Show header of a read when input FASTQ sample has invalid format

iychoi · Aug 30, 2018 · 80c38eb · 80c38eb
1 parent 7c637fd
commit 80c38eb
Showing 1 changed file with 6 additions and 1 deletion.
diff --git 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;