Find(), ConstFind() dictionary methods, .gitignore

.gitignore

@@ -0,0 +1,9 @@
+build
+bin
+lib
+include
+bamtools_version.h
+*.swp
+.DS_Store
+._.*
+

README.md

@@ -0,0 +1,23 @@
+Fork of **bamtools** from <https://github.com/pezmaster31/bamtools/>.  I love
+the bamtools API and will put mods here that could potentially be part of the
+general bamtools offering.  More extensive mods (such as my desire to create a
+version that can be dropped into an existing Makefile-driven project) will go
+in another fork.
+
+#### Reduced header-associated memory usage
+
+I added the methods
+```c++
+const SamHeader& BamReader::GetConstSamHeader() const { }
+```
+to the public interface for `BamReader`,
+```c++
+const SamHeader& BamReaderPrivate::GetConstSamHeader() const { }
+```
+to the public interface for `Internal::BamReaderPrivate` and
+```c++
+const SamHeader& BamHeader::ToConstSamHeader() const { }
+```
+to the `Internal::BamHeader` class, this is the method that ultimately provides
+the reference requested by `BamReader::GetConstSamHeader()`.
+

src/api/BamWriter.h

@@ -1,69 +1,69 @@
-// ***************************************************************************
-// BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// ---------------------------------------------------------------------------
-// Last modified: 10 October 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides the basic functionality for producing BAM files
-// ***************************************************************************
-
-#ifndef BAMWRITER_H
-#define BAMWRITER_H
-
-#include "api/api_global.h"
-#include "api/BamAux.h"
-#include <string>
-
-namespace BamTools {
-
-class BamAlignment;
-class SamHeader;
-
-//! \cond
-namespace Internal {
-    class BamWriterPrivate;
-} // namespace Internal
-//! \endcond
-
-class API_EXPORT BamWriter {
-
-    // enums
-    public:
-        enum CompressionMode { Compressed = 0
-                             , Uncompressed
-                             };
-
-    // ctor & dtor
-    public:
-        BamWriter(void);
-        ~BamWriter(void);
-
-    // public interface
-    public:
-        //  closes the current BAM file
-        void Close(void);
-        // returns a human-readable description of the last error that occurred
-        std::string GetErrorString(void) const;
-        // returns true if BAM file is open for writing
-        bool IsOpen(void) const;
-        // opens a BAM file for writing
-        bool Open(const std::string& filename, 
-                  const std::string& samHeaderText,
-                  const RefVector& referenceSequences);
-        // opens a BAM file for writing
-        bool Open(const std::string& filename,
-                  const SamHeader& samHeader,
-                  const RefVector& referenceSequences);
-        // saves the alignment to the alignment archive
-        bool SaveAlignment(const BamAlignment& alignment);
-        // sets the output compression mode
-        void SetCompressionMode(const BamWriter::CompressionMode& compressionMode);
-
-    // private implementation
-    private:
-        Internal::BamWriterPrivate* d;
-};
-
-} // namespace BamTools
-
-#endif // BAMWRITER_H
+// ***************************************************************************
+// BamWriter.h (c) 2009 Michael Str�mberg, Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 10 October 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides the basic functionality for producing BAM files
+// ***************************************************************************
+
+#ifndef BAMWRITER_H
+#define BAMWRITER_H
+
+#include "api/api_global.h"
+#include "api/BamAux.h"
+#include <string>
+
+namespace BamTools {
+
+class BamAlignment;
+struct SamHeader;
+
+//! \cond
+namespace Internal {
+    class BamWriterPrivate;
+} // namespace Internal
+//! \endcond
+
+class API_EXPORT BamWriter {
+
+    // enums
+    public:
+        enum CompressionMode { Compressed = 0
+                             , Uncompressed
+                             };
+
+    // ctor & dtor
+    public:
+        BamWriter(void);
+        ~BamWriter(void);
+
+    // public interface
+    public:
+        //  closes the current BAM file
+        void Close(void);
+        // returns a human-readable description of the last error that occurred
+        std::string GetErrorString(void) const;
+        // returns true if BAM file is open for writing
+        bool IsOpen(void) const;
+        // opens a BAM file for writing
+        bool Open(const std::string& filename, 
+                  const std::string& samHeaderText,
+                  const RefVector& referenceSequences);
+        // opens a BAM file for writing
+        bool Open(const std::string& filename,
+                  const SamHeader& samHeader,
+                  const RefVector& referenceSequences);
+        // saves the alignment to the alignment archive
+        bool SaveAlignment(const BamAlignment& alignment);
+        // sets the output compression mode
+        void SetCompressionMode(const BamWriter::CompressionMode& compressionMode);
+
+    // private implementation
+    private:
+        Internal::BamWriterPrivate* d;
+};
+
+} // namespace BamTools
+
+#endif // BAMWRITER_H

