ngs_server 0.1

data/ext/bamtools/src/api/SamSequenceDictionary.cpp

@@ -0,0 +1,292 @@
+// ***************************************************************************
+// SamSequenceDictionary.cpp (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 18 April 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides methods for operating on a collection of SamSequence entries.
+// *************************************************************************
+
+#include <api/SamSequenceDictionary.h>
+using namespace BamTools;
+
+#include <iostream>
+using namespace std;
+
+/*! \class BamTools::SamSequenceDictionary
+    \brief Container of SamSequence entries.
+
+    Provides methods for operating on a collection of SamSequence entries.
+*/
+
+/*! \fn SamSequenceDictionary::SamSequenceDictionary(void)
+    \brief constructor
+*/
+SamSequenceDictionary::SamSequenceDictionary(void) { }
+
+/*! \fn SamSequenceDictionary::SamSequenceDictionary(const SamSequenceDictionary& other)
+    \brief copy constructor
+*/
+SamSequenceDictionary::SamSequenceDictionary(const SamSequenceDictionary& other)
+    : m_data(other.m_data)
+{ }
+
+/*! \fn SamSequenceDictionary::~SamSequenceDictionary(void)
+    \brief destructor
+*/
+SamSequenceDictionary::~SamSequenceDictionary(void) { }
+
+/*! \fn void SamSequenceDictionary::Add(const SamSequence& sequence)
+    \brief Adds a sequence to the dictionary.
+
+    Duplicate entries are silently discarded.
+
+    \param sequence entry to be added
+*/
+void SamSequenceDictionary::Add(const SamSequence& sequence) {
+
+    // TODO: report error on attempted duplicate?
+
+    if ( IsEmpty() || !Contains(sequence) )
+        m_data.push_back(sequence);
+}
+
+/*! \fn void SamSequenceDictionary::Add(const std::string& name, const int& length)
+    \brief Adds a sequence to the dictionary.
+
+    This is an overloaded function.
+
+    \param name name of sequence entry to be added
+    \param length length of sequence entry to be added
+    \sa Add()
+*/
+void SamSequenceDictionary::Add(const std::string& name, const int& length) {
+    Add( SamSequence(name, length) );
+}
+
+/*! \fn void SamSequenceDictionary::Add(const std::vector<SamSequence>& sequences)
+    \brief Adds multiple sequences to the dictionary.
+
+    This is an overloaded function.
+
+    \param sequences entries to be added
+    \sa Add()
+*/
+void SamSequenceDictionary::Add(const std::vector<SamSequence>& sequences) {
+    vector<SamSequence>::const_iterator seqIter = sequences.begin();
+    vector<SamSequence>::const_iterator seqEnd  = sequences.end();
+    for ( ; seqIter!= seqEnd; ++seqIter )
+        Add(*seqIter);
+}
+
+/*! \fn void SamSequenceDictionary::Add(const std::map<std::string, int>& sequenceMap)
+    \brief Adds multiple sequences to the dictionary.
+
+    This is an overloaded function.
+
+    \param sequenceMap map of sequence entries (name => length) to be added
+    \sa Add()
+*/
+void SamSequenceDictionary::Add(const std::map<std::string, int>& sequenceMap) {
+    map<string, int>::const_iterator seqIter = sequenceMap.begin();
+    map<string, int>::const_iterator seqEnd  = sequenceMap.end();
+    for ( ; seqIter != seqEnd; ++seqIter ) {
+        const string& name = (*seqIter).first;
+        const int& length = (*seqIter).second;
+        Add( SamSequence(name, length) );
+    }
+}
+
+/*! \fn SamSequenceIterator SamSequenceDictionary::Begin(void)
+    \return an STL iterator pointing to the first sequence
+    \sa ConstBegin(), End()
+*/
+SamSequenceIterator SamSequenceDictionary::Begin(void) {
+    return m_data.begin();
+}
+
+/*! \fn SamSequenceConstIterator SamSequenceDictionary::Begin(void) const
+    \return an STL const_iterator pointing to the first sequence
+
+    This is an overloaded function.
+
+    \sa ConstBegin(), End()
+*/
+SamSequenceConstIterator SamSequenceDictionary::Begin(void) const {
+    return m_data.begin();
+}
+
+/*! \fn void SamSequenceDictionary::Clear(void)
+    \brief Clears all sequence entries.
+*/
+void SamSequenceDictionary::Clear(void) {
+    m_data.clear();
+}
+
+/*! \fn SamSequenceConstIterator SamSequenceDictionary::ConstBegin(void) const
+    \return an STL const_iterator pointing to the first sequence
+    \sa Begin(), ConstEnd()
+*/
+SamSequenceConstIterator SamSequenceDictionary::ConstBegin(void) const {
+    return m_data.begin();
+}
+
+/*! \fn SamSequenceConstIterator SamSequenceDictionary::ConstEnd(void) const
+    \return an STL const_iterator pointing to the imaginary entry after the last sequence
+    \sa End(), ConstBegin()
+*/
+SamSequenceConstIterator SamSequenceDictionary::ConstEnd(void) const {
+    return m_data.end();
+}
+
+/*! \fn bool SamSequenceDictionary::Contains(const std::string& sequenceName) const
+    \brief Returns true if dictionary contains sequence.
+    \param sequenceName search for sequence matching this name
+    \return \c true if dictionary contains a sequence with this name
+*/
+bool SamSequenceDictionary::Contains(const std::string& sequenceName) const {
