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minor changes in case something goes wrong

This commit is contained in:
Heng Li 2011-10-19 13:50:50 -04:00
parent 1f02acbe09
commit b6d807b0b7
1 changed files with 5 additions and 5 deletions
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10
bwt_gen/bwt_gen.c
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@ -161,7 +161,7 @@ static void BWTIncSetBuildSizeAndTextAddr(BWTInc *bwtInc)
if (bwtInc->bwt->textLength == 0) { if (bwtInc->bwt->textLength == 0) {
// initial build // initial build
// Minus 2 because n+1 entries of seq and rank needed for n char // Minus 2 because n+1 entries of seq and rank needed for n char
maxBuildSize = (bwtInc->availableWord - 2 * (sizeof(bgint_t) / 4) - OCC_INTERVAL / CHAR_PER_WORD) maxBuildSize = (bwtInc->availableWord - (2 + OCC_INTERVAL / CHAR_PER_WORD) * (sizeof(bgint_t) / 4))
/ (2 * CHAR_PER_WORD + 1) * CHAR_PER_WORD / (sizeof(bgint_t) / 4); / (2 * CHAR_PER_WORD + 1) * CHAR_PER_WORD / (sizeof(bgint_t) / 4);
if (bwtInc->initialMaxBuildSize > 0) { if (bwtInc->initialMaxBuildSize > 0) {
bwtInc->buildSize = min(bwtInc->initialMaxBuildSize, maxBuildSize); bwtInc->buildSize = min(bwtInc->initialMaxBuildSize, maxBuildSize);
@ -171,8 +171,8 @@ static void BWTIncSetBuildSizeAndTextAddr(BWTInc *bwtInc)
} else { } else {
// Minus 3 because n+1 entries of sorted rank, seq and rank needed for n char // Minus 3 because n+1 entries of sorted rank, seq and rank needed for n char
// Minus numberOfIterationDone because bwt slightly shift to left in each iteration // Minus numberOfIterationDone because bwt slightly shift to left in each iteration
maxBuildSize = (bwtInc->availableWord - bwtInc->bwt->bwtSizeInWord - bwtInc->bwt->occSizeInWord - 3 * (sizeof(bgint_t) / 4) maxBuildSize = (bwtInc->availableWord - bwtInc->bwt->bwtSizeInWord - bwtInc->bwt->occSizeInWord
- bwtInc->numberOfIterationDone * OCC_INTERVAL / BIT_PER_CHAR) - (3 + bwtInc->numberOfIterationDone * OCC_INTERVAL / BIT_PER_CHAR) * (sizeof(bgint_t) / 4))
/ 3 / (sizeof(bgint_t) / 4); / 3 / (sizeof(bgint_t) / 4);
if (maxBuildSize < CHAR_PER_WORD) { if (maxBuildSize < CHAR_PER_WORD) {
fprintf(stderr, "BWTIncSetBuildSizeAndTextAddr(): Not enough space allocated to continue construction!\n"); fprintf(stderr, "BWTIncSetBuildSizeAndTextAddr(): Not enough space allocated to continue construction!\n");
@ -1399,7 +1399,7 @@ static void BWTIncConstruct(BWTInc *bwtInc, const bgint_t numChar)
// Merge BWT; relativeRank may be overwritten by mergedBwt // 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; // minus numberOfIteration * occInterval to create a buffer for merging - bwtInc->numberOfIterationDone * OCC_INTERVAL / BIT_PER_CHAR * (sizeof(bgint_t) / 4); // minus numberOfIteration * occInterval to create a buffer for merging
assert(mergedBwt >= insertBwt + numChar); 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);
} }
@ -1545,7 +1545,7 @@ void BWTSaveBwtCodeAndOcc(const BWT *bwt, const char *bwtFileName, const char *o
void bwt_bwtgen(const char *fn_pac, const char *fn_bwt) void bwt_bwtgen(const char *fn_pac, const char *fn_bwt)
{ {
BWTInc *bwtInc; BWTInc *bwtInc;
bwtInc = BWTIncConstructFromPacked(fn_pac, 5.0, 10000000, 10000000); bwtInc = BWTIncConstructFromPacked(fn_pac, 4.4, 10000000, 10000000);
printf("[bwt_gen] Finished constructing BWT in %u iterations.\n", bwtInc->numberOfIterationDone); printf("[bwt_gen] Finished constructing BWT in %u iterations.\n", bwtInc->numberOfIterationDone);
BWTSaveBwtCodeAndOcc(bwtInc->bwt, fn_bwt, 0); BWTSaveBwtCodeAndOcc(bwtInc->bwt, fn_bwt, 0);
BWTIncFree(bwtInc); BWTIncFree(bwtInc);