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fix bad memory allocation with initX #787

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fix bad memory allocation with initX #787

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18 changes: 8 additions & 10 deletions src/util/msa2profile.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -157,8 +157,6 @@ int msa2profile(int argc, const char **argv, const Command &command) {

Sequence sequence(maxSeqLength + 1, Parameters::DBTYPE_AMINO_ACIDS, &subMat, 0, false, par.compBiasCorrection != 0);

char *msaContent = (char*) mem_align(ALIGN_INT, sizeof(char) * (maxSeqLength + 1) * maxSetSize);

float *seqWeight = new float[maxSetSize];
float *pNullBuffer = new float[maxSeqLength + 1];
bool *maskedColumns = new bool[maxSeqLength + 1];
Expand All @@ -168,7 +166,8 @@ int msa2profile(int argc, const char **argv, const Command &command) {
kseq_buffer_t d;
kseq_t *seq = kseq_init(&d);

char **msaSequences = (char**) mem_align(ALIGN_INT, sizeof(char*) * maxSetSize);
char **msaSequences = MultipleAlignment::initX(maxSeqLength + 1, maxSetSize);

std::vector<Matcher::result_t> alnResults;
alnResults.reserve(maxSetSize);

Expand All @@ -182,8 +181,6 @@ int msa2profile(int argc, const char **argv, const Command &command) {

unsigned int queryKey = qDbr.getDbKey(id);

size_t msaPos = 0;

unsigned int setSize = 0;
unsigned int centerLengthWithGaps = 0;
unsigned int maskedCount = 0;
Expand Down Expand Up @@ -247,6 +244,8 @@ int msa2profile(int argc, const char **argv, const Command &command) {
continue;
}

size_t msaPos = 0;

// first sequence is always the query
if (setSize == 0) {
centerLengthWithGaps = seq->seq.l;
Expand All @@ -273,7 +272,6 @@ int msa2profile(int argc, const char **argv, const Command &command) {
}

sequence.mapSequence(0, 0, seq->seq.s, seq->seq.l);
msaSequences[setSize] = msaContent + msaPos;

for (size_t i = 0; i < centerLengthWithGaps; ++i) {
if (maskByFirst == true && maskedColumns[i] == true) {
Expand All @@ -285,7 +283,7 @@ int msa2profile(int argc, const char **argv, const Command &command) {
continue;
}

msaContent[msaPos++] = (seq->seq.s[i] == '-') ? (int)MultipleAlignment::GAP : sequence.numSequence[i];
msaSequences[setSize][msaPos++] = (seq->seq.s[i] == '-') ? (int)MultipleAlignment::GAP : sequence.numSequence[i];
}

// construct backtrace for all but the query sequence
Expand Down Expand Up @@ -314,7 +312,7 @@ int msa2profile(int argc, const char **argv, const Command &command) {
size_t rowSize = msaPos / (VECSIZE_INT*4);
rowSize = (rowSize+1) * (VECSIZE_INT*4);
while(msaPos < rowSize) {
msaContent[msaPos++] = MultipleAlignment::GAP;
msaSequences[setSize][msaPos++] = MultipleAlignment::GAP;
}

setSize++;
Expand Down Expand Up @@ -431,11 +429,11 @@ int msa2profile(int argc, const char **argv, const Command &command) {
result.clear();
}
kseq_destroy(seq);
free(msaSequences);
free(msaContent);
free(msaSequences[0]);
delete[] pNullBuffer;
delete[] maskedColumns;
delete[] seqWeight;
delete[] msaSequences;
}
headerWriter.close(true);
resultWriter.close(true);
Expand Down