// ***************************************************************************
// bamtools_count.cpp (c) 2010 Derek Barnett, Erik Garrison
// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 2 June 2010
+// Last modified: 10 December 2012
// ---------------------------------------------------------------------------
-// Prints alignment count for BAM file
-//
-// ** Expand to multiple??
-//
+// Prints alignment count for BAM file(s)
// ***************************************************************************
+#include "bamtools_count.h"
+
+#include <api/BamAlgorithms.h>
+#include <api/BamMultiReader.h>
+#include <utils/bamtools_options.h>
+#include <utils/bamtools_utilities.h>
+using namespace BamTools;
+
+#include <fstream>
#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
// flags
bool HasInput;
+ bool HasInputFilelist;
bool HasRegion;
// filenames
vector<string> InputFiles;
+ string InputFilelist;
string Region;
// constructor
CountSettings(void)
: HasInput(false)
+ , HasInputFilelist(false)
, HasRegion(false)
{ }
};
// ---------------------------------------------
-// CountTool implementation
+// CountToolPrivate 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);
-}
+struct CountTool::CountToolPrivate {
-CountTool::~CountTool(void) {
- delete m_settings;
- m_settings = 0;
-}
+ // ctor & dtro
+ public:
+ CountToolPrivate(CountTool::CountSettings* settings)
+ : m_settings(settings)
+ { }
-int CountTool::Help(void) {
- Options::DisplayHelp();
- return 0;
-}
+ ~CountToolPrivate(void) { }
-int CountTool::Run(int argc, char* argv[]) {
+ // interface
+ public:
+ bool Run(void);
- // parse command line arguments
- Options::Parse(argc, argv, 1);
+ // data members
+ private:
+ CountTool::CountSettings* m_settings;
+};
- if ( !m_settings->HasInput )
+bool CountTool::CountToolPrivate::Run(void) {
+
+ // set to default input if none provided
+ if ( !m_settings->HasInput && !m_settings->HasInputFilelist )
m_settings->InputFiles.push_back(Options::StandardIn());
-
+
+ // add files in the filelist to the input file list
+ if ( m_settings->HasInputFilelist ) {
+
+ ifstream filelist(m_settings->InputFilelist.c_str(), ios::in);
+ if ( !filelist.is_open() ) {
+ cerr << "bamtools count ERROR: could not open input BAM file list... Aborting." << endl;
+ return false;
+ }
+
+ string line;
+ while ( getline(filelist, line) )
+ m_settings->InputFiles.push_back(line);
+ }
+
// open reader without index
BamMultiReader reader;
- reader.Open(m_settings->InputFiles, false, true);
+ if ( !reader.Open(m_settings->InputFiles) ) {
+ cerr << "bamtools count ERROR: could not open input BAM file(s)... Aborting." << endl;
+ return false;
+ }
// alignment counter
+ BamAlignment al;
int alignmentCount(0);
-
- // set up error handling
- ostringstream errorStream("");
- bool foundError(false);
-
- // if no region specified, count entire file
+
+ // if no region specified, count entire file
if ( !m_settings->HasRegion ) {
- BamAlignment al;
- while ( reader.GetNextAlignmentCore(al) )
+ while ( reader.GetNextAlignmentCore(al) )
++alignmentCount;
}
-
- // more complicated - region specified
+
+ // otherwise attempt to use region as constraint
else {
-
+
+ // if region string parses OK
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;
+ // attempt to find index files
+ reader.LocateIndexes();
+
+ // if index data available for all BAM files, we can use SetRegion
+ if ( reader.HasIndexes() ) {
+
+ // attempt to set region on reader
+ if ( !reader.SetRegion(region.LeftRefID, region.LeftPosition, region.RightRefID, region.RightPosition) ) {
+ cerr << "bamtools count ERROR: set region failed. Check that REGION describes a valid range" << endl;
+ reader.Close();
+ return false;
}
+
+ // everything checks out, just iterate through specified region, counting alignments
+ while ( reader.GetNextAlignmentCore(al) )
+ ++alignmentCount;
}
-
- // 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) ) {
+
+ // no index data available, we have to iterate through until we
+ // find overlapping alignments
+ else {
+ while ( reader.GetNextAlignmentCore(al) ) {
if ( (al.RefID >= region.LeftRefID) && ( (al.Position + al.Length) >= region.LeftPosition ) &&
- (al.RefID <= region.RightRefID) && ( al.Position <= region.RightPosition) )
+ (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;
+ }
+
+ // error parsing REGION string
+ else {
+ cerr << "bamtools count ERROR: could not parse REGION - " << m_settings->Region << endl;
+ cerr << "Check that REGION is in valid format (see documentation) and that the coordinates are valid"
+ << endl;
+ reader.Close();
+ return false;
}
}
-
- // print errors OR results
- if ( foundError )
- cerr << errorStream.str() << endl;
- else
- cout << alignmentCount << endl;
-
- // clean & exit
+
+ // print results
+ cout << alignmentCount << endl;
+
+ // clean up & exit
reader.Close();
- return (int)foundError;
+ return true;
+}
+
+// ---------------------------------------------
+// CountTool implementation
+
+CountTool::CountTool(void)
+ : AbstractTool()
+ , m_settings(new CountSettings)
+ , m_impl(0)
+{
+ // set program details
+ Options::SetProgramInfo("bamtools count", "prints number of alignments in BAM file(s)",
+ "[-in <filename> -in <filename> ... | -list <filelist>] [-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::StandardIn());
+ Options::AddValueOption("-list", "filename", "the input BAM file list, one line per file", "", m_settings->HasInputFilelist, m_settings->InputFilelist, IO_Opts);
+ Options::AddValueOption("-region", "REGION",
+ "genomic region. Index file is recommended for better performance, and is used automatically if it exists. See \'bamtools help index\' for more details on creating one",
+ "", m_settings->HasRegion, m_settings->Region, IO_Opts);
+}
+
+CountTool::~CountTool(void) {
+
+ delete m_settings;
+ m_settings = 0;
+
+ delete m_impl;
+ m_impl = 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);
+
+ // initialize CountTool with settings
+ m_impl = new CountToolPrivate(m_settings);
+
+ // run CountTool, return success/fail
+ if ( m_impl->Run() )
+ return 0;
+ else
+ return 1;
}
projects / bamtools.git / blobdiff