From d75665f1559980266e86bf3f8392612f62bcf0a8 Mon Sep 17 00:00:00 2001
From: Chris Norman <cnorman@broadinstitute.org>
Date: Mon, 22 May 2017 13:39:56 -0400
Subject: [PATCH] Fix ordering of assignments in FastQReader constructor.

---
 .../java/htsjdk/samtools/fastq/FastqReader.java    |  2 +-
 .../samtools/fastq/FastqReaderWriterTest.scala     | 29 +++++++++++++++++++++-
 2 files changed, 29 insertions(+), 2 deletions(-)

diff --git a/src/main/java/htsjdk/samtools/fastq/FastqReader.java b/src/main/java/htsjdk/samtools/fastq/FastqReader.java
index 76ead119d..c5d52f8dc 100755
--- a/src/main/java/htsjdk/samtools/fastq/FastqReader.java
+++ b/src/main/java/htsjdk/samtools/fastq/FastqReader.java
@@ -90,8 +90,8 @@ public FastqReader(final BufferedReader reader) {
     public FastqReader(final File file, final BufferedReader reader,boolean skipBlankLines) {
         this.fastqFile = file;
         this.reader = reader;
-        this.nextRecord = readNextRecord();
         this.skipBlankLines = skipBlankLines;
+        this.nextRecord = readNextRecord();
     }
 
     public FastqReader(final File file, final BufferedReader reader) {
diff --git a/src/test/scala/htsjdk/samtools/fastq/FastqReaderWriterTest.scala b/src/test/scala/htsjdk/samtools/fastq/FastqReaderWriterTest.scala
index 60e08efbd..00f62e91a 100644
--- a/src/test/scala/htsjdk/samtools/fastq/FastqReaderWriterTest.scala
+++ b/src/test/scala/htsjdk/samtools/fastq/FastqReaderWriterTest.scala
@@ -3,7 +3,7 @@ package htsjdk.samtools.fastq
 import java.io.{BufferedReader, File, StringReader}
 
 import htsjdk.UnitSpec
-import htsjdk.samtools.SAMUtils
+import htsjdk.samtools.{SAMException, SAMUtils}
 import htsjdk.samtools.util.IOUtil
 
 import scala.util.Random
@@ -106,6 +106,33 @@ class FastqReaderWriterTest extends UnitSpec {
     in.close()
   }
 
+  it should "honor skipBlankLines when requested" in {
+    val fastq =
+      """
+        |
+        |@SL-XBG:1:1:4:1663#0/2
+        |NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+        |+SL-XBG:1:1:4:1663#0/2
+        |BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+      """.stripMargin
+    val reader = new BufferedReader(new StringReader(fastq))
+    val in = new FastqReader(null, reader, true)
+    while (in.hasNext) in.next()
+  }
+
+  it should "fail on blank lines when skipBlankLines is false" in {
+    val fastq =
+      """
+        |
+        |@SL-XBG:1:1:4:1663#0/2
+        |NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
+        |+SL-XBG:1:1:4:1663#0/2
+        |BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB
+      """.stripMargin
+    val reader = new BufferedReader(new StringReader(fastq))
+    an[SAMException] shouldBe thrownBy { val in = new FastqReader(null, reader, false) }
+  }
+
   it should "fail on a truncated file" in {
     val fastq =
       """