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added a few assertions

This commit is contained in:
Heng Li 2011-10-19 00:26:56 -04:00
parent 573ad0c98f
commit 1f02acbe09
1 changed files with 16 additions and 11 deletions
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27
bwt_gen/bwt_gen.c
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@ -83,7 +83,6 @@ typedef struct BWTInc {
unsigned int numberOfIterationDone; unsigned int numberOfIterationDone;
bgint_t *cumulativeCountInCurrentBuild; bgint_t *cumulativeCountInCurrentBuild;
bgint_t availableWord; bgint_t availableWord;
float targetNBit;
bgint_t buildSize; bgint_t buildSize;
bgint_t initialMaxBuildSize; bgint_t initialMaxBuildSize;
bgint_t incMaxBuildSize; bgint_t incMaxBuildSize;
@ -362,18 +361,16 @@ BWTInc *BWTIncCreate(const unsigned int textLength, const float targetNBit,
bwtInc->bwt = BWTCreate(textLength, NULL); bwtInc->bwt = BWTCreate(textLength, NULL);
bwtInc->initialMaxBuildSize = initialMaxBuildSize; bwtInc->initialMaxBuildSize = initialMaxBuildSize;
bwtInc->incMaxBuildSize = incMaxBuildSize; bwtInc->incMaxBuildSize = incMaxBuildSize;
bwtInc->targetNBit = targetNBit;
bwtInc->cumulativeCountInCurrentBuild = (bgint_t*)calloc((ALPHABET_SIZE + 1), sizeof(bgint_t)); bwtInc->cumulativeCountInCurrentBuild = (bgint_t*)calloc((ALPHABET_SIZE + 1), sizeof(bgint_t));
initializeVAL_bg(bwtInc->cumulativeCountInCurrentBuild, ALPHABET_SIZE + 1, 0); initializeVAL_bg(bwtInc->cumulativeCountInCurrentBuild, ALPHABET_SIZE + 1, 0);
// Build frequently accessed data // Build frequently accessed data
bwtInc->packedShift = (unsigned*)calloc(CHAR_PER_WORD, sizeof(unsigned int)); bwtInc->packedShift = (unsigned*)calloc(CHAR_PER_WORD, sizeof(unsigned int));
for (i=0; i<CHAR_PER_WORD; i++) { for (i=0; i<CHAR_PER_WORD; i++)
bwtInc->packedShift[i] = BITS_IN_WORD - (i+1) * BIT_PER_CHAR; bwtInc->packedShift[i] = BITS_IN_WORD - (i+1) * BIT_PER_CHAR;
}
bwtInc->availableWord = (bgint_t)((textLength + OCC_INTERVAL - 1) / OCC_INTERVAL * OCC_INTERVAL / BITS_IN_WORD * bwtInc->targetNBit); bwtInc->availableWord = (bgint_t)((textLength + OCC_INTERVAL - 1) / OCC_INTERVAL * OCC_INTERVAL / BITS_IN_WORD * targetNBit);
if (bwtInc->availableWord < MIN_AVAILABLE_WORD) bwtInc->availableWord = MIN_AVAILABLE_WORD; if (bwtInc->availableWord < MIN_AVAILABLE_WORD) bwtInc->availableWord = MIN_AVAILABLE_WORD; // lh3: otherwise segfaul when availableWord is too small
if (bwtInc->availableWord < BWTResidentSizeInWord(textLength) + BWTOccValueMinorSizeInWord(textLength)) { if (bwtInc->availableWord < BWTResidentSizeInWord(textLength) + BWTOccValueMinorSizeInWord(textLength)) {
fprintf(stderr, "BWTIncCreate() : targetNBit is too low!\n"); fprintf(stderr, "BWTIncCreate() : targetNBit is too low!\n");
exit(1); exit(1);
@ -1317,8 +1314,13 @@ static void BWTIncConstruct(BWTInc *bwtInc, const bgint_t numChar)
// Set address // Set address
seq = (bgint_t*)bwtInc->workingMemory; seq = (bgint_t*)bwtInc->workingMemory;
relativeRank = seq + bwtInc->buildSize + 1; relativeRank = seq + bwtInc->buildSize + 1;
// mergedBwt and packedTex may share memory
mergedBwt = insertBwt = bwtInc->workingMemory + bwtInc->availableWord - mergedBwtSizeInWord; // build in place mergedBwt = insertBwt = bwtInc->workingMemory + bwtInc->availableWord - mergedBwtSizeInWord; // build in place
assert((void*)(relativeRank + bwtInc->buildSize + 1) <= (void*)bwtInc->packedText);
assert((void*)(relativeRank + bwtInc->buildSize + 1) <= (void*)mergedBwt);
