Removed SamTool (bamtools sam ...) from toolkit. This functionality is covered by...

diff --git a/bamtools_sam.cpp b/bamtools_sam.cpp
deleted file mode 100644 (file)
index 89da132..0000000
--- a/bamtools_sam.cpp
+++ /dev/null
@@ -1,244 +0,0 @@
-// ***************************************************************************
-// bamtools_sam.cpp (c) 2010 Derek Barnett, Erik Garrison
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 2 June 2010
-// ---------------------------------------------------------------------------
-// Prints a BAM file in the text-based SAM format.
-// ***************************************************************************
-
-#include <cstdlib>
-#include <iostream>
-#include <sstream>
-#include <string>
-
-#include "bamtools_sam.h"
-#include "bamtools_options.h"
-#include "BamReader.h"
-#include "BGZF.h"
-
-using namespace std;
-using namespace BamTools;
-
-static RefVector references;
-
-// ---------------------------------------------
-// print BamAlignment in SAM format
-
-void PrintSAM(const BamAlignment& a) {
-  
-    // tab-delimited
-    // <QNAME> <FLAG> <RNAME> <POS> <MAPQ> <CIGAR> <MRNM> <MPOS> <ISIZE> <SEQ> <QUAL> [ <TAG>:<VTYPE>:<VALUE> [...] ]
-  
-    ostringstream sb("");
-    
-    // write name & alignment flag
-    cout << a.Name << "\t" << a.AlignmentFlag << "\t";
-    
-    // write reference name
-    if ( (a.RefID >= 0) && (a.RefID < (int)references.size()) ) cout << references[a.RefID].RefName << "\t";
-    else cout << "*\t";
-    
-    // write position & map quality
-    cout << a.Position+1 << "\t" << a.MapQuality << "\t";
-    
-    // write CIGAR
-    const vector<CigarOp>& cigarData = a.CigarData;
-    if ( cigarData.empty() ) cout << "*\t";
-    else {
-        vector<CigarOp>::const_iterator cigarIter = cigarData.begin();
-        vector<CigarOp>::const_iterator cigarEnd  = cigarData.end();
-        for ( ; cigarIter != cigarEnd; ++cigarIter ) {
-            const CigarOp& op = (*cigarIter);
-            cout << op.Length << op.Type;
-        }
-        cout << "\t";
-    }
-    
-    // write mate reference name, mate position, & insert size
-    if ( a.IsPaired() && (a.MateRefID >= 0) && (a.MateRefID < (int)references.size()) ) {
-        if ( a.MateRefID == a.RefID ) cout << "=\t";
-        else cout << references[a.MateRefID].RefName << "\t";
-        cout << a.MatePosition+1 << "\t" << a.InsertSize << "\t";
-    } 
-    else cout << "*\t0\t0\t";
-    
-    // write sequence
-    if ( a.QueryBases.empty() ) cout << "*\t";
-    else cout << a.QueryBases << "\t";
-    
-    // write qualities
-    if ( a.Qualities.empty() ) cout << "*";
-    else cout << a.Qualities;
-    
-    // write tag data
-    const char* tagData = a.TagData.c_str();
-    const size_t tagDataLength = a.TagData.length();
-    size_t index = 0;
-    while ( index < tagDataLength ) {
-        
-        // write tag name
-        cout << "\t" << a.TagData.substr(index, 2) << ":";
-        index += 2;
-        
-        // get data type
-        char type = a.TagData.at(index);
-        ++index;
-        
-        switch (type) {
-            case('A') : 
-                cout << "A:" << tagData[index]; 
-                ++index; 
-                break;
-            
-            case('C') : 
-                cout << "i:" << atoi(&tagData[index]); 
-                ++index; 
-                break;
-            
-            case('c') : 
-                cout << "i:" << atoi(&tagData[index]);
-                ++index; 
-                break;
-            
-            case('S') : 
-                cout << "i:" << BgzfData::UnpackUnsignedShort(&tagData[index]); 
-                index += 2; 
-                break;
-                
-            case('s') : 
-                cout << "i:" << BgzfData::UnpackSignedShort(&tagData[index]);
-                index += 2; 
-                break;
-            
-            case('I') : 
-                cout << "i:" << BgzfData::UnpackUnsignedInt(&tagData[index]);
-                index += 4; 
-                break;
-            
-            case('i') : 
-                cout << "i:" << BgzfData::UnpackSignedInt(&tagData[index]);
-                index += 4; 
-                break;
-            
-            case('f') : 
-                cout << "f:" << BgzfData::UnpackFloat(&tagData[index]);
-                index += 4; 
-                break;