+    return ( IndexOf(sequenceName) != (int)m_data.size() );
+}
+
+/*! \fn bool SamSequenceDictionary::Contains(const SamSequence& sequence) const
+    \brief Returns true if dictionary contains sequence (matches on name).
+
+    This is an overloaded function.
+
+    \param sequence search for this sequence
+    \return \c true if dictionary contains sequence (matching on name)
+*/
+bool SamSequenceDictionary::Contains(const SamSequence& sequence) const {
+    return ( IndexOf(sequence.Name) != (int)m_data.size() );
+}
+
+/*! \fn SamSequenceIterator SamSequenceDictionary::End(void)
+    \return an STL iterator pointing to the imaginary entry after the last sequence
+    \sa Begin(), ConstEnd()
+*/
+SamSequenceIterator SamSequenceDictionary::End(void) {
+    return m_data.end();
+}
+
+/*! \fn SamSequenceConstIterator SamSequenceDictionary::End(void) const
+    \return an STL const_iterator pointing to the imaginary entry after the last sequence
+
+    This is an overloaded function.
+
+    \sa Begin(), ConstEnd()
+*/
+SamSequenceConstIterator SamSequenceDictionary::End(void) const {
+    return m_data.end();
+}
+
+/*! \fn int SamSequenceDictionary::IndexOf(const std::string& name) const
+    \internal
+    \return index of sequence if found (matching on name).  Otherwise, returns vector::size() (invalid index).
+*/
+int SamSequenceDictionary::IndexOf(const std::string& name) const {
+    SamSequenceConstIterator begin = ConstBegin();
+    SamSequenceConstIterator iter  = begin;
+    SamSequenceConstIterator end   = ConstEnd();
+    for ( ; iter != end; ++iter ) {
+        const SamSequence& currentSeq = (*iter);
+        if ( currentSeq.Name == name )
+            break;
+    }
+    return distance( begin, iter );
+}
+
+/*! \fn bool SamSequenceDictionary::IsEmpty(void) const
+    \brief Returns \c true if dictionary contains no sequences
+    \sa Size()
+*/
+bool SamSequenceDictionary::IsEmpty(void) const {
+    return m_data.empty();
+}
+
+/*! \fn void SamSequenceDictionary::Remove(const SamSequence& sequence)
+    \brief Removes sequence from dictionary, if found (matches on name).
+
+    This is an overloaded function.
+
+    \param sequence SamSequence to remove (matching on name)
+*/
+void SamSequenceDictionary::Remove(const SamSequence& sequence) {
+    Remove( sequence.Name );
+}
+
+/*! \fn void SamSequenceDictionary::Remove(const std::string& sequenceName)
+    \brief Removes sequence from dictionary, if found.
+
+    \param sequenceName name of sequence to remove
+    \sa Remove()
+*/
+void SamSequenceDictionary::Remove(const std::string& sequenceName) {
+    if ( Contains(sequenceName) )
+        m_data.erase( m_data.begin() + IndexOf(sequenceName) );
+}
+
+/*! \fn void SamSequenceDictionary::Remove(const std::vector<SamSequence>& sequences)
+    \brief Removes multiple sequences from dictionary.
+
+    This is an overloaded function.
+
+    \param sequences sequences to remove
+    \sa Remove()
+*/
+void SamSequenceDictionary::Remove(const std::vector<SamSequence>& sequences) {
+    vector<SamSequence>::const_iterator rgIter = sequences.begin();
+    vector<SamSequence>::const_iterator rgEnd  = sequences.end();
+    for ( ; rgIter!= rgEnd; ++rgIter )
+        Remove(*rgIter);
+}
+
+/*! \fn void SamSequenceDictionary::Remove(const std::vector<std::string>& sequenceNames)
+    \brief Removes multiple sequences from dictionary.
+
+    This is an overloaded function.
+
+    \param sequenceNames names of the sequences to remove
+    \sa Remove()
+*/
+void SamSequenceDictionary::Remove(const std::vector<std::string>& sequenceNames) {
+    vector<string>::const_iterator rgIter = sequenceNames.begin();
+    vector<string>::const_iterator rgEnd  = sequenceNames.end();
+    for ( ; rgIter!= rgEnd; ++rgIter )
+        Remove(*rgIter);
+}
+
+/*! \fn int SamSequenceDictionary::Size(void) const
+    \brief Returns number of sequences in dictionary.
+    \sa IsEmpty()
+*/
+int SamSequenceDictionary::Size(void) const {
+    return m_data.size();
+}
+
+/*! \fn SamSequence& SamSequenceDictionary::operator[](const std::string& sequenceName)
+    \brief Retrieves the modifiable SamSequence that matches \a sequenceName.
+
+    NOTE - If the dictionary contains no sequence matching this name, this function inserts
+    a new one with this name (length:0), and returns a reference to it.
+
+    If you want to avoid this insertion behavior, check the result of Contains() before
+    using this operator.
+
+    \param sequenceName name of sequence to retrieve
+    \return a modifiable reference to the SamSequence associated with the name
+*/
+SamSequence& SamSequenceDictionary::operator[](const std::string& sequenceName) {
+
+    // look up sequence ID
+    int index = IndexOf(sequenceName);
+
+    // if found, return sequence at index
+    if ( index != (int)m_data.size() )
+        return m_data[index];
+
+    // otherwise, append new sequence and return reference
+    else {
+        m_data.push_back( SamSequence(sequenceName, 0) );
+        return m_data.back();
+    }
+}

