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49 CigarOp(
const char type =
'\0',
const uint32_t& length = 0)
68 RefData(
const std::string& name = std::string(),
const int32_t& length = 0)
98 BamRegion(
const int& leftID = -1,
const int& leftPos = -1,
const int& rightID = -1,
99 const int& rightPos = -1)
101 , LeftPosition(leftPos)
102 , RightRefID(rightID)
103 , RightPosition(rightPos)
108 : LeftRefID(other.LeftRefID)
109 , LeftPosition(other.LeftPosition)
110 , RightRefID(other.RightRefID)
111 , RightPosition(other.RightPosition)
126 return (LeftRefID >= 0 && LeftPosition >= 0);
132 return (!isLeftBoundSpecified() && !isRightBoundSpecified());
138 return (RightRefID >= 0 && RightPosition >= 1);
156 std::ifstream f(filename.c_str(), std::ifstream::in);
165 x = ((x >> 8) | (x << 8));
173 x = ((x >> 8) | (x << 8));
181 x = ((x >> 24) | ((x << 8) & 0x00FF0000) | ((x >> 8) & 0x0000FF00) | (x << 24));
189 x = ((x >> 24) | ((x << 8) & 0x00FF0000) | ((x >> 8) & 0x0000FF00) | (x << 24));
197 x = ((x >> 56) | ((x << 40) & 0x00FF000000000000ll) | ((x << 24) & 0x0000FF0000000000ll) |
198 ((x << 8) & 0x000000FF00000000ll) | ((x >> 8) & 0x00000000FF000000ll) |
199 ((x >> 24) & 0x0000000000FF0000ll) | ((x >> 40) & 0x000000000000FF00ll) | (x << 56));
207 x = ((x >> 56) | ((x << 40) & 0x00FF000000000000ll) | ((x << 24) & 0x0000FF0000000000ll) |
208 ((x << 8) & 0x000000FF00000000ll) | ((x >> 8) & 0x00000000FF000000ll) |
209 ((x >> 24) & 0x0000000000FF0000ll) | ((x >> 40) & 0x000000000000FF00ll) | (x << 56));
217 uint16_t& value = (uint16_t&)*data;
226 uint32_t& value = (uint32_t&)*data;
235 uint64_t& value = (uint64_t&)*data;
245 const uint16_t one = 0x0001;
246 return ((*(
char*)&one) == 0);
257 buffer[0] = (char)value;
258 buffer[1] = (char)(value >> 8);
259 buffer[2] = (char)(value >> 16);
260 buffer[3] = (char)(value >> 24);
271 buffer[0] = (char)value;
272 buffer[1] = (char)(value >> 8);
286 unsigned char valueBuffer[
sizeof(double)];
289 un.valueBuffer[0] = buffer[0];
290 un.valueBuffer[1] = buffer[1];
291 un.valueBuffer[2] = buffer[2];
292 un.valueBuffer[3] = buffer[3];
293 un.valueBuffer[4] = buffer[4];
294 un.valueBuffer[5] = buffer[5];
295 un.valueBuffer[6] = buffer[6];
296 un.valueBuffer[7] = buffer[7];
324 unsigned char valueBuffer[
sizeof(float)];
327 un.valueBuffer[0] = buffer[0];
328 un.valueBuffer[1] = buffer[1];
329 un.valueBuffer[2] = buffer[2];
330 un.valueBuffer[3] = buffer[3];
358 unsigned char valueBuffer[
sizeof(
signed int)];
361 un.valueBuffer[0] = buffer[0];
362 un.valueBuffer[1] = buffer[1];
363 un.valueBuffer[2] = buffer[2];
364 un.valueBuffer[3] = buffer[3];
392 unsigned char valueBuffer[
sizeof(
signed short)];
395 un.valueBuffer[0] = buffer[0];
396 un.valueBuffer[1] = buffer[1];
424 unsigned char valueBuffer[
sizeof(
unsigned int)];
427 un.valueBuffer[0] = buffer[0];
428 un.valueBuffer[1] = buffer[1];
429 un.valueBuffer[2] = buffer[2];
430 un.valueBuffer[3] = buffer[3];
457 unsigned short value;
458 unsigned char valueBuffer[
sizeof(
unsigned short)];
461 #if __BYTE_ORDER__ == __ORDER_LITTLE_ENDIAN__
462 un.valueBuffer[0] = buffer[0];
463 un.valueBuffer[1] = buffer[1];
464 #elif __BYTE_ORDER__ == __ORDER_BIG_ENDIAN__
465 un.valueBuffer[0] = buffer[1];
466 un.valueBuffer[1] = buffer[0];
468 #error "Unsupported hardware"
497 const std::size_t NumBytes;
500 RaiiBuffer(
const std::size_t n)
501 : Buffer(new char[n]())
513 memset(Buffer, 0, NumBytes);
#define API_EXPORT
Definition: api_global.h:18