From e6f542a368c368e85c3cc411fb4fb84fa694d441 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Mon, 10 Oct 2022 08:51:20 -0500
Subject: [PATCH] Change alignment getter for BAM.Record to use existing cigar
 constructor

Rather than keep a copy of the BioAlignments cigar constructor embedded in
this function, have it call the existing constructor. There may be
performance implications for using `cigar` instead of `cigar_rle`, but
having a second copy of the constructor here is an antipattern if I've ever
seen one, so prioritise stable code over performant code.
---
 src/bam/record.jl | 24 ++++--------------------
 1 file changed, 4 insertions(+), 20 deletions(-)

diff --git a/src/bam/record.jl b/src/bam/record.jl
index 6de18a5..bd092e8 100644
--- a/src/bam/record.jl
+++ b/src/bam/record.jl
@@ -430,27 +430,11 @@ end
 Get the alignment of `record`.
 """
 function alignment(record::Record)::BioAlignments.Alignment
-    checkfilled(record)
-    if !ismapped(record)
-        return BioAlignments.Alignment(BioAlignments.AlignmentAnchor[])
+    if ismapped(record)
+        return BioAlignments.Alignment(cigar(record), 1, position(record))
     end
-    seqpos = 0
-    refpos = position(record) - 1
-    anchors = [BioAlignments.AlignmentAnchor(seqpos, refpos, BioAlignments.OP_START)]
-    for (op, len) in zip(cigar_rle(record)...)
-        if BioAlignments.ismatchop(op)
-            seqpos += len
-            refpos += len
-        elseif BioAlignments.isinsertop(op)
-            seqpos += len
-        elseif BioAlignments.isdeleteop(op)
-            refpos += len
-        else
-            error("operation $(op) is not supported")
-        end
-        push!(anchors, BioAlignments.AlignmentAnchor(seqpos, refpos, op))
-    end
-    return BioAlignments.Alignment(anchors)
+
+    return BioAlignments.Alignment(BioAlignments.AlignmentAnchor[])
 end
 
 function hasalignment(record::Record)