Fix regidx out-of-bounds array access and double free#2533
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pd3 merged 1 commit intosamtools:developfrom Mar 31, 2026
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Fix regidx out-of-bounds array access and double free#2533pd3 merged 1 commit intosamtools:developfrom
pd3 merged 1 commit intosamtools:developfrom
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1. regidx_overlap: cap iend to nidx-1 instead of nidx, preventing an out-of-bounds read of list->idx[nidx] in the i<=iend loop. 2. regidx_init: set str.s = NULL after freeing it so the error path does not double-free when hts_close() fails.
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pd3
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Mar 31, 2026
| { | ||
| int iend = iBIN(end); | ||
| if ( iend > list->nidx ) iend = list->nidx; | ||
| if ( iend >= list->nidx ) iend = list->nidx - 1; |
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@daviesrob If correct, I think this affects also regidx.c code in htslib
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I'm not convinced that this is correct. The item count gets incremented by 1 when allocating list->idx, so it can accommodate looking up iend. I assume that it was written that way because the actual range is likely to end somewhere in the middle of the bin.
Because the array is big enough, there is no out of bounds access.
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As explained by #2533 (comment) the original code was correct
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Summary
iendtolist->nidx - 1instead oflist->nidxinregidx_overlap— the loopfor (i=ibeg; i<=iend; i++)could readlist->idx[nidx], one past the allocated arraystr.s = NULLafterfree(str.s)inregidx_init— prevents double free ifhts_close()fails and the error path freesstr.sagainTest plan