai") ) {
+ hasDefaultIndex = true;
+ ++defaultIndexCount;
+ }
+
+ if ( Utilities::FileExists(*f + ".bti") ) {
+ hasBamtoolsIndex = true;
+ ++bamtoolsIndexCount;
+ }
+
+ if ( !hasDefaultIndex && !hasBamtoolsIndex ) {
+ hasNoIndex = true;
+ cerr << "*WARNING - could not find index file for " << *f
+ << ", parsing whole file(s) to get alignment counts for target region"
+ << " (could be slow)" << endl;
+ break;
+ }
+ }
+
+ // determine if index file types are heterogeneous
+ bool hasDifferentIndexTypes = false;
+ if ( defaultIndexCount > 0 && bamtoolsIndexCount > 0 ) {
+ hasDifferentIndexTypes = true;
+ cerr << "*WARNING - different index file formats found"
+ << ", parsing whole file(s) to get alignment counts for target region"
+ << " (could be slow)" << endl;
+ }
+
+ // if any input file has no index, or if input files use different index formats
+ // can't use BamMultiReader to jump directly (**for now**)
+ if ( hasNoIndex || hasDifferentIndexTypes ) {
+
+ // read through sequentially, counting all overlapping reads
+ BamAlignment al;
+ while( reader.GetNextAlignmentCore(al) ) {
+ if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
+ (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
+ {
+ ++alignmentCount;
+ }
+ }
+ }
+
+ // has index file for each input file (and same format)
+ else {
+
+ // this is kind of a hack...?
+ BamMultiReader reader;
+ reader.Open(m_settings->InputFiles, true, true, hasDefaultIndex );
+
+ if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
+ foundError = true;
+ errorStream << "Could not set BamReader region to REGION: " << m_settings->Region << endl;
+ } else {
+ BamAlignment al;
+ while ( reader.GetNextAlignmentCore(al) )
+ ++alignmentCount;
+ }
+ }
+
+ } else {
+ foundError = true;
+ errorStream << "Could not parse REGION: " << m_settings->Region << endl;
+ errorStream << "Be sure REGION is in valid format (see README) and that coordinates are valid for selected references" << endl;
+ }
+ }
+
+ // print errors OR results
+ if ( foundError )
+ cerr << errorStream.str() << endl;
+ else
+ cout << alignmentCount << endl;
+
+ // clean & exit
+ reader.Close();
+ return (int)foundError;
+}
projects / bamtools.git / blobdiff