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Return failure status for invalid SAF indexes - #672

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thierrygosselin wants to merge 1 commit into
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thierrygosselin:fix-saf-reader-error-status
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thierrygosselin wants to merge 1 commit into
ANGSD:masterfrom
thierrygosselin:fix-saf-reader-error-status

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The SAF reader detects missing files, incompatible SAF versions, truncated index data, missing SAF data files and version mismatches, but several of these fatal paths previously terminated with exit(0).

This change makes those validation failures return EXIT_FAILURE.

No SAF data layout or statistical calculation is changed. The purpose is to prevent malformed or incompatible SAF files from appearing to have been read successfully by automated workflows.

Related to #637, #255 and #385.

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