added warning for duplicate @RG tag in header

[bamtools.git] / BGZF.h

diff --git a/BGZF.h b/BGZF.h
index e1adf25dc11de1fed2c70a4c2033134156157b6b..0cca24ccc344b893a04705f791d0de06d50ce090 100644 (file)
--- a/BGZF.h
+++ b/BGZF.h
@@ -108,12 +108,32 @@ struct BgzfData {
     static inline void PackUnsignedInt(char* buffer, unsigned int value);\r
     // packs an unsigned short into the specified buffer\r
     static inline void PackUnsignedShort(char* buffer, unsigned short value);\r
+    \r
     // unpacks a buffer into a signed int\r
     static inline signed int UnpackSignedInt(char* buffer);\r
-    // unpacks a buffer into a unsigned int\r
+    // unpacks a buffer into an unsigned int\r
     static inline unsigned int UnpackUnsignedInt(char* buffer);\r
-    // unpacks a buffer into a unsigned short\r
+    // unpacks a buffer into a signed short\r
+    static inline signed short UnpackSignedShort(char* buffer);\r
+    // unpacks a buffer into an unsigned short\r
     static inline unsigned short UnpackUnsignedShort(char* buffer);\r
+    // unpacks a buffer into a double\r
+    static inline double UnpackDouble(char* buffer);\r
+    // unpacks a buffer into a float\r
+    static inline float UnpackFloat(char* buffer); \r
+    \r
+    // unpacks a buffer into a signed int\r
+    static inline signed int UnpackSignedInt(const char* buffer);\r
+    // unpacks a buffer into an unsigned int\r
+    static inline unsigned int UnpackUnsignedInt(const char* buffer);\r
+    // unpacks a buffer into a signed short\r
+    static inline signed short UnpackSignedShort(const char* buffer);\r
+    // unpacks a buffer into an unsigned short\r
+    static inline unsigned short UnpackUnsignedShort(const char* buffer);\r
+    // unpacks a buffer into a double\r
+    static inline double UnpackDouble(const char* buffer);\r
+    // unpacks a buffer into a float\r
+    static inline float UnpackFloat(const char* buffer); \r
 };\r
 \r
 // -------------------------------------------------------------\r
@@ -170,6 +190,16 @@ unsigned int BgzfData::UnpackUnsignedInt(char* buffer) {
     return un.value;\r
 }\r
 \r
+// 'unpacks' a buffer into a signed short\r
+inline\r
+signed short BgzfData::UnpackSignedShort(char* buffer) {\r
+    union { signed short value; unsigned char valueBuffer[sizeof(signed short)]; } un;\r
+    un.value = 0;\r
+    un.valueBuffer[0] = buffer[0];\r
+    un.valueBuffer[1] = buffer[1];\r
+    return un.value;\r
+}\r
+\r
 // 'unpacks' a buffer into an unsigned short\r
 inline\r
 unsigned short BgzfData::UnpackUnsignedShort(char* buffer) {\r
@@ -180,6 +210,108 @@ unsigned short BgzfData::UnpackUnsignedShort(char* buffer) {
     return un.value;\r
 }\r
 \r
+// 'unpacks' a buffer into a double\r
+inline\r
+double BgzfData::UnpackDouble(char* buffer) {\r
+    union { double value; unsigned char valueBuffer[sizeof(double)]; } un;\r
+    un.value = 0;\r
+    un.valueBuffer[0] = buffer[0];\r
+    un.valueBuffer[1] = buffer[1];\r
+    un.valueBuffer[2] = buffer[2];\r
+    un.valueBuffer[3] = buffer[3];\r
