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Rehaul BAM and SAM accessor functions #28

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Rehaul BAM and SAM accessor functions #28

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cf168ac
Improve BAM.quality performance
CiaranOMara Jul 1, 2020
a6fff2b
Make BAM record layout match BAM specs
jakobnissen Jul 28, 2020
cfd4149
Change BAM accessor functions
jakobnissen Aug 7, 2020
198e031
Improve printing of BAM records
jakobnissen Aug 7, 2020
fc16f7d
Switch to CodecBGZF
jakobnissen Feb 28, 2021
8054407
Merge branch 'codecbgzf' into rehaul
jakobnissen Feb 28, 2021
fb886c0
Disable cross tests
jakobnissen Feb 28, 2021
3bc38ee
Add quality iter
jakobnissen Feb 28, 2021
8c219c2
Add no-copy AUX data
jakobnissen Feb 28, 2021
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Improve BAM.quality performance 
Closes https://github.com/BioJulia/BioAlignments.jl/pull/33/files.
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@CiaranOMara
CiaranOMara committed Jul 8, 2020
commit cf168acaa372308451e729708b0670a9e3f0ff3f
8 changes: 4 additions & 4 deletions src/bam/record.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -543,15 +543,15 @@ function hasseqlength(record::Record)
end

"""
quality(record::Record)::Vector{UInt8}
quality(record::Record)

Get the base quality of `record`.
Get the base quality of `record`.
"""
function quality(record::Record)::Vector{UInt8}
function quality(record::Record)
checkfilled(record)
seqlen = seqlength(record)
offset = seqname_length(record) + n_cigar_op(record, false) * 4 + cld(seqlen, 2)
return [reinterpret(Int8, record.data[i+offset]) for i in 1:seqlen]
return record.data[(1+offset):(seqlen+offset)]
end

function hasquality(record::Record)
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