From 7443237129aee4b0f043d929c0b2ad51f62f567a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Ciara=CC=81n=20O=E2=80=99Mara?= <Ciaran.OMara@utas.edu.au>
Date: Sun, 16 May 2021 12:20:55 +1000
Subject: [PATCH] Adjust BGZFStreams.virtualoffset

https://github.com/BioJulia/BGZFStreams.jl/issues/22#issuecomment-874491338
---
 src/bam/bam.jl | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)

diff --git a/src/bam/bam.jl b/src/bam/bam.jl
index 6fd1174..09552ae 100644
--- a/src/bam/bam.jl
+++ b/src/bam/bam.jl
@@ -15,6 +15,22 @@ import BioGenerics: isfilled, header
 
 import GenomicFeatures: eachoverlap
 
+# Overwrite virtualoffset method as per https://github.com/BioJulia/BGZFStreams.jl/issues/22#issuecomment-874491338.
+function BGZFStreams.virtualoffset(stream::BGZFStreams.BGZFStream)
+    if stream.mode == BGZFStreams.READ_MODE
+        i = BGZFStreams.ensure_buffered_data(stream)
+        if i == 0
+            # Provide a VirtualOffset beyond the bounds of the stream.
+            block = stream.blocks[end]
+            return BGZFStreams.VirtualOffset(block.block_offset, 0) + (block.position - 1)
+        else
+            block = stream.blocks[i]
+        end
+    else
+        block = stream.blocks[1]
+    end
+    return BGZFStreams.VirtualOffset(block.block_offset, block.position - 1)
+end
 
 include("bai.jl")
 include("auxdata.jl")