data/ext/bamtools/src/api/SamSequenceDictionary.h

@@ -0,0 +1,88 @@
+// ***************************************************************************
+// SamSequenceDictionary.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 18 April 2011
+// ---------------------------------------------------------------------------
+// Provides methods for operating on a collection of SamSequence entries.
+// ***************************************************************************
+
+#ifndef SAM_SEQUENCE_DICTIONARY_H
+#define SAM_SEQUENCE_DICTIONARY_H
+
+#include <api/api_global.h>
+#include <api/SamSequence.h>
+#include <string>
+#include <map>
+#include <vector>
+
+namespace BamTools {
+
+typedef std::vector<SamSequence>             SamSequenceContainer;
+typedef SamSequenceContainer::iterator       SamSequenceIterator;
+typedef SamSequenceContainer::const_iterator SamSequenceConstIterator;
+
+class API_EXPORT SamSequenceDictionary {
+
+    // ctor & dtor
+    public:
+        SamSequenceDictionary(void);
+        SamSequenceDictionary(const SamSequenceDictionary& other);
+        ~SamSequenceDictionary(void);
+
+    // query/modify sequence data
+    public:
+        // adds a sequence
+        void Add(const SamSequence& sequence);
+        void Add(const std::string& name, const int& length);
+
+        // adds multiple sequences
+        void Add(const std::vector<SamSequence>& sequences);
+        void Add(const std::map<std::string, int>& sequenceMap);
+
+        // clears all sequence entries
+        void Clear(void);
+
+        // returns true if dictionary contains this sequence
+        bool Contains(const SamSequence& sequence) const;
+        bool Contains(const std::string& sequenceName) const;
+
+        // returns true if dictionary is empty
+        bool IsEmpty(void) const;
+
+        // removes sequence, if found
+        void Remove(const SamSequence& sequence);
+        void Remove(const std::string& sequenceName);
+
+        // removes multiple sequences
+        void Remove(const std::vector<SamSequence>& sequences);
+        void Remove(const std::vector<std::string>& sequenceNames);
+
+        // returns number of sequences in dictionary
+        int Size(void) const;
+
+        // retrieves a modifiable reference to the SamSequence object associated with this name
+        SamSequence& operator[](const std::string& sequenceName);
+
+    // retrieve STL-compatible iterators
+    public:
+        SamSequenceIterator      Begin(void);               // returns iterator to begin()
+        SamSequenceConstIterator Begin(void) const;         // returns const_iterator to begin()
+        SamSequenceConstIterator ConstBegin(void) const;    // returns const_iterator to begin()
+        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()
+
+    // internal methods
+    private:
+        int IndexOf(const std::string& name) const;
+
+    // data members
+    private:
+        SamSequenceContainer m_data;
+};
+
+} // namespace BamTools
+
+#endif // SAM_SEQUENCE_DICTIONARY_H
+

