Fix possible array bounds violation in bed_minoff()#1962
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Confusion over how to check the number of items in bed_reglist_t::idx could lead to either attempting to read off the end of the array, or returning a value smaller than it should have. The latter was harmless, apart from making lookups slightly slower, but the former could lead to crashes or results not being returned. The correct limit wasn't actually stored directly although it could be calculated from the last range in bed_reglist_t::a. For easier look-ups, it's now stored in bed_reglist_t::max_idx. bed_index_core() is rewritten to store max_idx; add more error and input range checking; and be more efficient. It no longer leaves gaps (filled with -1) in the index it builds, so the code that dealt with them in bed_minoff() can be removed. Some additional changes are made so failures can be passed back and handled appropriately.
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Added some minor tidying up... |
jkbonfield
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Apr 12, 2024
If we run out of memory while calling bed_index then it rightly fails, but in doing so frees ks and str.vs twice. Under normal conditions there were no memory errors. This is a minor error handling glitch that arrived with samtools#1962.
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Confusion over how to check the number of items in bed_reglist_t::idx could lead to either attempting to read off the end of the array, or returning a value smaller than it should have. The latter was harmless, apart from making lookups slightly slower, but the former could lead to crashes or results not being returned.
The correct limit wasn't actually stored directly although it could be calculated from the last range in bed_reglist_t::a. For easier look-ups, it's now stored in bed_reglist_t::max_idx.
bed_index_core() is rewritten to store max_idx; add more error and input range checking; and be more efficient. It no longer leaves gaps (filled with -1) in the index it builds, so the code that dealt with them in bed_minoff() can be removed.
Some additional changes are made so failures can be passed back and handled appropriately.
Fixes #1961