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Fixed BWTIncFree() memory leaks 

[Based on PR #37 with the additions below.]

Don't free non-malloced items in BWTFree().  If BWTCreate() is ever
called with a non-NULL decodeTable, BWTFree() will need to not free
decodeTable -- see FIXME comment.

Close packedFile in BWTIncConstructFromPacked() in the normal case.
Ignore it in error cases, as they immediately call exit() anyway.
This commit is contained in:
Gwen Ives 2014-12-09 10:24:46 +01:00 committed by John Marshall
parent 1972a97813
commit 6a5caf764f
1 changed files with 6 additions and 3 deletions
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9
bwt_gen.c
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@ -338,6 +338,7 @@ BWT *BWTCreate(const bgint_t textLength, unsigned int *decodeTable)
bwt->decodeTable = (unsigned*)calloc(DNA_OCC_CNT_TABLE_SIZE_IN_WORD, sizeof(unsigned int)); bwt->decodeTable = (unsigned*)calloc(DNA_OCC_CNT_TABLE_SIZE_IN_WORD, sizeof(unsigned int));
GenerateDNAOccCountTable(bwt->decodeTable); GenerateDNAOccCountTable(bwt->decodeTable);
} else { } else {
// FIXME Prevent BWTFree() from freeing decodeTable in this case
bwt->decodeTable = decodeTable; bwt->decodeTable = decodeTable;
} }
@ -1538,6 +1539,8 @@ BWTInc *BWTIncConstructFromPacked(const char *inputFileName, bgint_t initialMaxB
(long)bwtInc->numberOfIterationDone, (long)processedTextLength); (long)bwtInc->numberOfIterationDone, (long)processedTextLength);
} }
} }
fclose(packedFile);
return bwtInc; return bwtInc;
} }
@ -1545,8 +1548,6 @@ void BWTFree(BWT *bwt)
{ {
if (bwt == 0) return; if (bwt == 0) return;
free(bwt->cumulativeFreq); free(bwt->cumulativeFreq);
free(bwt->bwtCode);
free(bwt->occValue);
free(bwt->occValueMajor); free(bwt->occValueMajor);
free(bwt->decodeTable); free(bwt->decodeTable);
free(bwt); free(bwt);
@ -1555,8 +1556,10 @@ void BWTFree(BWT *bwt)
void BWTIncFree(BWTInc *bwtInc) void BWTIncFree(BWTInc *bwtInc)
{ {
if (bwtInc == 0) return; if (bwtInc == 0) return;
free(bwtInc->bwt); BWTFree(bwtInc->bwt);
free(bwtInc->workingMemory); free(bwtInc->workingMemory);
free(bwtInc->cumulativeCountInCurrentBuild);
free(bwtInc->packedShift);
free(bwtInc); free(bwtInc);
} }