ngs_server 0.1

data/ext/bamtools/src/api/internal/SamHeaderVersion_p.h

@@ -0,0 +1,134 @@
+// ***************************************************************************
+// SamHeaderVersion.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 24 February 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides functionality for comparing SAM header versions
+// *************************************************************************
+
+#ifndef SAM_HEADERVERSION_P_H
+#define SAM_HEADERVERSION_P_H
+
+//  -------------
+//  W A R N I N G
+//  -------------
+//
+// This file is not part of the BamTools API.  It exists purely as an
+// implementation detail. This header file may change from version to version
+// without notice, or even be removed.
+//
+// We mean it.
+
+#include <api/SamConstants.h>
+#include <sstream>
+#include <string>
+
+namespace BamTools {
+namespace Internal {
+
+class SamHeaderVersion {
+
+    // ctors & dtor
+    public:
+        SamHeaderVersion(void)
+            : m_majorVersion(0)
+            , m_minorVersion(0)
+        { }
+
+        explicit SamHeaderVersion(const std::string& version)
+            : m_majorVersion(0)
+            , m_minorVersion(0)
+        {
+            SetVersion(version);
+        }
+
+        SamHeaderVersion(const unsigned int& major, const unsigned int& minor)
+            : m_majorVersion(major)
+            , m_minorVersion(minor)
+        { }
+
+        ~SamHeaderVersion(void) {
+            m_majorVersion = 0;
+            m_minorVersion = 0;
+        }
+    
+    // acess data
+    public:
+        unsigned int MajorVersion(void) const { return m_majorVersion; }
+        unsigned int MinorVersion(void) const { return m_minorVersion; }
+
+        void SetVersion(const std::string& version);
+        std::string ToString(void) const;
+
+    // data members
+    private:
+        unsigned int m_majorVersion;
+        unsigned int m_minorVersion;
+};
+
+inline
+void SamHeaderVersion::SetVersion(const std::string& version) {
+
+    // do nothing if version is empty
+    if ( !version.empty() ) {
+
+        std::stringstream versionStream("");
+
+        // do nothing if period not found
+        const size_t periodFound = version.find(Constants::SAM_PERIOD);
+        if ( periodFound != std::string::npos ) {
+
+            // store major version if non-empty and contains only digits
+            const std::string& majorVersion = version.substr(0, periodFound);
+            versionStream.str(majorVersion);
+            if ( !majorVersion.empty() ) {
+                const size_t nonDigitFound = majorVersion.find_first_not_of(Constants::SAM_DIGITS);
+                if ( nonDigitFound == std::string::npos )
+                    versionStream >> m_majorVersion;
+            }
+
+            // store minor version if non-empty and contains only digits
+            const std::string& minorVersion = version.substr(periodFound + 1);
+            versionStream.str(minorVersion);
+            if ( !minorVersion.empty() ) {
+                const size_t nonDigitFound = minorVersion.find_first_not_of(Constants::SAM_DIGITS);
+                if ( nonDigitFound == std::string::npos )
+                    versionStream >> m_minorVersion;
+            }
+        }
+    }
+}
+
+// -----------------------------------------------------
+// printing
+
+inline std::string SamHeaderVersion::ToString(void) const {
+    std::stringstream version;
+    version << m_majorVersion << Constants::SAM_PERIOD << m_minorVersion;
+    return version.str();
+}
+
+// -----------------------------------------------------
+// comparison operators
+
+inline bool operator==(const SamHeaderVersion& lhs, const SamHeaderVersion& rhs) {
+    return (lhs.MajorVersion() == rhs.MajorVersion()) &&
+           (lhs.MinorVersion() == rhs.MinorVersion());
+}
+
+inline bool operator<(const SamHeaderVersion& lhs, const SamHeaderVersion& rhs) {
+    if ( lhs.MajorVersion() == rhs.MajorVersion() )
+        return lhs.MinorVersion() < rhs.MinorVersion();
+    else 
+        return lhs.MajorVersion() < rhs.MajorVersion();
+}
+
+inline bool operator> (const SamHeaderVersion& lhs, const SamHeaderVersion& rhs) { return rhs < lhs;  }
+inline bool operator<=(const SamHeaderVersion& lhs, const SamHeaderVersion& rhs) { return !(lhs>rhs); }
+inline bool operator>=(const SamHeaderVersion& lhs, const SamHeaderVersion& rhs) { return !(lhs<rhs); }
+
+} // namespace Internal 
+} // namespace BamTools
+
+#endif // SAM_HEADERVERSION_P_H

