cigar_from_alignment.hpp File Reference

Provides the function seqan3::cigar_from_alignment and a helper struct seqan3::cigar_clipped_bases. More...

#include <vector>
#include <seqan3/alphabet/cigar/cigar.hpp>
#include <seqan3/alphabet/gap/gap.hpp>
#include <seqan3/utility/views/zip.hpp>

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Classes
struct	seqan3::cigar_clipped_bases
	Helper struct to specialise soft and hard clipping when using seqan3::cigar_from_alignment. More...

Namespaces
namespace	seqan3
	The main SeqAn3 namespace.

Functions
template<typename alignment_type >
auto	seqan3::cigar_from_alignment (alignment_type const &alignment, cigar_clipped_bases const &clipped_bases={}, bool const extended_cigar=false)
	Creates a CIGAR string (SAM format) given a seqan3::detail::pairwise_alignment represented by two seqan3::aligned_sequences.

Detailed Description

Provides the function seqan3::cigar_from_alignment and a helper struct seqan3::cigar_clipped_bases.

Author

Svenja Mehringer <svenja.mehringer AT fu-berlin.de>