+    un.valueBuffer[4] = buffer[4];\r
+    un.valueBuffer[5] = buffer[5];\r
+    un.valueBuffer[6] = buffer[6];\r
+    un.valueBuffer[7] = buffer[7];\r
+    return un.value;\r
+}\r
+\r
+// 'unpacks' a buffer into a float\r
+inline\r
+float BgzfData::UnpackFloat(char* buffer) {\r
+    union { float value; unsigned char valueBuffer[sizeof(float)]; } un;\r
+    un.value = 0;\r
+    un.valueBuffer[0] = buffer[0];\r
+    un.valueBuffer[1] = buffer[1];\r
+    un.valueBuffer[2] = buffer[2];\r
+    un.valueBuffer[3] = buffer[3];\r
+    return un.value;\r
+}\r
+\r
+// ---------\r
+\r
+// 'unpacks' a buffer into a signed int\r
+inline\r
+signed int BgzfData::UnpackSignedInt(const char* buffer) {\r
+    union { signed int value; unsigned char valueBuffer[sizeof(signed int)]; } un;\r
+    un.value = 0;\r
+    un.valueBuffer[0] = buffer[0];\r
+    un.valueBuffer[1] = buffer[1];\r
+    un.valueBuffer[2] = buffer[2];\r
+    un.valueBuffer[3] = buffer[3];\r
+    return un.value;\r
+}\r
+\r
+// 'unpacks' a buffer into an unsigned int\r
+inline\r
+unsigned int BgzfData::UnpackUnsignedInt(const char* buffer) {\r
+    union { unsigned int value; unsigned char valueBuffer[sizeof(unsigned int)]; } un;\r
+    un.value = 0;\r
+    un.valueBuffer[0] = buffer[0];\r
+    un.valueBuffer[1] = buffer[1];\r
+    un.valueBuffer[2] = buffer[2];\r
+    un.valueBuffer[3] = buffer[3];\r
+    return un.value;\r
+}\r
+\r
+// 'unpacks' a buffer into a signed short\r
+inline\r
+signed short BgzfData::UnpackSignedShort(const char* buffer) {\r
+    union { signed short value; unsigned char valueBuffer[sizeof(signed short)]; } un;\r
+    un.value = 0;\r
+    un.valueBuffer[0] = buffer[0];\r
+    un.valueBuffer[1] = buffer[1];\r
+    return un.value;\r
+}\r
+\r
+// 'unpacks' a buffer into an unsigned short\r
+inline\r
+unsigned short BgzfData::UnpackUnsignedShort(const char* buffer) {\r
+    union { unsigned short value; unsigned char valueBuffer[sizeof(unsigned short)]; } un;\r
+    un.value = 0;\r
+    un.valueBuffer[0] = buffer[0];\r
+    un.valueBuffer[1] = buffer[1];\r
+    return un.value;\r
+}\r
+\r
+// 'unpacks' a buffer into a double\r
+inline\r
+double BgzfData::UnpackDouble(const char* buffer) {\r
+    union { double value; unsigned char valueBuffer[sizeof(double)]; } un;\r
+    un.value = 0;\r
+    un.valueBuffer[0] = buffer[0];\r
+    un.valueBuffer[1] = buffer[1];\r
+    un.valueBuffer[2] = buffer[2];\r
+    un.valueBuffer[3] = buffer[3];\r
+    un.valueBuffer[4] = buffer[4];\r
+    un.valueBuffer[5] = buffer[5];\r
+    un.valueBuffer[6] = buffer[6];\r
+    un.valueBuffer[7] = buffer[7];\r
+    return un.value;\r
+}\r
+\r
+// 'unpacks' a buffer into a float\r
+inline\r
+float BgzfData::UnpackFloat(const char* buffer) {\r
+    union { float value; unsigned char valueBuffer[sizeof(float)]; } un;\r
+    un.value = 0;\r
+    un.valueBuffer[0] = buffer[0];\r
+    un.valueBuffer[1] = buffer[1];\r
+    un.valueBuffer[2] = buffer[2];\r
+    un.valueBuffer[3] = buffer[3];\r
+    return un.value;\r
+}\r
+\r
 } // namespace BamTools\r
 \r
 #endif // BGZF_H\r