// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 21 March 2011
+// Last modified: 7 April 2011
// ---------------------------------------------------------------------------
// Prints general alignment statistics for BAM file(s).
// ***************************************************************************
// ctor & dtor
public:
StatsToolPrivate(StatsTool::StatsSettings* _settings);
- ~StatsToolPrivate(void);
+ ~StatsToolPrivate(void) { }
// 'public' interface
public:
// data members
private:
- StatsTool::StatsSettings* settings;
- unsigned int numReads;
- unsigned int numPaired;
- unsigned int numProperPair;
- unsigned int numMapped;
- unsigned int numBothMatesMapped;
- unsigned int numForwardStrand;
- unsigned int numReverseStrand;
- unsigned int numFirstMate;
- unsigned int numSecondMate;
- unsigned int numSingletons;
- unsigned int numFailedQC;
- unsigned int numDuplicates;
- vector<int> insertSizes;
+ StatsTool::StatsSettings* m_settings;
+ unsigned int m_numReads;
+ unsigned int m_numPaired;
+ unsigned int m_numProperPair;
+ unsigned int m_numMapped;
+ unsigned int m_numBothMatesMapped;
+ unsigned int m_numForwardStrand;
+ unsigned int m_numReverseStrand;
+ unsigned int m_numFirstMate;
+ unsigned int m_numSecondMate;
+ unsigned int m_numSingletons;
+ unsigned int m_numFailedQC;
+ unsigned int m_numDuplicates;
+ vector<int> m_insertSizes;
};
-StatsTool::StatsToolPrivate::StatsToolPrivate(StatsTool::StatsSettings* _settings)
- : settings(_settings)
- , numReads(0)
- , numPaired(0)
- , numProperPair(0)
- , numMapped(0)
- , numBothMatesMapped(0)
- , numForwardStrand(0)
- , numReverseStrand(0)
- , numFirstMate(0)
- , numSecondMate(0)
- , numSingletons(0)
- , numFailedQC(0)
- , numDuplicates(0)
+StatsTool::StatsToolPrivate::StatsToolPrivate(StatsTool::StatsSettings* settings)
+ : m_settings(settings)
+ , m_numReads(0)
+ , m_numPaired(0)
+ , m_numProperPair(0)
+ , m_numMapped(0)
+ , m_numBothMatesMapped(0)
+ , m_numForwardStrand(0)
+ , m_numReverseStrand(0)
+ , m_numFirstMate(0)
+ , m_numSecondMate(0)
+ , m_numSingletons(0)
+ , m_numFailedQC(0)
+ , m_numDuplicates(0)
{
- insertSizes.reserve(100000);
+ m_insertSizes.reserve(100000);
}
-StatsTool::StatsToolPrivate::~StatsToolPrivate(void) { }
-
// median is of type double because in the case of even number of data elements,
// we need to return the average of middle 2 elements
bool StatsTool::StatsToolPrivate::CalculateMedian(vector<int>& data, double& median) {
cout << "Stats for BAM file(s): " << endl;
cout << "**********************************************" << endl;
cout << endl;
- cout << "Total reads: " << numReads << endl;
- cout << "Mapped reads: " << numMapped << "\t(" << ((float)numMapped/numReads)*100 << "%)" << endl;
- cout << "Forward strand: " << numForwardStrand << "\t(" << ((float)numForwardStrand/numReads)*100 << "%)" << endl;
- cout << "Reverse strand: " << numReverseStrand << "\t(" << ((float)numReverseStrand/numReads)*100 << "%)" << endl;
- cout << "Failed QC: " << numFailedQC << "\t(" << ((float)numFailedQC/numReads)*100 << "%)" << endl;
- cout << "Duplicates: " << numDuplicates << "\t(" << ((float)numDuplicates/numReads)*100 << "%)" << endl;
- cout << "Paired-end reads: " << numPaired << "\t(" << ((float)numPaired/numReads)*100 << "%)" << endl;
+ cout << "Total reads: " << m_numReads << endl;
+ cout << "Mapped reads: " << m_numMapped << "\t(" << ((float)m_numMapped/m_numReads)*100 << "%)" << endl;
+ cout << "Forward strand: " << m_numForwardStrand << "\t(" << ((float)m_numForwardStrand/m_numReads)*100 << "%)" << endl;
+ cout << "Reverse strand: " << m_numReverseStrand << "\t(" << ((float)m_numReverseStrand/m_numReads)*100 << "%)" << endl;
+ cout << "Failed QC: " << m_numFailedQC << "\t(" << ((float)m_numFailedQC/m_numReads)*100 << "%)" << endl;
+ cout << "Duplicates: " << m_numDuplicates << "\t(" << ((float)m_numDuplicates/m_numReads)*100 << "%)" << endl;
+ cout << "Paired-end reads: " << m_numPaired << "\t(" << ((float)m_numPaired/m_numReads)*100 << "%)" << endl;
- if ( numPaired != 0 ) {
- cout << "'Proper-pairs': " << numProperPair << "\t(" << ((float)numProperPair/numPaired)*100 << "%)" << endl;
