From 535a8e1f56c9abb89e1d102adacb8dee7f0c23c8 Mon Sep 17 00:00:00 2001
From: magicDGS <daniel.gomez.sanchez@hotmail.es>
Date: Sun, 20 Nov 2016 14:24:56 +0100
Subject: [PATCH] make CustomGzipOutputStream public to be able to set
 compression level

---
 .../samtools/util/CustomGzipOutputStream.java      | 24 ++++++++++++++++++++++
 src/main/java/htsjdk/samtools/util/IOUtil.java     | 19 -----------------
 2 files changed, 24 insertions(+), 19 deletions(-)
 create mode 100644 src/main/java/htsjdk/samtools/util/CustomGzipOutputStream.java

diff --git a/src/main/java/htsjdk/samtools/util/CustomGzipOutputStream.java b/src/main/java/htsjdk/samtools/util/CustomGzipOutputStream.java
new file mode 100644
index 000000000..cb3652ed5
--- /dev/null
+++ b/src/main/java/htsjdk/samtools/util/CustomGzipOutputStream.java
@@ -0,0 +1,24 @@
+package htsjdk.samtools.util;
+
+import java.io.IOException;
+import java.io.OutputStream;
+import java.util.zip.GZIPOutputStream;
+
+/**
+ * Hacky little class used to allow us to set the compression level on a GZIP output stream which, for some
+ * bizarre reason, is not exposed in the standard API.
+ *
+ * @author Tim Fennell
+ */
+public class CustomGzipOutputStream extends GZIPOutputStream {
+    CustomGzipOutputStream(final OutputStream outputStream, final int bufferSize, final int compressionLevel) throws
+            IOException {
+        super(outputStream, bufferSize);
+        this.def.setLevel(compressionLevel);
+    }
+
+    CustomGzipOutputStream(final OutputStream outputStream, final int compressionLevel) throws IOException {
+        super(outputStream);
+        this.def.setLevel(compressionLevel);
+    }
+}
diff --git a/src/main/java/htsjdk/samtools/util/IOUtil.java b/src/main/java/htsjdk/samtools/util/IOUtil.java
index 7f0495d4b..b87b40978 100644
--- a/src/main/java/htsjdk/samtools/util/IOUtil.java
+++ b/src/main/java/htsjdk/samtools/util/IOUtil.java
@@ -944,22 +944,3 @@ public static String slurp(final InputStream is, final Charset charSet) {
         return output;
     }
 }
-
-
-/**
- * Hacky little class used to allow us to set the compression level on a GZIP output stream which, for some
- * bizarre reason, is not exposed in the standard API.
- *
- * @author Tim Fennell
- */
-class CustomGzipOutputStream extends GZIPOutputStream {
-    CustomGzipOutputStream(final OutputStream outputStream, final int bufferSize, final int compressionLevel) throws IOException {
-        super(outputStream, bufferSize);
-        this.def.setLevel(compressionLevel);
-    }
-
-    CustomGzipOutputStream(final OutputStream outputStream, final int compressionLevel) throws IOException {
-        super(outputStream);
-        this.def.setLevel(compressionLevel);
-    }
-}