Fix SamLocusIterator so that read position is not incorrectly offset …#1758
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Fix SamLocusIterator so that read position is not incorrectly offset …#1758
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…after transiting insertions that fail the base quality check.
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yfarjoun
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Mar 24, 2026
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please add an assert that "proves" that the code evaluates the assertion on L848.
Also a few nits to make the documentation less time-dependent.
| for (final SamLocusIterator.RecordAndOffset rao : li.getInsertedInRecord()) { | ||
| // The second insertion's first base is at read offset 12. | ||
| // Before the fix, the drifted readBase would report offset 11. | ||
| Assert.assertEquals(rao.getOffset(), 12, |
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please assert that we got to here (i.e. that the loops were not all trivially empty)
Co-authored-by: Yossi Farjoun <farjoun@gmail.com>
nh13
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Apr 4, 2026
Co-authored-by: Nils Homer <nh13@users.noreply.github.com>
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…after transiting insertions that fail the base quality check.
Description
This fixes a bug in SamLocusIterator where during accumulation of indels, the position in the read (
readBase) was incorrectly failling to count indels that failed a base quality check. The result of this is that indels later in the read were then accumulated with incorrect read offsets.This affects any tool that uses the pileup engine with a base quality filter and cares about indels!
The added test fails without the accompanying change to SamLocusIterator.