data/ext/bamtools/src/api/api_global.h

@@ -0,0 +1,21 @@
+// ***************************************************************************
+// api_global.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 19 November 2010 (DB)
+// ---------------------------------------------------------------------------
+// Provides macros for exporting & importing BamTools API library symbols
+// ***************************************************************************
+
+#ifndef API_GLOBAL_H
+#define API_GLOBAL_H
+
+#include "shared/bamtools_global.h"
+
+#ifdef BAMTOOLS_API_LIBRARY
+#  define API_EXPORT BAMTOOLS_LIBRARY_EXPORT
+#else
+#  define API_EXPORT BAMTOOLS_LIBRARY_IMPORT
+#endif
+
+#endif // API_GLOBAL_H

data/ext/bamtools/src/api/cmake_install.cmake

@@ -0,0 +1,122 @@
+# Install script for directory: /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api
+
+# Set the install prefix
+IF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+  SET(CMAKE_INSTALL_PREFIX "/usr/local")
+ENDIF(NOT DEFINED CMAKE_INSTALL_PREFIX)
+STRING(REGEX REPLACE "/$" "" CMAKE_INSTALL_PREFIX "${CMAKE_INSTALL_PREFIX}")
+
+# Set the install configuration name.
+IF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+  IF(BUILD_TYPE)
+    STRING(REGEX REPLACE "^[^A-Za-z0-9_]+" ""
+           CMAKE_INSTALL_CONFIG_NAME "${BUILD_TYPE}")
+  ELSE(BUILD_TYPE)
+    SET(CMAKE_INSTALL_CONFIG_NAME "Release")
+  ENDIF(BUILD_TYPE)
+  MESSAGE(STATUS "Install configuration: \"${CMAKE_INSTALL_CONFIG_NAME}\"")
+ENDIF(NOT DEFINED CMAKE_INSTALL_CONFIG_NAME)
+
+# Set the component getting installed.
+IF(NOT CMAKE_INSTALL_COMPONENT)
+  IF(COMPONENT)
+    MESSAGE(STATUS "Install component: \"${COMPONENT}\"")
+    SET(CMAKE_INSTALL_COMPONENT "${COMPONENT}")
+  ELSE(COMPONENT)
+    SET(CMAKE_INSTALL_COMPONENT)
+  ENDIF(COMPONENT)
+ENDIF(NOT CMAKE_INSTALL_COMPONENT)
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/bamtools" TYPE SHARED_LIBRARY FILES
+    "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/lib/libbamtools.1.0.2.dylib"
+    "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/lib/libbamtools.dylib"
+    )
+  FOREACH(file
+      "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/bamtools/libbamtools.1.0.2.dylib"
+      "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/bamtools/libbamtools.dylib"
+      )
+    IF(EXISTS "${file}" AND
+       NOT IS_SYMLINK "${file}")
+      EXECUTE_PROCESS(COMMAND "/usr/bin/install_name_tool"
+        -id "libbamtools.1.0.2.dylib"
+        "${file}")
+      IF(CMAKE_INSTALL_DO_STRIP)
+        EXECUTE_PROCESS(COMMAND "/usr/bin/strip" "${file}")
+      ENDIF(CMAKE_INSTALL_DO_STRIP)
+    ENDIF()
+  ENDFOREACH()
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/lib/bamtools" TYPE STATIC_LIBRARY FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/lib/libbamtools.a")
+  IF(EXISTS "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/bamtools/libbamtools.a" AND
+     NOT IS_SYMLINK "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/bamtools/libbamtools.a")
+    EXECUTE_PROCESS(COMMAND "/usr/bin/ranlib" "$ENV{DESTDIR}${CMAKE_INSTALL_PREFIX}/lib/bamtools/libbamtools.a")
+  ENDIF()
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/api_global.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/BamAlignment.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/BamAux.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/BamConstants.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/BamIndex.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/BamMultiReader.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/BamReader.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/BamWriter.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamConstants.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamHeader.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamProgram.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamProgramChain.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamReadGroup.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamReadGroupDictionary.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamSequence.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+  FILE(INSTALL DESTINATION "${CMAKE_INSTALL_PREFIX}/include/bamtools/api" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/SamSequenceDictionary.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+