data/ext/bamtools/src/cmake_install.cmake

@@ -0,0 +1,42 @@
+# Install script for directory: /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src
+
+# 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}/include/bamtools/shared" TYPE FILE FILES "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/shared/bamtools_global.h")
+ENDIF(NOT CMAKE_INSTALL_COMPONENT OR "${CMAKE_INSTALL_COMPONENT}" STREQUAL "Unspecified")
+
+IF(NOT CMAKE_INSTALL_LOCAL_ONLY)
+  # Include the install script for each subdirectory.
+  INCLUDE("/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/api/cmake_install.cmake")
+  INCLUDE("/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/utils/cmake_install.cmake")
+  INCLUDE("/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/cmake_install.cmake")
+  INCLUDE("/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/toolkit/cmake_install.cmake")
+
+ENDIF(NOT CMAKE_INSTALL_LOCAL_ONLY)
+

data/ext/bamtools/src/shared/bamtools_global.h

@@ -0,0 +1,78 @@
+// ***************************************************************************
+// bamtools_global.h (c) 2010 Derek Barnett
+// Marth Lab, Department of Biology, Boston College
+// ---------------------------------------------------------------------------
+// Last modified: 3 March 2011 (DB)
+// ---------------------------------------------------------------------------
+// Provides the basic definitions for exporting & importing library symbols.
+// Also provides some platform-specific rules for definitions.
+// ***************************************************************************
+
+#ifndef BAMTOOLS_GLOBAL_H
+#define BAMTOOLS_GLOBAL_H
+
+/*! \brief Library export macro
+    \internal
+*/
+#ifndef BAMTOOLS_LIBRARY_EXPORT
+#  if defined(WIN32)
+#    define BAMTOOLS_LIBRARY_EXPORT __declspec(dllexport)
+#  else
+#    define BAMTOOLS_LIBRARY_EXPORT __attribute__((visibility("default")))
+#  endif
+#endif // BAMTOOLS_LIBRARY_EXPORT
+
+/*! \brief Library import macro
+    \internal
+*/
+#ifndef BAMTOOLS_LIBRARY_IMPORT
+#  if defined(WIN32)
+#    define BAMTOOLS_LIBRARY_IMPORT __declspec(dllimport)
+#  else
+#    define BAMTOOLS_LIBRARY_IMPORT
+#  endif
+#endif // BAMTOOLS_LIBRARY_IMPORT
+
+/*! \brief Platform-specific type definitions
+    \internal
+*/
+#ifndef BAMTOOLS_LFS
+#define BAMTOOLS_LFS
+    #ifdef WIN32
+        #define ftell64(a)     _ftelli64(a)
+        #define fseek64(a,b,c) _fseeki64(a,b,c)
+    #else
+        #define ftell64(a)     ftello(a)
+        #define fseek64(a,b,c) fseeko(a,b,c)
+    #endif
+#endif // BAMTOOLS_LFS
+
+/*! \def ftell64(a)
+    \brief Platform-independent tell() operation.
+    \internal
+*/
+/*! \def fseek64(a,b,c)
+    \brief Platform-independent seek() operation.
+    \internal
+*/
+
+/*! \brief Platform-specific type definitions
+    \internal
+*/
+#ifndef BAMTOOLS_TYPES
+#define BAMTOOLS_TYPES
+    #ifdef _MSC_VER
+        typedef char                 int8_t;
+        typedef unsigned char       uint8_t;
+        typedef short               int16_t;
+        typedef unsigned short     uint16_t;
+        typedef int                 int32_t;
+        typedef unsigned int       uint32_t;
+        typedef long long           int64_t;
+        typedef unsigned long long uint64_t;
+    #else
+        #include <stdint.h>
+    #endif
+#endif // BAMTOOLS_TYPES
+
+#endif // BAMTOOLS_GLOBAL_H

