From 9e97d389c33d5a8b099acfe1c76ef16dd39d74a4 Mon Sep 17 00:00:00 2001
From: kortschak <dan.kortschak@adelaide.edu.au>
Date: Tue, 15 Sep 2015 11:31:33 +0930
Subject: [PATCH] bgzf/index: use correct end of chunk for identification

Fixes #10.
---
 bgzf/index/index.go | 20 ++++++++++++++++----
 1 file changed, 16 insertions(+), 4 deletions(-)

diff --git a/bgzf/index/index.go b/bgzf/index/index.go
index 1aa5898..1c9d95b 100644
--- a/bgzf/index/index.go
+++ b/bgzf/index/index.go
@@ -50,7 +50,11 @@ func NewChunkReader(r *bgzf.Reader, chunks []bgzf.Chunk) (*ChunkReader, error) {
 
 // Read satisfies the io.Reader interface.
 func (r *ChunkReader) Read(p []byte) (int, error) {
-	if len(r.chunks) == 0 || vOffset(r.r.LastChunk().End) >= vOffset(r.chunks[0].End) {
+	if len(r.chunks) == 0 {
+		return 0, io.EOF
+	}
+	last := r.r.LastChunk()
+	if vOffset(last.End) >= vOffset(r.chunks[0].End) {
 		return 0, io.EOF
 	}
 
@@ -58,9 +62,13 @@ func (r *ChunkReader) Read(p []byte) (int, error) {
 	// the current chunk. We do not need to consider reading
 	// beyond the end of the block because the bgzf.Reader is in
 	// blocked mode and so will stop there anyway.
-	if r.r.LastChunk().End.File == r.chunks[0].End.File {
-		p = p[:min(len(p), int(r.chunks[0].End.Block-r.r.LastChunk().End.Block))]
+	// If we are in the same block as the last read, set the
+	// cursor to the end of that read.
+	var cursor uint16
+	if last.Begin.File == r.chunks[0].Begin.File {
+		cursor = last.End.Block
 	}
+	p = p[:min(len(p), int(r.chunks[0].End.Block-cursor))]
 
 	n, err := r.r.Read(p)
 	if err != nil {
@@ -69,13 +77,17 @@ func (r *ChunkReader) Read(p []byte) (int, error) {
 		}
 		return n, err
 	}
-	if len(r.chunks) != 0 && vOffset(r.r.LastChunk().End) >= vOffset(r.chunks[0].End) {
+
+	// Check for non-progress and terminate when this happens.
+	this := r.r.LastChunk()
+	if this == last || vOffset(this.End) >= vOffset(r.chunks[0].End) {
 		r.chunks = r.chunks[1:]
 		if len(r.chunks) == 0 {
 			return n, io.EOF
 		}
 		err = r.r.Seek(r.chunks[0].Begin)
 	}
+
 	return n, err
 }