// ->packedText is not used any more and may be overwritten by mergedBwt
BWTIncPutPackedTextToRank(bwtInc->packedText, relativeRank, bwtInc->cumulativeCountInCurrentBuild, numChar); BWTIncPutPackedTextToRank(bwtInc->packedText, relativeRank, bwtInc->cumulativeCountInCurrentBuild, numChar);
firstCharInThisIteration = relativeRank[0]; firstCharInThisIteration = relativeRank[0];
@ -1342,8 +1344,11 @@ static void BWTIncConstruct(BWTInc *bwtInc, const bgint_t numChar)
sortedRank = (bgint_t*)bwtInc->workingMemory; sortedRank = (bgint_t*)bwtInc->workingMemory;
seq = sortedRank + bwtInc->buildSize + 1; seq = sortedRank + bwtInc->buildSize + 1;
insertBwt = (unsigned*)seq; // insertBwt and seq share memory insertBwt = (unsigned*)seq; // insertBwt and seq share memory
// relativeRank and ->packedText may share memory
relativeRank = seq + bwtInc->buildSize + 1; relativeRank = seq + bwtInc->buildSize + 1;
assert((void*)relativeRank <= (void*)bwtInc->packedText);
// Store the first character of this iteration // Store the first character of this iteration
firstCharInThisIteration = bwtInc->packedText[0] >> (BITS_IN_WORD - BIT_PER_CHAR); firstCharInThisIteration = bwtInc->packedText[0] >> (BITS_IN_WORD - BIT_PER_CHAR);
@ -1357,6 +1362,7 @@ static void BWTIncConstruct(BWTInc *bwtInc, const bgint_t numChar)
// Get rank of new suffix among processed suffix // Get rank of new suffix among processed suffix
// The seq array is built into ALPHABET_SIZE + 2 groups; ALPHABET_SIZE groups + 1 group divided into 2 by inverseSa0 + inverseSa0 as 1 group // The seq array is built into ALPHABET_SIZE + 2 groups; ALPHABET_SIZE groups + 1 group divided into 2 by inverseSa0 + inverseSa0 as 1 group
// ->packedText is not used any more and will be overwritten by relativeRank
oldInverseSa0RelativeRank = BWTIncGetAbsoluteRank(bwtInc->bwt, sortedRank, seq, bwtInc->packedText, oldInverseSa0RelativeRank = BWTIncGetAbsoluteRank(bwtInc->bwt, sortedRank, seq, bwtInc->packedText,
numChar, bwtInc->cumulativeCountInCurrentBuild, bwtInc->firstCharInLastIteration); numChar, bwtInc->cumulativeCountInCurrentBuild, bwtInc->firstCharInLastIteration);
@ -1388,15 +1394,14 @@ static void BWTIncConstruct(BWTInc *bwtInc, const bgint_t numChar)
sortedRank[newInverseSa0RelativeRank] = 0; // a special value so that this is skipped in the merged bwt sortedRank[newInverseSa0RelativeRank] = 0; // a special value so that this is skipped in the merged bwt
// Build BWT // Build BWT; seq is overwritten by insertBwt
BWTIncBuildBwt(insertBwt, relativeRank, numChar, bwtInc->cumulativeCountInCurrentBuild); BWTIncBuildBwt(insertBwt, relativeRank, numChar, bwtInc->cumulativeCountInCurrentBuild);
// Merge BWT // Merge BWT; relativeRank may be overwritten by mergedBwt
mergedBwt = bwtInc->workingMemory + bwtInc->availableWord - mergedBwtSizeInWord mergedBwt = bwtInc->workingMemory + bwtInc->availableWord - mergedBwtSizeInWord
- bwtInc->numberOfIterationDone * OCC_INTERVAL / BIT_PER_CHAR; - bwtInc->numberOfIterationDone * OCC_INTERVAL / BIT_PER_CHAR; // minus numberOfIteration * occInterval to create a buffer for merging
// minus numberOfIteration * occInterval to create a buffer for merging assert(mergedBwt >= insertBwt + numChar);
BWTIncMergeBwt(sortedRank, bwtInc->bwt->bwtCode, insertBwt, mergedBwt, bwtInc->bwt->textLength, numChar); BWTIncMergeBwt(sortedRank, bwtInc->bwt->bwtCode, insertBwt, mergedBwt, bwtInc->bwt->textLength, numChar);
} }
// Build auxiliary structure and update info and pointers in BWT // Build auxiliary structure and update info and pointers in BWT