Replace assert() with proper error handling for user-triggerable conditions#2535
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sirus20x6 wants to merge 1 commit intosamtools:developfrom
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Replace assert() with proper error handling for user-triggerable conditions#2535sirus20x6 wants to merge 1 commit intosamtools:developfrom
sirus20x6 wants to merge 1 commit intosamtools:developfrom
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assert() is compiled out in release builds (NDEBUG), causing silent
undefined behavior or buffer overflows when triggered by malformed input.
- consensus.c: Replace asserts on variant overlap trimming, unreachable
overlap case, and fasta buffer bounds with error() calls
- convert.c: Replace GT type asserts with warning+skip; add allele index
bounds checks in process_tgt and process_iupac_gt
- vcfconcat.c: Replace bgzf block size assert with error() call
- filter.c: Add NULL check for getenv("HOME") and getenv("HOMEDRIVE")/
getenv("HOMEPATH") in expand_path()
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Summary
Several
assert()calls guard conditions that can be triggered by user input. In release builds with NDEBUG, these are compiled out, causing silent undefined behavior or buffer overflows.error()callsline->d.allele[ial]accesserror()callgetenv("HOME")before passing tokputsTest plan