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Bring up-to-date with master branch of BioAlignments.jl
Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
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parent
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commit
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3 changed files with 14 additions and 11 deletions
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@ -91,7 +91,7 @@ function Base.empty!(record::Record)
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record.tlen = 0
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#Note: data will be overwritten and indexed using data_size.
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return record
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end
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@ -436,7 +436,9 @@ function alignment(record::Record)::BioAlignments.Alignment
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end
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seqpos = 0
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refpos = position(record) - 1
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anchors = [BioAlignments.AlignmentAnchor(seqpos, refpos, BioAlignments.OP_START)]
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alnpos = 0
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anchors = [BioAlignments.AlignmentAnchor(seqpos, refpos, alnpos, BioAlignments.OP_START)]
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for (op, len) in zip(cigar_rle(record)...)
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if BioAlignments.ismatchop(op)
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seqpos += len
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@ -448,7 +450,8 @@ function alignment(record::Record)::BioAlignments.Alignment
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else
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error("operation $(op) is not supported")
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end
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push!(anchors, BioAlignments.AlignmentAnchor(seqpos, refpos, op))
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alnpos += len
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push!(anchors, BioAlignments.AlignmentAnchor(seqpos, refpos, alnpos, op))
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end
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return BioAlignments.Alignment(anchors)
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end
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@ -79,10 +79,10 @@
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@test BAM.flag(record) === UInt16(16)
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@test BAM.cigar(record) == "27M1D73M"
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@test BAM.alignment(record) == Alignment([
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AlignmentAnchor( 0, 1, OP_START),
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AlignmentAnchor( 27, 28, OP_MATCH),
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AlignmentAnchor( 27, 29, OP_DELETE),
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AlignmentAnchor(100, 102, OP_MATCH)])
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AlignmentAnchor( 0, 1, 0, OP_START),
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AlignmentAnchor( 27, 28, 27, OP_MATCH),
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AlignmentAnchor( 27, 29, 28, OP_DELETE),
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AlignmentAnchor(100, 102, 101, OP_MATCH)])
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@test record["XG"] == 1
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@test record["XM"] == 5
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@test record["XN"] == 0
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@ -104,10 +104,10 @@
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@test SAM.flag(record) == 16
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@test SAM.cigar(record) == "27M1D73M"
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@test SAM.alignment(record) == Alignment([
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AlignmentAnchor( 0, 1, OP_START),
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AlignmentAnchor( 27, 28, OP_MATCH),
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AlignmentAnchor( 27, 29, OP_DELETE),
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AlignmentAnchor(100, 102, OP_MATCH)])
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AlignmentAnchor( 0, 1, 0, OP_START),
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AlignmentAnchor( 27, 28, 27, OP_MATCH),
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AlignmentAnchor( 27, 29, 28, OP_DELETE),
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AlignmentAnchor(100, 102, 101, OP_MATCH)])
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@test record["XG"] == 1
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@test record["XM"] == 5
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@test record["XN"] == 0
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