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fix off-by-one assumption regarding vector indexing dating to 2011

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This commit is contained in:
Vern Paxson 2021-02-24 16:11:27 -08:00
parent 3179df9ab2
commit e64805430b
4 changed files with 29 additions and 31 deletions
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7
src/SmithWaterman.cc
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@ -86,12 +86,12 @@ VectorVal* Substring::VecToPolicy(Vec* vec)
align_val->Assign(0, make_intrusive<StringVal>(new String(*align.string)));
align_val->Assign(1, val_mgr->Count(align.index));
aligns->Assign(j + 1, std::move(align_val));
aligns->Assign(j, std::move(align_val));
}
st_val->Assign(1, std::move(aligns));
st_val->Assign(2, val_mgr->Bool(bst->IsNewAlignment()));
result->Assign(i + 1, std::move(st_val));
result->Assign(i, std::move(st_val));
}
}
@ -102,8 +102,7 @@ Substring::Vec* Substring::VecFromPolicy(VectorVal* vec)
{
Vec* result = new Vec();
// VectorVals start at index 1!
for ( unsigned int i = 1; i <= vec->Size(); ++i )
for ( unsigned int i = 0; i < vec->Size(); ++i )
{
const auto& v = vec->At(i); // get the RecordVal
if ( ! v )