data/ext/bamtools/src/api/internal/BamHeader_p.cpp

@@ -0,0 +1,132 @@
+// ***************************************************************************
+// BamHeader_p.cpp (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 21 March 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides the basic functionality for handling BAM headers.
+// ***************************************************************************
+
+#include <api/BamAux.h>
+#include <api/BamConstants.h>
+#include <api/internal/BamHeader_p.h>
+#include <api/internal/BgzfStream_p.h>
+using namespace BamTools;
+using namespace BamTools::Internal;
+
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>
+#include <iostream>
+using namespace std;
+
+// ctor
+BamHeader::BamHeader(void) { }
+
+// dtor
+BamHeader::~BamHeader(void) { }
+
+// reads magic number from BGZF stream, returns true if valid
+bool BamHeader::CheckMagicNumber(BgzfStream* stream) {
+
+    // try to read magic number
+    char buffer[Constants::BAM_HEADER_MAGIC_LENGTH];
+    if ( stream->Read(buffer, Constants::BAM_HEADER_MAGIC_LENGTH) != (int)Constants::BAM_HEADER_MAGIC_LENGTH ) {
+        fprintf(stderr, "BamHeader ERROR: could not read magic number\n");
+        return false;
+    }
+
+    // validate magic number
+    if ( strncmp(buffer, Constants::BAM_HEADER_MAGIC, Constants::BAM_HEADER_MAGIC_LENGTH) != 0 ) {
+        fprintf(stderr, "BamHeader ERROR: invalid magic number\n");
+        return false;
+    }
+
+    // all checks out
+    return true;
+}
+
+// clear SamHeader data
+void BamHeader::Clear(void) {
+    m_header.Clear();
+}
+
+// return true if SamHeader data is valid
+bool BamHeader::IsValid(void) const {
+    return m_header.IsValid();
+}
+
+// load BAM header ('magic number' and SAM header text) from BGZF stream
+// returns true if all OK
+bool BamHeader::Load(BgzfStream* stream) {
+
+    // cannot load if invalid stream
+    if ( stream == 0 )
+        return false;
+
+    // cannot load if magic number is invalid
+    if ( !CheckMagicNumber(stream) )
+        return false;
+
+    // cannot load header if cannot read header length
+    uint32_t length(0);
+    if ( !ReadHeaderLength(stream, length) )
+        return false;
+
+    // cannot load header if cannot read header text
+    if ( !ReadHeaderText(stream, length) )
+        return false;
+
+    // otherwise, everything OK
+    return true;
+}
+
+// reads SAM header text length from BGZF stream, stores it in @length
+// returns read success/fail status
+bool BamHeader::ReadHeaderLength(BgzfStream* stream, uint32_t& length) {
+
+    // attempt to read BAM header text length
+    char buffer[sizeof(uint32_t)];
+    if ( stream->Read(buffer, sizeof(uint32_t)) != sizeof(uint32_t) ) {
+        fprintf(stderr, "BamHeader ERROR: could not read header length\n");
+        return false;
+    }
+
+    // convert char buffer to length, return success
+    length = BamTools::UnpackUnsignedInt(buffer);
+    if ( BamTools::SystemIsBigEndian() )
+        BamTools::SwapEndian_32(length);
+    return true;
+}
+
+// reads SAM header text from BGZF stream, stores in SamHeader object
+// returns read success/fail status
+bool BamHeader::ReadHeaderText(BgzfStream* stream, const uint32_t& length) {
+
+    // set up destination buffer
+    char* headerText = (char*)calloc(length + 1, 1);
+
+    // attempt to read header text
+    const unsigned bytesRead = stream->Read(headerText, length);
+    const bool readOk = ( bytesRead == length );
+    if ( readOk )
+        m_header.SetHeaderText( (string)((const char*)headerText) );
+    else
+        fprintf(stderr, "BamHeader ERROR: could not read header text\n");
+
+    // clean up calloc-ed temp variable (on success or fail)
+    free(headerText);
+
+    // return read success
+    return readOk;
+}
+
+// returns *copy* of SamHeader data object
+SamHeader BamHeader::ToSamHeader(void) const {
+    return m_header;
+}
+
+// returns SAM-formatted string of header data
+string BamHeader::ToString(void) const {
+    return m_header.ToString();
+}