data/ext/bamtools/src/third_party/CMakeFiles/CMakeDirectoryInformation.cmake

@@ -0,0 +1,22 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 2.8
+
+# Relative path conversion top directories.
+SET(CMAKE_RELATIVE_PATH_TOP_SOURCE "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools")
+SET(CMAKE_RELATIVE_PATH_TOP_BINARY "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools")
+
+# Force unix paths in dependencies.
+SET(CMAKE_FORCE_UNIX_PATHS 1)
+
+# The C and CXX include file search paths:
+SET(CMAKE_C_INCLUDE_PATH
+  "src"
+  )
+SET(CMAKE_CXX_INCLUDE_PATH ${CMAKE_C_INCLUDE_PATH})
+SET(CMAKE_Fortran_INCLUDE_PATH ${CMAKE_C_INCLUDE_PATH})
+
+# The C and CXX include file regular expressions for this directory.
+SET(CMAKE_C_INCLUDE_REGEX_SCAN "^.*$")
+SET(CMAKE_C_INCLUDE_REGEX_COMPLAIN "^$")
+SET(CMAKE_CXX_INCLUDE_REGEX_SCAN ${CMAKE_C_INCLUDE_REGEX_SCAN})
+SET(CMAKE_CXX_INCLUDE_REGEX_COMPLAIN ${CMAKE_C_INCLUDE_REGEX_COMPLAIN})

data/ext/bamtools/src/third_party/CMakeFiles/progress.marks

@@ -0,0 +1 @@
+3

data/ext/bamtools/src/third_party/CMakeLists.txt

@@ -0,0 +1,10 @@
+# ==========================
+# BamTools CMakeLists.txt
+# (c) 2010 Derek Barnett
+#
+# src/third-party/
+# ==========================
+
+# list third-party subdirectories to build in
+add_subdirectory (jsoncpp)
+