- cout << "Both pairs mapped: " << numBothMatesMapped << "\t(" << ((float)numBothMatesMapped/numPaired)*100 << "%)" << endl;
- cout << "Read 1: " << numFirstMate << endl;
- cout << "Read 2: " << numSecondMate << endl;
- cout << "Singletons: " << numSingletons << "\t(" << ((float)numSingletons/numPaired)*100 << "%)" << endl;
+ if ( m_numPaired != 0 ) {
+ cout << "'Proper-pairs': " << m_numProperPair << "\t(" << ((float)m_numProperPair/m_numPaired)*100 << "%)" << endl;
+ cout << "Both pairs mapped: " << m_numBothMatesMapped << "\t(" << ((float)m_numBothMatesMapped/m_numPaired)*100 << "%)" << endl;
+ cout << "Read 1: " << m_numFirstMate << endl;
+ cout << "Read 2: " << m_numSecondMate << endl;
+ cout << "Singletons: " << m_numSingletons << "\t(" << ((float)m_numSingletons/m_numPaired)*100 << "%)" << endl;
}
- if ( settings->IsShowingInsertSizeSummary ) {
+ if ( m_settings->IsShowingInsertSizeSummary ) {
double avgInsertSize = 0.0;
- if ( !insertSizes.empty() ) {
- avgInsertSize = ( accumulate(insertSizes.begin(), insertSizes.end(), 0.0) / (double)insertSizes.size() );
+ if ( !m_insertSizes.empty() ) {
+ avgInsertSize = ( accumulate(m_insertSizes.begin(), m_insertSizes.end(), 0.0) / (double)m_insertSizes.size() );
cout << "Average insert size (absolute value): " << avgInsertSize << endl;
}
double medianInsertSize = 0.0;
- if ( CalculateMedian(insertSizes, medianInsertSize) )
+ if ( CalculateMedian(m_insertSizes, medianInsertSize) )
cout << "Median insert size (absolute value): " << medianInsertSize << endl;
}
cout << endl;
void StatsTool::StatsToolPrivate::ProcessAlignment(const BamAlignment& al) {
// increment total alignment counter
- ++numReads;
+ ++m_numReads;
- // check the paired-independent flags
- if ( al.IsDuplicate() ) ++numDuplicates;
- if ( al.IsFailedQC() ) ++numFailedQC;
- if ( al.IsMapped() ) ++numMapped;
+ // incrememt counters for pairing-independent flags
+ if ( al.IsDuplicate() ) ++m_numDuplicates;
+ if ( al.IsFailedQC() ) ++m_numFailedQC;
+ if ( al.IsMapped() ) ++m_numMapped;
- // check forward/reverse strand
+ // increment strand counters
if ( al.IsReverseStrand() )
- ++numReverseStrand;
+ ++m_numReverseStrand;
else
- ++numForwardStrand;
+ ++m_numForwardStrand;
// if alignment is paired-end
if ( al.IsPaired() ) {
// increment PE counter
- ++numPaired;
+ ++m_numPaired;
// increment first mate/second mate counters
- if ( al.IsFirstMate() ) ++numFirstMate;
- if ( al.IsSecondMate() ) ++numSecondMate;
+ if ( al.IsFirstMate() ) ++m_numFirstMate;
+ if ( al.IsSecondMate() ) ++m_numSecondMate;
// if alignment is mapped, check mate status
if ( al.IsMapped() ) {
// if mate mapped
if ( al.IsMateMapped() )
- ++numBothMatesMapped;
+ ++m_numBothMatesMapped;
// else singleton
else
- ++numSingletons;
+ ++m_numSingletons;
}
// check for explicit proper pair flag
- if ( al.IsProperPair() ) ++numProperPair;
+ if ( al.IsProperPair() ) ++m_numProperPair;
// store insert size for first mate
- if ( settings->IsShowingInsertSizeSummary && al.IsFirstMate() && (al.InsertSize != 0) ) {
+ if ( m_settings->IsShowingInsertSizeSummary && al.IsFirstMate() && (al.InsertSize != 0) ) {
int insertSize = abs(al.InsertSize);
- insertSizes.push_back( insertSize );
+ m_insertSizes.push_back( insertSize );
}
}
}
bool StatsTool::StatsToolPrivate::Run() {
+ // set to default input if none provided
+ if ( !m_settings->HasInput )
+ m_settings->InputFiles.push_back(Options::StandardIn());
+
// open the BAM files
BamMultiReader reader;
- if ( !reader.Open(settings->InputFiles) ) {
+ if ( !reader.Open(m_settings->InputFiles) ) {
cerr << "bamtools stats ERROR: could not open input BAM file(s)... Aborting." << endl;
reader.Close();
return false;
}
StatsTool::~StatsTool(void) {
+
delete m_settings;
m_settings = 0;
// parse command line arguments
Options::Parse(argc, argv, 1);
-
- // set to default input if none provided
- if ( !m_settings->HasInput )
- m_settings->InputFiles.push_back(Options::StandardIn());
- // run internal StatsTool implementation, return success/fail
+ // initialize StatsTool with settings
m_impl = new StatsToolPrivate(m_settings);
- if ( m_impl->Run() ) return 0;
- else return 1;
+ // run StatsTool, return success/fail
+ if ( m_impl->Run() )
+ return 0;
+ else
+ return 1;
}
projects / bamtools.git / blobdiff