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Remove CIGAR(::BAMCIGAR, ::Vector{UInt8}), cigar_view!,
BAMCIGAR(::CIGAR, ::Vector{UInt8}), and
BAMCIGAR(::MutableMemoryView{UInt8}, ::CIGAR), which were
deprecated in favor of encode!/encode_append!.
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## master #13 +/- ##
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- Coverage 91.34% 91.31% -0.04%
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Files 3 3
Lines 543 541 -2
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- Hits 496 494 -2
Misses 47 47
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added 2 commits
February 12, 2026 09:01
I had misunderstood what OP_H means. While it is true that, like OP_S, it means that the alignment is local and does not extend to the ends of the aligned query, its meaning is still different. OP_H indicates that the unaligned ends of the query has been removed, meaning that the observed query is a truncated version of the true query. Therefore, hard clipped bases are not part of the query at all, and so they are not consumed by OP_H.
These are more efficient for the compiler, and therefore generates better code.
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Breaking:
BAMCIGAR(::MutableMemoryView{UInt8}, ::CIGAR), which were deprecated in favor of encode!/encode_append!.
OP_Hno longer consumes the query.Other
Various bugfixes