Reading bigWig files sometimes fails: Uninitialized bwRTree_t->root variable

[pbenner]

pyBigWig/libBigWig/bwValues.c

Line 36 in 339ebc8

node = malloc(sizeof(bwRTree_t));

A new root node is allocated here using malloc (not calloc), which leaves node->root uninitialized.

pyBigWig/libBigWig/bwValues.c

Line 302 in 339ebc8

fp->idx = readRTreeIdx(fp, fp->hdr->indexOffset);

Here the index is read.

pyBigWig/libBigWig/bwValues.c

Line 308 in 339ebc8

if(!fp->idx->root) fp->idx->root = bwGetRTreeNode(fp, 0);

And here the RTree is parsed only if idx->root is not zero, assuming that it was initialized to zero by readRTreeIdx, which is not the case.

Possible fix:

--- a/libBigWig/bwValues.c
+++ b/libBigWig/bwValues.c
@@ -35,6 +35,7 @@ static bwRTree_t *readRTreeIdx(bigWigFile_t *fp, uint64_t offset) {
 
     node = malloc(sizeof(bwRTree_t));
     if(!node) return NULL;
+    node->root = 0;
 
     if(bwRead(&(node->blockSize), sizeof(uint32_t), 1, fp) != 1) goto error;
     if(bwRead(&(node->nItems), sizeof(uint64_t), 1, fp) != 1) goto error;

[dpryan79]

Good catch, I'll change that to calloc.

[dpryan79]

I'll push out a version with this fixed now.