Fix silent truncation in IteratorRowAllRefs on I/O errors#1379
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gileshall wants to merge 1 commit intopysam-developers:masterfrom
Open
Fix silent truncation in IteratorRowAllRefs on I/O errors#1379gileshall wants to merge 1 commit intopysam-developers:masterfrom
gileshall wants to merge 1 commit intopysam-developers:masterfrom
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IteratorRowAllRefs.__next__() only checked `retval > 0` to decide whether a record was available. All non-positive return values, including I/O errors (retval < -1) and truncated files (retval == -2), were silently treated as end-of-reference and the iterator advanced to the next tid. This caused `samfile.fetch()` without a region to silently yield truncated results on read errors with no exception. Add explicit error checks matching the pattern already used by IteratorRowRegion: raise IOError on retval < -1, only treat retval == -1 as normal end-of-reference.
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Summary
IteratorRowAllRefs.__next__()(used bysamfile.fetch()without a region) only checkedretval > 0to decide whether a record was available. All non-positive return values — including I/O errors (retval < -1) and truncated files (retval == -2) — were silently treated as end-of-reference, causing the iterator to advance to the nexttid. On a read error mid-file, callers getStopIterationinstead of an exception and have no indication that results are incomplete.Every other iterator in pysam (
IteratorRowRegion,IteratorRowAll,IteratorRowHead,IteratorRowSelection,VariantFile, etc.) already distinguishes EOF from error.IteratorRowAllRefswas the only one missing this check.Add explicit error checks matching the pattern used by
IteratorRowRegion: raiseIOErroronretval < -1, only treatretval == -1as normal end-of-reference.