src/api/SamSequenceDictionary.cpp

@@ -196,6 +196,45 @@ SamSequenceConstIterator SamSequenceDictionary::End(void) const {
     return m_data.end();
 }
 
+/*! \fn SamSequenceIterator SamSequenceDictionary::Find(const std::string& sequenceName)
+    \return an STL iterator pointing to the sequence having sequenceName, otherwise End()
+    \sa ConstFind(), Begin(), End()
+*/
+SamSequenceIterator SamSequenceDictionary::Find(const std::string& sequenceName) {
+    if ( m_lookupData.find(sequenceName) == m_lookupData.end() )
+        return End();
+    SamSequenceIterator it = m_data.begin();
+    const size_t index = m_lookupData.find(sequenceName)->second;
+    return it + index;
+}
+
+/*! \fn SamSequenceConstIterator SamSequenceDictionary::Find(void) const
+    \return an STL const_iterator pointing to the sequence having sequenceName, otherwise End()
+
+    This is an overloaded function.
+
+    \sa ConstFind(), Begin(), End()
+*/
+SamSequenceConstIterator SamSequenceDictionary::Find(const std::string& sequenceName) const {
+    if ( m_lookupData.find(sequenceName) == m_lookupData.end() )
+        return End();
+    SamSequenceConstIterator it = m_data.begin();
+    const size_t index = m_lookupData.find(sequenceName)->second;
+    return it + index;
+}
+
+/*! \fn SamSequenceConstIterator SamSequenceDictionary::ConstFind(void) const
+    \return an STL const_iterator pointing to the sequence having sequenceName, otherwise End()
+    \sa Find(), ConstBegin(), ConstEnd()
+*/
+SamSequenceConstIterator SamSequenceDictionary::ConstFind(const std::string& sequenceName) const {
+    if ( m_lookupData.find(sequenceName) == m_lookupData.end() )
+        return ConstEnd();
+    SamSequenceConstIterator it = m_data.begin();
+    const size_t index = m_lookupData.find(sequenceName)->second;
+    return it + index;
+}
+
 /*! \fn bool SamSequenceDictionary::IsEmpty(void) const
     \brief Returns \c true if dictionary contains no sequences
     \sa Size()

src/api/SamSequenceDictionary.h

@@ -73,6 +73,10 @@ class API_EXPORT SamSequenceDictionary {
         SamSequenceIterator      End(void);                 // returns iterator to end()
         SamSequenceConstIterator End(void) const;           // returns const_iterator to end()
         SamSequenceConstIterator ConstEnd(void) const;      // returns const_iterator to end()
+        SamSequenceIterator      Find(const std::string& sequenceName);
+        SamSequenceConstIterator Find(const std::string& sequenceName) const;
+        SamSequenceConstIterator ConstFind(const std::string& sequenceName) const;
+
 
     // data members
     private:

src/toolkit/bamtools.cpp

@@ -146,7 +146,7 @@ int Version(void) {
 int main(int argc, char* argv[]) {
 
     // just 'bamtools'
-    if ( (argc == 1) ) return Help(argc, argv);
+    if ( argc == 1 ) return Help(argc, argv);
 
     // 'bamtools help', 'bamtools --help', or 'bamtools -h'
     if ( IsHelp(argv[1]) ) return Help(argc, argv);