Fix regidx out-of-bounds array access and double free#2533
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sirus20x6 wants to merge 1 commit intosamtools:developfrom
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Fix regidx out-of-bounds array access and double free#2533sirus20x6 wants to merge 1 commit intosamtools:developfrom
sirus20x6 wants to merge 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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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