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This release adds support for newer compilers and C++ standards (17, 20, 23). It also improves interoperability with SeqAn3.
To avoid namespace conflicts with other libraries in the SeqAn ecosystem, the namespace was changed
from seqan to .
seqan2To use version 2.5.0, you will need to update your code. Depending on how you use seqan in your project, the following changes are required:
// Before
using namespace seqan;
// After
using namespace seqan2;
// Before
auto foo(seqan::StringSet<seqan::DnaString> const & sequences)
{
return seqan::length(sequences);
}
// After
auto foo(seqan2::StringSet<seqan2::DnaString> const & sequences)
{
return seqan2::length(sequences);
}
A script to automatically update your code may look like this:
for file in $(git grep -l 'namespace seqan'); do sed -i 's/namespace seqan/namespace seqan2/g' ${file}; done
for file in $(git grep -l 'seqan::'); do sed -i 's/seqan::/seqan2::/g' ${file}; done
.fas.seqan2::bi_fm_index.seqan2::VcfIOContext via seqan2::context now works correctly.--out-alignment) in conjunction with bisulfite sequencing (--enable-bs-seq) now yields correct reference begin positions.