data/ext/bamtools/src/third_party/Makefile

@@ -0,0 +1,167 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 2.8
+
+# Default target executed when no arguments are given to make.
+default_target: all
+.PHONY : default_target
+
+#=============================================================================
+# Special targets provided by cmake.
+
+# Disable implicit rules so canoncical targets will work.
+.SUFFIXES:
+
+# Remove some rules from gmake that .SUFFIXES does not remove.
+SUFFIXES =
+
+.SUFFIXES: .hpux_make_needs_suffix_list
+
+# Suppress display of executed commands.
+$(VERBOSE).SILENT:
+
+# A target that is always out of date.
+cmake_force:
+.PHONY : cmake_force
+
+#=============================================================================
+# Set environment variables for the build.
+
+# The shell in which to execute make rules.
+SHELL = /bin/sh
+
+# The CMake executable.
+CMAKE_COMMAND = /usr/local/Cellar/cmake/2.8.4/bin/cmake
+
+# The command to remove a file.
+RM = /usr/local/Cellar/cmake/2.8.4/bin/cmake -E remove -f
+
+# The program to use to edit the cache.
+CMAKE_EDIT_COMMAND = /usr/local/Cellar/cmake/2.8.4/bin/ccmake
+
+# The top-level source directory on which CMake was run.
+CMAKE_SOURCE_DIR = /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools
+
+# The top-level build directory on which CMake was run.
+CMAKE_BINARY_DIR = /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools
+
+#=============================================================================
+# Targets provided globally by CMake.
+
+# Special rule for the target edit_cache
+edit_cache:
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake cache editor..."
+	/usr/local/Cellar/cmake/2.8.4/bin/ccmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
+.PHONY : edit_cache
+
+# Special rule for the target edit_cache
+edit_cache/fast: edit_cache
+.PHONY : edit_cache/fast
+
+# Special rule for the target install
+install: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+	/usr/local/Cellar/cmake/2.8.4/bin/cmake -P cmake_install.cmake
+.PHONY : install
+
+# Special rule for the target install
+install/fast: preinstall/fast
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Install the project..."
+	/usr/local/Cellar/cmake/2.8.4/bin/cmake -P cmake_install.cmake
+.PHONY : install/fast
+
+# Special rule for the target install/local
+install/local: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing only the local directory..."
+	/usr/local/Cellar/cmake/2.8.4/bin/cmake -DCMAKE_INSTALL_LOCAL_ONLY=1 -P cmake_install.cmake
+.PHONY : install/local
+
+# Special rule for the target install/local
+install/local/fast: install/local
+.PHONY : install/local/fast
+
+# Special rule for the target install/strip
+install/strip: preinstall
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Installing the project stripped..."
+	/usr/local/Cellar/cmake/2.8.4/bin/cmake -DCMAKE_INSTALL_DO_STRIP=1 -P cmake_install.cmake
+.PHONY : install/strip
+
+# Special rule for the target install/strip
+install/strip/fast: install/strip
+.PHONY : install/strip/fast
+
+# Special rule for the target list_install_components
+list_install_components:
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Available install components are: \"Unspecified\""
+.PHONY : list_install_components
+
+# Special rule for the target list_install_components
+list_install_components/fast: list_install_components
+.PHONY : list_install_components/fast
+
+# Special rule for the target rebuild_cache
+rebuild_cache:
+	@$(CMAKE_COMMAND) -E cmake_echo_color --switch=$(COLOR) --cyan "Running CMake to regenerate build system..."
+	/usr/local/Cellar/cmake/2.8.4/bin/cmake -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR)
+.PHONY : rebuild_cache
+
+# Special rule for the target rebuild_cache
+rebuild_cache/fast: rebuild_cache
+.PHONY : rebuild_cache/fast
+
+# The main all target
+all: cmake_check_build_system
+	cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(CMAKE_COMMAND) -E cmake_progress_start /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/CMakeFiles /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/CMakeFiles/progress.marks
+	cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f CMakeFiles/Makefile2 src/third_party/all
+	$(CMAKE_COMMAND) -E cmake_progress_start /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/CMakeFiles 0
+.PHONY : all
+
+# The main clean target
+clean:
+	cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f CMakeFiles/Makefile2 src/third_party/clean
+.PHONY : clean
+
+# The main clean target
+clean/fast: clean
+.PHONY : clean/fast
+
+# Prepare targets for installation.
+preinstall: all
+	cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f CMakeFiles/Makefile2 src/third_party/preinstall
+.PHONY : preinstall
+
+# Prepare targets for installation.
+preinstall/fast:
+	cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(MAKE) -f CMakeFiles/Makefile2 src/third_party/preinstall
+.PHONY : preinstall/fast
+
+# clear depends
+depend:
+	cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 1
+.PHONY : depend
+
+# Help Target
+help:
+	@echo "The following are some of the valid targets for this Makefile:"
+	@echo "... all (the default if no target is provided)"
+	@echo "... clean"
+	@echo "... depend"
+	@echo "... edit_cache"
+	@echo "... install"
+	@echo "... install/local"
+	@echo "... install/strip"
+	@echo "... list_install_components"
+	@echo "... rebuild_cache"
+.PHONY : help
+
+
+
+#=============================================================================
+# Special targets to cleanup operation of make.
+
+# Special rule to run CMake to check the build system integrity.
+# No rule that depends on this can have commands that come from listfiles
+# because they might be regenerated.
+cmake_check_build_system:
+	cd /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools && $(CMAKE_COMMAND) -H$(CMAKE_SOURCE_DIR) -B$(CMAKE_BINARY_DIR) --check-build-system CMakeFiles/Makefile.cmake 0
+.PHONY : cmake_check_build_system
+

