From de252188e81c37ddba77e511ef3d57a4f5649aae Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Thu, 27 Jan 2022 11:11:45 -0600
Subject: [PATCH] Bring up-to-date with master branch of BioAlignments.jl

Signed-off-by: Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com>
---
 src/bam/record.jl | 9 ++++++---
 test/test_bam.jl  | 8 ++++----
 test/test_sam.jl  | 8 ++++----
 3 files changed, 14 insertions(+), 11 deletions(-)

diff --git a/src/bam/record.jl b/src/bam/record.jl
index b545600..b861d1f 100644
--- a/src/bam/record.jl
+++ b/src/bam/record.jl
@@ -91,7 +91,7 @@ function Base.empty!(record::Record)
     record.tlen       = 0
 
     #Note: data will be overwritten and indexed using data_size.
-    
+
     return record
 end
 
@@ -436,7 +436,9 @@ function alignment(record::Record)::BioAlignments.Alignment
     end
     seqpos = 0
     refpos = position(record) - 1
-    anchors = [BioAlignments.AlignmentAnchor(seqpos, refpos, BioAlignments.OP_START)]
+    alnpos = 0
+
+    anchors = [BioAlignments.AlignmentAnchor(seqpos, refpos, alnpos, BioAlignments.OP_START)]
     for (op, len) in zip(cigar_rle(record)...)
         if BioAlignments.ismatchop(op)
             seqpos += len
@@ -448,7 +450,8 @@ function alignment(record::Record)::BioAlignments.Alignment
         else
             error("operation $(op) is not supported")
         end
-        push!(anchors, BioAlignments.AlignmentAnchor(seqpos, refpos, op))
+        alnpos += len
+        push!(anchors, BioAlignments.AlignmentAnchor(seqpos, refpos, alnpos, op))
     end
     return BioAlignments.Alignment(anchors)
 end
diff --git a/test/test_bam.jl b/test/test_bam.jl
index beb6d03..b5823ed 100644
--- a/test/test_bam.jl
+++ b/test/test_bam.jl
@@ -79,10 +79,10 @@
         @test BAM.flag(record) === UInt16(16)
         @test BAM.cigar(record) == "27M1D73M"
         @test BAM.alignment(record) == Alignment([
-            AlignmentAnchor(  0,   1, OP_START),
-            AlignmentAnchor( 27,  28, OP_MATCH),
-            AlignmentAnchor( 27,  29, OP_DELETE),
-            AlignmentAnchor(100, 102, OP_MATCH)])
+            AlignmentAnchor(  0,   1,  0, OP_START),
+            AlignmentAnchor( 27,  28, 27, OP_MATCH),
+            AlignmentAnchor( 27,  29, 28, OP_DELETE),
+            AlignmentAnchor(100, 102, 101, OP_MATCH)])
         @test record["XG"] == 1
         @test record["XM"] == 5
         @test record["XN"] == 0
diff --git a/test/test_sam.jl b/test/test_sam.jl
index 195288d..e1c09bb 100644
--- a/test/test_sam.jl
+++ b/test/test_sam.jl
@@ -104,10 +104,10 @@
         @test SAM.flag(record) == 16
         @test SAM.cigar(record) == "27M1D73M"
         @test SAM.alignment(record) == Alignment([
-            AlignmentAnchor(  0,   1, OP_START),
-            AlignmentAnchor( 27,  28, OP_MATCH),
-            AlignmentAnchor( 27,  29, OP_DELETE),
-            AlignmentAnchor(100, 102, OP_MATCH)])
+            AlignmentAnchor(  0,   1,  0, OP_START),
+            AlignmentAnchor( 27,  28, 27, OP_MATCH),
+            AlignmentAnchor( 27,  29, 28, OP_DELETE),
+            AlignmentAnchor(100, 102, 101, OP_MATCH)])
         @test record["XG"] == 1
         @test record["XM"] == 5
         @test record["XN"] == 0