-            
-            case('d') : 
-                cout << "d:" << BgzfData::UnpackDouble(&tagData[index]);
-                index += 8; 
-                break;
-            
-            case('Z') :
-            case('H') : 
-                cout << type << ":"; 
-                while (tagData[index]) {
-                    cout << tagData[index];
-                    ++index;
-                }
-                ++index; 
-                break;      
-        }
-    }
-    
-    // write stream to stdout
-    cout << sb.str() << endl;
-}
-
-// ---------------------------------------------
-// SamSettings implementation
-
-struct SamTool::SamSettings {
-
-    // flags
-    bool HasInputBamFilename;
-    bool HasMaximumOutput;
-    bool IsOmittingHeader;
-
-    // filenames
-    string InputBamFilename;
-    
-    // other parameters
-    int MaximumOutput;
-    
-    // constructor
-    SamSettings(void)
-        : HasInputBamFilename(false)
-        , HasMaximumOutput(false)
-        , IsOmittingHeader(false)
-        , InputBamFilename(Options::StandardIn())
-    { }
-};  
-
-// ---------------------------------------------
-// SamTool implementation
-
-SamTool::SamTool(void)
-    : AbstractTool()
-    , m_settings(new SamSettings)
-{
-    // set program details
-    Options::SetProgramInfo("bamtools sam", "prints BAM file in SAM text format", "-in <filename>");
-    
-    // set up options 
-    OptionGroup* IO_Opts = Options::CreateOptionGroup("Input & Output");
-    Options::AddValueOption("-in", "BAM filename", "the input BAM file", "", m_settings->HasInputBamFilename, m_settings->InputBamFilename, IO_Opts, Options::StandardIn());
-    
-    OptionGroup* FilterOpts = Options::CreateOptionGroup("Filters");
-    Options::AddOption("-noheader", "omit the SAM header from output", m_settings->IsOmittingHeader, FilterOpts);
-    Options::AddValueOption("-num", "N", "maximum number of alignments to output", "", m_settings->HasMaximumOutput, m_settings->MaximumOutput, FilterOpts);
-}
-
-SamTool::~SamTool(void) {
-    delete m_settings;
-    m_settings = 0;
-}
-
-int SamTool::Help(void) {
-    Options::DisplayHelp();
-    return 0;
-}
-
-int SamTool::Run(int argc, char* argv[]) {
-  
-    // parse command line arguments
-    Options::Parse(argc, argv, 1);
-    
-    // open our BAM reader
-    BamReader reader;
-    reader.Open(m_settings->InputBamFilename);
-    
-    // if header desired, retrieve and print to stdout
-    if ( !m_settings->IsOmittingHeader ) {
-        string header = reader.GetHeaderText();
-        cout << header << endl;
-    }
-
-    // store reference data
-    references = reader.GetReferenceData();
-
-    // print all alignments to stdout in SAM format
-    if ( !m_settings->HasMaximumOutput ) {
-        BamAlignment ba;
-        while( reader.GetNextAlignment(ba) ) {
-            PrintSAM(ba);
-        }
-    }  
-    
-    // print first N alignments to stdout in SAM format
-    else {
-        BamAlignment ba;
-        int alignmentsPrinted = 0;
-        while ( reader.GetNextAlignment(ba) && (alignmentsPrinted < m_settings->MaximumOutput) ) {
-            PrintSAM(ba);
-            ++alignmentsPrinted;
-        }
-    }
-    
-    // clean & exit
-    reader.Close();
-    return 0;
-}

diff --git a/bamtools_sam.h b/bamtools_sam.h
deleted file mode 100644 (file)
index a0f5cc3..0000000
--- a/bamtools_sam.h
+++ /dev/null
@@ -1,35 +0,0 @@
-// ***************************************************************************
-// bamtools_sam.h (c) 2010 Derek Barnett, Erik Garrison
-// Marth Lab, Department of Biology, Boston College
-// All rights reserved.
-// ---------------------------------------------------------------------------
-// Last modified: 1 June 2010
-// ---------------------------------------------------------------------------
-// Prints a BAM file in the text-based SAM format.
-// ***************************************************************************
-
-#ifndef BAMTOOLS_SAM_H
-#define BAMTOOLS_SAM_H
-
-#include "bamtools_tool.h"
-
-namespace BamTools {
-  
-class SamTool : public AbstractTool {
-  
-    public:
-        SamTool(void);
-        ~SamTool(void);
-  
-    public:
-        int Help(void);
-        int Run(int argc, char* argv[]); 
-        
-    private:
-        struct SamSettings;
-        SamSettings* m_settings;
-};
-  
-} // namespace BamTools
-
-#endif // BAMTOOLS_SAM_H