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

@@ -0,0 +1,35 @@
+# Install script for directory: /Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party
+
+# 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_LOCAL_ONLY)
+  # Include the install script for each subdirectory.
+  INCLUDE("/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/cmake_install.cmake")
+
+ENDIF(NOT CMAKE_INSTALL_LOCAL_ONLY)
+

data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/CMakeDirectoryInformation.cmake

@@ -0,0 +1,22 @@
+# CMAKE generated file: DO NOT EDIT!
+# Generated by "Unix Makefiles" Generator, CMake Version 2.8
+
+# Relative path conversion top directories.
+SET(CMAKE_RELATIVE_PATH_TOP_SOURCE "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools")
+SET(CMAKE_RELATIVE_PATH_TOP_BINARY "/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools")
+
+# Force unix paths in dependencies.
+SET(CMAKE_FORCE_UNIX_PATHS 1)
+
+# The C and CXX include file search paths:
+SET(CMAKE_C_INCLUDE_PATH
+  "src"
+  )
+SET(CMAKE_CXX_INCLUDE_PATH ${CMAKE_C_INCLUDE_PATH})
+SET(CMAKE_Fortran_INCLUDE_PATH ${CMAKE_C_INCLUDE_PATH})
+
+# The C and CXX include file regular expressions for this directory.
+SET(CMAKE_C_INCLUDE_REGEX_SCAN "^.*$")
+SET(CMAKE_C_INCLUDE_REGEX_COMPLAIN "^$")
+SET(CMAKE_CXX_INCLUDE_REGEX_SCAN ${CMAKE_C_INCLUDE_REGEX_SCAN})
+SET(CMAKE_CXX_INCLUDE_REGEX_COMPLAIN ${CMAKE_C_INCLUDE_REGEX_COMPLAIN})

data/ext/bamtools/src/third_party/jsoncpp/CMakeFiles/jsoncpp.dir/CXX.includecache

@@ -0,0 +1,144 @@
+#IncludeRegexLine: ^[ 	]*#[ 	]*(include|import)[ 	]*[<"]([^">]+)([">])
+
+#IncludeRegexScan: ^.*$
+
+#IncludeRegexComplain: ^$
+
+#IncludeRegexTransform: 
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_batchallocator.h
+stdlib.h
+-
+assert.h
+-
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_config.h
+shared/bamtools_global.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/shared/bamtools_global.h
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_features.h
+json_forwards.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_forwards.h
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_forwards.h
+json_config.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_config.h
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_internalarray.inl
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_internalmap.inl
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_reader.cpp
+json_reader.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_reader.h
+json_value.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_value.h
+json_tool.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_tool.h
+utility
+-
+cstdio
+-
+cassert
+-
+cstring
+-
+iostream
+-
+stdexcept
+-
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_reader.h
+json_features.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_features.h
+json_value.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_value.h
+deque
+-
+stack
+-
+string
+-
+iostream
+-
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_tool.h
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_value.cpp
+iostream
+-
+json_value.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_value.h
+json_writer.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_writer.h
+utility
+-
+stdexcept
+-
+cstring
+-
+cassert
+-
+cpptl/conststring.h
+-
+cstddef
+-
+json_batchallocator.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_batchallocator.h
+json_internalarray.inl
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_internalarray.inl
+json_internalmap.inl
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_internalmap.inl
+json_valueiterator.inl
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_valueiterator.inl
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_value.h
+json_forwards.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_forwards.h
+string
+-
+vector
+-
+map
+-
+cpptl/smallmap.h
+-
+cpptl/forwards.h
+-
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_valueiterator.inl
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_writer.cpp
+json_writer.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_writer.h
+json_tool.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_tool.h
+utility
+-
+assert.h
+-
+stdio.h
+-
+string.h
+-
+iostream
+-
+sstream
+-
+iomanip
+-
+
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_writer.h
+json_value.h
+/Users/chase/Desktop/tmp_workspace/ngs_server/ext/bamtools/src/third_party/jsoncpp/json_value.h
+vector
+-
+string
+-
+iostream
+-
+
+src/shared/bamtools_global.h
+stdint.h
+-
+