slow5lib-sys 0.2.0

Low-level bindings to the slow5lib C library
Documentation 
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#include "streamvbyte.h"

#if defined(_MSC_VER)
/* Microsoft C/C++-compatible compiler */
#include <intrin.h>
#elif defined(__GNUC__) && (defined(__x86_64__) || defined(__i386__))
/* GCC-compatible compiler, targeting x86/x86-64 */
#include <x86intrin.h>
#elif defined(__GNUC__) && defined(__ARM_NEON__)
/* GCC-compatible compiler, targeting ARM with NEON */
#include <arm_neon.h>
#elif defined(__GNUC__) && defined(__IWMMXT__)
/* GCC-compatible compiler, targeting ARM with WMMX */
#include <mmintrin.h>
#elif (defined(__GNUC__) || defined(__xlC__)) &&                               \
    (defined(__VEC__) || defined(__ALTIVEC__))
/* XLC or GCC-compatible compiler, targeting PowerPC with VMX/VSX */
#include <altivec.h>
#elif defined(__GNUC__) && defined(__SPE__)
/* GCC-compatible compiler, targeting PowerPC with SPE */
#include <spe.h>
#endif

#include <string.h> // for memcpy
#include "streamvbyte_shuffle_tables_encode.h"

#ifdef STREAMVBYTE_SSSE3
#include "streamvbyte_x64_encode.c"
#else

static uint8_t _encode_data(uint32_t val, uint8_t *__restrict__ *dataPtrPtr) {
  uint8_t *dataPtr = *dataPtrPtr;
  uint8_t code;

  if (val < (1 << 8)) { // 1 byte
    *dataPtr = (uint8_t)(val);
    *dataPtrPtr += 1;
    code = 0;
  } else if (val < (1 << 16)) { // 2 bytes
    memcpy(dataPtr, &val, 2);   // assumes little endian
    *dataPtrPtr += 2;
    code = 1;
  } else if (val < (1 << 24)) { // 3 bytes
    memcpy(dataPtr, &val, 3);   // assumes little endian
    *dataPtrPtr += 3;
    code = 2;
  } else { // 4 bytes
    memcpy(dataPtr, &val, sizeof(uint32_t));
    *dataPtrPtr += sizeof(uint32_t);
    code = 3;
  }

  return code;
}

static uint8_t *svb_encode_scalar(const uint32_t *in,
                                  uint8_t *__restrict__ keyPtr,
                                  uint8_t *__restrict__ dataPtr,
                                  uint32_t count) {
  if (count == 0)
    return dataPtr; // exit immediately if no data

  uint8_t shift = 0; // cycles 0, 2, 4, 6, 0, 2, 4, 6, ...
  uint8_t key = 0;
  for (uint32_t c = 0; c < count; c++) {
    if (shift == 8) {
      shift = 0;
      *keyPtr++ = key;
      key = 0;
    }
    uint32_t val = in[c];
    uint8_t code = _encode_data(val, &dataPtr);
    key |= code << shift;
    shift += 2;
  }

  *keyPtr = key;  // write last key (no increment needed)
  return dataPtr; // pointer to first unused data byte
}
#endif


#ifdef __ARM_NEON__
#include "streamvbyte_arm_encode.c"
#endif



// Encode an array of a given length read from in to bout in streamvbyte format.
// Returns the number of bytes written.
// Note: I am appending a __slow5_ to prevent any name collision with the original library
size_t __slow5_streamvbyte_encode(const uint32_t *in, uint32_t count, uint8_t *out) {
#ifdef STREAMVBYTE_SSSE3
return streamvbyte_encode_SSSE3(in,count,out);
#else
  uint8_t *keyPtr = out;
  uint32_t keyLen = (count + 3) / 4;  // 2-bits rounded to full byte
  uint8_t *dataPtr = keyPtr + keyLen; // variable byte data after all keys

#if defined(__ARM_NEON__)

  uint32_t count_quads = count / 4;
  count -= 4 * count_quads;

  for (uint32_t c = 0; c < count_quads; c++) {
    dataPtr += streamvbyte_encode_quad(in, dataPtr, keyPtr);
    keyPtr++;
    in += 4;
  }

#endif

  return svb_encode_scalar(in, keyPtr, dataPtr, count) - out;
#endif// no AVX
}