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ASAN fixes for GNU-specific pointer arithmetic #66

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Merged
dpryan79 merged 1 commit into from
Jan 17, 2025
Merged

ASAN fixes for GNU-specific pointer arithmetic #66

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4 changes: 2 additions & 2 deletions bwStats.c
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Original file line number Diff line number Diff line change
Expand Up @@ -70,7 +70,7 @@ static struct vals_t *getVals(bigWigFile_t *fp, bwOverlapBlock_t *o, int i, uint

if(sz) {
compressed = 1;
buf = malloc(sz);
buf = malloc(sz);
}
sz = 0; //This is now the size of the compressed buffer

Expand All @@ -96,7 +96,7 @@ static struct vals_t *getVals(bigWigFile_t *fp, bwOverlapBlock_t *o, int i, uint
}

p = buf;
while(((uLongf) ((void*)p-buf)) < sz) {
while(((uLongf) ((char*)p - (char*)buf)) < sz) {
vtid = p[0];
vstart = p[1];
vend = p[2];
Expand Down
10 changes: 5 additions & 5 deletions bwValues.c
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Original file line number Diff line number Diff line change
Expand Up @@ -524,15 +524,15 @@ bbOverlappingEntries_t *bbGetOverlappingEntriesCore(bigWigFile_t *fp, bwOverlapB
tmp = o->size[i]; //TODO: Is this correct? Do non-gzipped bigBeds exist?
}

bufEnd = buf + tmp;
bufEnd = (char*)buf + tmp;
while(buf < bufEnd) {
entryTid = ((uint32_t*)buf)[0];
start = ((uint32_t*)buf)[1];
end = ((uint32_t*)buf)[2];
buf += 12;
buf = (char*)buf + 12;
str = (char*)buf;
slen = strlen(str) + 1;
buf += slen;
buf = (char*)buf + slen;

if(entryTid < tid) continue;
if(entryTid > tid) break;
Expand All @@ -543,7 +543,7 @@ bbOverlappingEntries_t *bbGetOverlappingEntriesCore(bigWigFile_t *fp, bwOverlapB
if(!pushBBIntervals(output, start, end, str, withString)) goto error;
}

buf = bufEnd - tmp; //reset the buffer pointer
buf = (char*)bufEnd - tmp; //reset the buffer pointer
}

if(compressed && buf) free(buf);
Expand All @@ -552,7 +552,7 @@ bbOverlappingEntries_t *bbGetOverlappingEntriesCore(bigWigFile_t *fp, bwOverlapB

error:
fprintf(stderr, "[bbGetOverlappingEntriesCore] Got an error\n");
buf = bufEnd - tmp;
buf = (char*)bufEnd - tmp;
if(output) bbDestroyOverlappingEntries(output);
if(compressed && buf) free(buf);
if(compBuf) free(compBuf);
Expand Down
52 changes: 26 additions & 26 deletions bwWrite.c
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Original file line number Diff line number Diff line change
Expand Up @@ -317,12 +317,12 @@ static int flushBuffer(bigWigFile_t *fp) {
if(!wb->ltype) return 0;

//Fill in the header
if(!memcpy(wb->p, &(wb->tid), sizeof(uint32_t))) return 1;
if(!memcpy(wb->p+4, &(wb->start), sizeof(uint32_t))) return 2;
if(!memcpy(wb->p+8, &(wb->end), sizeof(uint32_t))) return 3;
if(!memcpy(wb->p+12, &(wb->step), sizeof(uint32_t))) return 4;
if(!memcpy(wb->p+16, &(wb->span), sizeof(uint32_t))) return 5;
if(!memcpy(wb->p+20, &(wb->ltype), sizeof(uint8_t))) return 6;
if(!memcpy((char*)wb->p, &(wb->tid), sizeof(uint32_t))) return 1;
if(!memcpy((char*)wb->p+4, &(wb->start), sizeof(uint32_t))) return 2;
if(!memcpy((char*)wb->p+8, &(wb->end), sizeof(uint32_t))) return 3;
if(!memcpy((char*)wb->p+12, &(wb->step), sizeof(uint32_t))) return 4;
if(!memcpy((char*)wb->p+16, &(wb->span), sizeof(uint32_t))) return 5;
if(!memcpy((char*)wb->p+20, &(wb->ltype), sizeof(uint8_t))) return 6;
//1 byte padding
//Determine the number of items
switch(wb->ltype) {
Expand All @@ -338,7 +338,7 @@ static int flushBuffer(bigWigFile_t *fp) {
default:
return 7;
}
if(!memcpy(wb->p+22, &nItems, sizeof(uint16_t))) return 8;
if(!memcpy((char*)wb->p+22, &nItems, sizeof(uint16_t))) return 8;

if(sz) {
//compress
Expand Down Expand Up @@ -399,9 +399,9 @@ int bwAddIntervals(bigWigFile_t *fp, const char* const* chrom, const uint32_t *s
wb->span = 0;
wb->step = 0;
}
if(!memcpy(wb->p+wb->l, start, sizeof(uint32_t))) return 7;
if(!memcpy(wb->p+wb->l+4, end, sizeof(uint32_t))) return 8;
if(!memcpy(wb->p+wb->l+8, values, sizeof(float))) return 9;
if(!memcpy((char*)wb->p+wb->l, start, sizeof(uint32_t))) return 7;
if(!memcpy((char*)wb->p+wb->l+4, end, sizeof(uint32_t))) return 8;
if(!memcpy((char*)wb->p+wb->l+8, values, sizeof(float))) return 9;
updateStats(fp, end[0]-start[0], values[0]);
wb->l += 12;

