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Fix some minor undefined behaviours #1810

Merged
merged 3 commits into from
Jul 18, 2024
Merged

Fix some minor undefined behaviours #1810

merged 3 commits into from
Jul 18, 2024

Commits on Jul 18, 2024

  1. Remove undefined behavior in expression language. 

    The bit-wise AND, OR and XOR logic works on the overloaded double
(res->d), but casting this to int64_t for NAN is undefined behaviour.

Infact the current cast doesn't even yield the correct bit-wise layout
for NAN, as (long)d and *(long *)&d give different results for d==NAN.
However the result wasn't used anyway as it's promptly cleared again
in the subsequent `if (undef) hts_expr_val_undef(res)` code.  Hence
undefined or otherwise, it made no difference.
    @jkbonfield
    jkbonfield committed Jul 18, 2024
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  2. Fix signed overflow for hts_parse_decimal. 

    Obviously there can still be overflows if we attempt to parse numbers
which are too big, but for the legally accepted range of this, parsing
"-9,223,372,036,854,775,808" as tested in test/sam.c triggered a
problem as the positive version doesn't fit in "long long".

We parse as unsigned and only switch to signed via the implicit return
type conversion (and probably exploiting twos-complement, but that's a
fair assumption).
    @jkbonfield
    jkbonfield committed Jul 18, 2024
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  3. Fix an undefined addition to a NULL pointer in vcf_format. 

    The pointer was never used, but the NULL+0 still triggers clang's ubsan.
    @jkbonfield
    jkbonfield committed Jul 18, 2024
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