From 80c38eb4a54975f38d002c4c3c78de9264dd38ce Mon Sep 17 00:00:00 2001
From: Illyoung Choi <iychoi@email.arizona.edu>
Date: Thu, 30 Aug 2018 12:35:53 -0700
Subject: [PATCH] Show header of a read when input FASTQ sample has invalid
 format

---
 src/libra/common/sequence/Read.java | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/src/libra/common/sequence/Read.java b/src/libra/common/sequence/Read.java
index b49bf87..5d1ed18 100644
--- a/src/libra/common/sequence/Read.java
+++ b/src/libra/common/sequence/Read.java
@@ -116,8 +116,13 @@ public void parseFasta(List<String> lines) throws IOException {
     public void parseFastq(List<String> lines) throws IOException {
         clear();
         
+        if(lines.size() == 0) {
+            return;
+        }
+        
         if(lines.size() != 4) {
-            throw new IOException(String.format("invalid fastq read format - line num is %d", lines.size()));
+            String header = lines.get(0);
+            throw new IOException(String.format("invalid fastq read format - a read (%s) has %d lines", header, lines.size()));
         }
         
         int lineNo = 0;