Expand All @@ -420,9 +420,9 @@ int bwAddIntervals(bigWigFile_t *fp, const char* const* chrom, const uint32_t *s
flushBuffer(fp);
wb->start = start[i];
}
if(!memcpy(wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 11;
if(!memcpy(wb->p+wb->l+4, &(end[i]), sizeof(uint32_t))) return 12;
if(!memcpy(wb->p+wb->l+8, &(values[i]), sizeof(float))) return 13;
if(!memcpy((char*)wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 11;
if(!memcpy((char*)wb->p+wb->l+4, &(end[i]), sizeof(uint32_t))) return 12;
if(!memcpy((char*)wb->p+wb->l+8, &(values[i]), sizeof(float))) return 13;
updateStats(fp, end[i]-start[i], values[i]);
wb->l += 12;
}
Expand All @@ -447,9 +447,9 @@ int bwAppendIntervals(bigWigFile_t *fp, const uint32_t *start, const uint32_t *e
flushBuffer(fp);
wb->start = start[i];
}
if(!memcpy(wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 4;
if(!memcpy(wb->p+wb->l+4, &(end[i]), sizeof(uint32_t))) return 5;
if(!memcpy(wb->p+wb->l+8, &(values[i]), sizeof(float))) return 6;
if(!memcpy((char*)wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 4;
if(!memcpy((char*)wb->p+wb->l+4, &(end[i]), sizeof(uint32_t))) return 5;
if(!memcpy((char*)wb->p+wb->l+8, &(values[i]), sizeof(float))) return 6;
updateStats(fp, end[i]-start[i], values[i]);
wb->l += 12;
}
Expand Down Expand Up @@ -482,8 +482,8 @@ int bwAddIntervalSpans(bigWigFile_t *fp, const char *chrom, const uint32_t *star
flushBuffer(fp);
wb->start = start[i];
}
if(!memcpy(wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 5;
if(!memcpy(wb->p+wb->l+4, &(values[i]), sizeof(float))) return 6;
if(!memcpy((char*)wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 5;
if(!memcpy((char*)wb->p+wb->l+4, &(values[i]), sizeof(float))) return 6;
updateStats(fp, span, values[i]);
wb->l += 8;
}
Expand All @@ -506,8 +506,8 @@ int bwAppendIntervalSpans(bigWigFile_t *fp, const uint32_t *start, const float *
flushBuffer(fp);
wb->start = start[i];
}
if(!memcpy(wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 4;
if(!memcpy(wb->p+wb->l+4, &(values[i]), sizeof(float))) return 5;
if(!memcpy((char*)wb->p+wb->l, &(start[i]), sizeof(uint32_t))) return 4;
if(!memcpy((char*)wb->p+wb->l+4, &(values[i]), sizeof(float))) return 5;
updateStats(fp, wb->span, values[i]);
wb->l += 8;
}
Expand Down Expand Up @@ -540,7 +540,7 @@ int bwAddIntervalSpanSteps(bigWigFile_t *fp, const char *chrom, uint32_t start,
flushBuffer(fp);
wb->start = wb->end;
}
if(!memcpy(wb->p+wb->l, &(values[i]), sizeof(float))) return 5;
if(!memcpy((char*)wb->p+wb->l, &(values[i]), sizeof(float))) return 5;
updateStats(fp, wb->span, values[i]);
wb->l += 4;
}
Expand All @@ -563,7 +563,7 @@ int bwAppendIntervalSpanSteps(bigWigFile_t *fp, const float *values, uint32_t n)
flushBuffer(fp);
wb->start = wb->end;
}
if(!memcpy(wb->p+wb->l, &(values[i]), sizeof(float))) return 4;
if(!memcpy((char*)wb->p+wb->l, &(values[i]), sizeof(float))) return 4;
updateStats(fp, wb->span, values[i]);
wb->l += 4;
}
Expand Down Expand Up @@ -754,7 +754,7 @@ int writeIndex(bigWigFile_t *fp) {
}
if(!root) return 4;
fp->idx->root = root;

ll = fp->writeBuffer->firstIndexNode;
while(ll) {
p = ll->next;
Expand Down Expand Up @@ -994,8 +994,8 @@ int addIntervalValue(bigWigFile_t *fp, uint64_t *nEntries, double *sum, double *
newBuffer->p = calloc(itemsPerSlot, 32);
if(!newBuffer->p) goto error;
newBuffer->m = itemsPerSlot*32;
memcpy(newBuffer->p, buffer->p+buffer->l-32, 4);
memcpy(newBuffer->p+4, buffer->p+buffer->l-28, 4);
memcpy(newBuffer->p, (unsigned char*)buffer->p+buffer->l-32, 4);
memcpy((unsigned char*)newBuffer->p+4, (unsigned char*)buffer->p + buffer->l-28, 4);
((uint32_t*) newBuffer->p)[2] = ((uint32_t*) newBuffer->p)[1] + zoom;
*sum = *sumsq = 0.0;
rv = updateInterval(fp, newBuffer, sum, sumsq, zoom, tid, start, end, value);
Expand Down Expand Up @@ -1122,7 +1122,7 @@ int writeZoomLevels(bigWigFile_t *fp) {
while(ll) {
p = ll->next;
free(ll);
ll=p;
ll=p;
}


Expand Down
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