extern int
BWTSeqPosHasLocateInfo(const BWTSeq *bwtSeq, Seqpos pos,
struct extBitsRetrieval *extBits)
{
if (bwtSeq->featureToggles & BWTLocateBitmap)
{
EISRetrieveExtraBits(bwtSeq->seqIdx, pos, EBRF_RETRIEVE_CWBITS, extBits,
bwtSeq->hint);
return gt_bsGetBit(extBits->cwPart,
extBits->cwOffset + pos - extBits->start);
}
else if (bwtSeq->featureToggles & BWTLocateCount)
{
BitOffset markOffset = searchLocateCountMark(bwtSeq, pos, extBits);
return markOffset != 0;
}
#ifndef NDEBUG
else
{
fputs("Trying to locate in BWT sequence index without locate information.",
stderr);
abort();
}
#endif
return 0;
}
int
gt_bitPackStringInt8_unit_test(GtError *err)
{
BitString bitStore = NULL;
BitString bitStoreCopy = NULL;
uint8_t *randSrc = NULL; /*< create random ints here for input as bit
* store */
uint8_t *randCmp = NULL; /*< used for random ints read back */
unsigned *numBitsList = NULL;
size_t i, numRnd;
BitOffset offsetStart, offset;
int had_err = 0;
offset = offsetStart = random()%(sizeof (uint8_t) * CHAR_BIT);
numRnd = random() % (MAX_RND_NUMS_uint8_t + 1);
gt_log_log("offset=%lu, numRnd=%lu\n",
(long unsigned)offsetStart, (long unsigned)numRnd);
{
BitOffset numBits = sizeof (uint8_t) * CHAR_BIT * numRnd + offsetStart;
randSrc = gt_malloc(sizeof (uint8_t)*numRnd);
bitStore = gt_malloc(bitElemsAllocSize(numBits) * sizeof (BitElem));
bitStoreCopy = gt_calloc(bitElemsAllocSize(numBits), sizeof (BitElem));
randCmp = gt_malloc(sizeof (uint8_t)*numRnd);
}
/* first test unsigned types */
gt_log_log("gt_bsStoreUInt8/gt_bsGetUInt8: ");
for (i = 0; i < numRnd; ++i)
{
#if 8 > 32 && LONG_BIT < 8
uint8_t v = randSrc[i] = (uint8_t)random() << 32 | random();
#else /* 8 > 32 && LONG_BIT < 8 */
uint8_t v = randSrc[i] = random();
#endif /* 8 > 32 && LONG_BIT < 8 */
int bits = gt_requiredUInt8Bits(v);
gt_bsStoreUInt8(bitStore, offset, bits, v);
offset += bits;
}
offset = offsetStart;
for (i = 0; i < numRnd; ++i)
{
uint8_t v = randSrc[i];
int bits = gt_requiredUInt8Bits(v);
uint8_t r = gt_bsGetUInt8(bitStore, offset, bits);
gt_ensure(had_err, r == v);
if (had_err)
{
gt_log_log("Expected %"PRIu8", got %"PRIu8", i = %lu\n",
v, r, (unsigned long)i);
freeResourcesAndReturn(had_err);
}
offset += bits;
}
gt_log_log("passed\n");
if (numRnd > 0)
{
uint8_t v = randSrc[0], r = 0;
unsigned numBits = gt_requiredUInt8Bits(v);
BitOffset i = offsetStart + numBits;
uint8_t mask = ~(uint8_t)0;
if (numBits < 8)
mask = ~(mask << numBits);
gt_log_log("bsSetBit, gt_bsClearBit, bsToggleBit, gt_bsGetBit: ");
while (v)
{
int lowBit = v & 1;
v >>= 1;
gt_ensure(had_err, lowBit == (r = gt_bsGetBit(bitStore, --i)));
if (had_err)
{
gt_log_log("Expected %d, got %d, i = %llu\n",
lowBit, (int)r, (unsigned long long)i);
freeResourcesAndReturn(had_err);
}
}
i = offsetStart + numBits;
gt_bsClear(bitStoreCopy, offsetStart, numBits, random()&1);
v = randSrc[0];
while (i)
{
int lowBit = v & 1;
v >>= 1;
if (lowBit)
bsSetBit(bitStoreCopy, --i);
else
gt_bsClearBit(bitStoreCopy, --i);
}
v = randSrc[0];
r = gt_bsGetUInt8(bitStoreCopy, offsetStart, numBits);
gt_ensure(had_err, r == v);
if (had_err)
{
gt_log_log("Expected %"PRIu8", got %"PRIu8"\n", v, r);
freeResourcesAndReturn(had_err);
}
for (i = 0; i < numBits; ++i)
bsToggleBit(bitStoreCopy, offsetStart + i);
r = gt_bsGetUInt8(bitStoreCopy, offsetStart, numBits);
gt_ensure(had_err, r == (v = (~v & mask)));
if (had_err)
{
gt_log_log("Expected %"PRIu8", got %"PRIu8"\n", v, r);
freeResourcesAndReturn(had_err);
}
gt_log_log("passed\n");
}
