Return failure status for invalid SAF likelihoods - #669
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thierrygosselin wants to merge 1 commit into
Open
thierrygosselin wants to merge 1 commit into
thierrygosselin wants to merge 1 commit into
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ANGSD’s SAF code detected invalid genotype probabilities and normalization failures, but terminated with
exit(0). This reports a successful process exit even though the SAF calculation failed.This change makes those fatal paths return
EXIT_FAILURE.The likelihood calculations are unchanged. The change only ensures that malformed or numerically invalid SAF input cannot silently appear to have completed successfully.
This is important for automated pipelines, where the exit status is often the only signal that a calculation failed.