bump htsjdk dependency version to 0.20.3

HadoopGenomics · Sep 11, 2019 · 9cd7d67 · 9cd7d67
1 parent 9f974cf
commit 9cd7d67
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Showing 6 changed files with 13 additions and 8 deletions.
diff --git a/pom.xml b/pom.xml
@@ -40,7 +40,7 @@
 
     <properties>
         <java.version>1.8</java.version>
-        <htsjdk.version>2.14.2</htsjdk.version>
+        <htsjdk.version>2.20.3</htsjdk.version>
         <!-- CHANGE THIS FOR A DIFFERENT VERSION OF HADOOP -->
         <hadoop.version>2.9.0</hadoop.version>
         <!--

diff --git a/src/main/java/org/seqdoop/hadoop_bam/BAMRecordWriter.java b/src/main/java/org/seqdoop/hadoop_bam/BAMRecordWriter.java
@@ -23,6 +23,7 @@
 package org.seqdoop.hadoop_bam;
 
 import htsjdk.samtools.util.BlockCompressedStreamConstants;
+import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
 import java.io.StringWriter;
@@ -109,11 +110,11 @@ private void init(
 		origOutput = output;
 
 		if (useIntelDeflater) {
-			compressedOut = new BlockCompressedOutputStream(origOutput, null,
+                    compressedOut = new BlockCompressedOutputStream(origOutput, (File) null,
 					BlockCompressedStreamConstants.DEFAULT_COMPRESSION_LEVEL,
 					IntelGKLAccessor.newDeflaterFactory());
 		} else {
-			compressedOut = new BlockCompressedOutputStream(origOutput, null);
+                    compressedOut = new BlockCompressedOutputStream(origOutput, (File) null);
 		}
 
 		binaryCodec = new BinaryCodec(compressedOut);

diff --git a/src/main/java/org/seqdoop/hadoop_bam/BCFRecordWriter.java b/src/main/java/org/seqdoop/hadoop_bam/BCFRecordWriter.java
@@ -22,6 +22,7 @@
 
 package org.seqdoop.hadoop_bam;
 
+import java.io.File;
 import java.io.FilterOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
@@ -166,7 +167,7 @@ final class BCFStoppableOutputStream extends FilterOutputStream {
 	private final OutputStream origOut;
 
 	public BCFStoppableOutputStream(boolean startStopped, OutputStream out) {
-		super(new BlockCompressedOutputStream(out, null));
+            super(new BlockCompressedOutputStream(out, (File) null));
 		origOut = out;
 		stopped = startStopped;
 	}

diff --git a/src/main/java/org/seqdoop/hadoop_bam/util/BGZFCompressionOutputStream.java b/src/main/java/org/seqdoop/hadoop_bam/util/BGZFCompressionOutputStream.java
@@ -1,6 +1,7 @@
 package org.seqdoop.hadoop_bam.util;
 
 import htsjdk.samtools.util.BlockCompressedOutputStream;
+import java.io.File;
 import java.io.IOException;
 import java.io.OutputStream;
 import org.apache.hadoop.io.compress.CompressionOutputStream;
@@ -20,7 +21,7 @@ class BGZFCompressionOutputStream extends CompressionOutputStream {
   public BGZFCompressionOutputStream(OutputStream out)
       throws IOException {
     super(out);
-    this.output = new BlockCompressedOutputStream(out, null);
+    this.output = new BlockCompressedOutputStream(out, (File) null);
   }
 
   public void write(int b) throws IOException {
@@ -37,7 +38,7 @@ public void finish() throws IOException {
 
   public void resetState() throws IOException {
     output.flush();
-    output = new BlockCompressedOutputStream(out, null);
+    output = new BlockCompressedOutputStream(out, (File) null);
   }
 
   public void close() throws IOException {

diff --git a/src/main/java/org/seqdoop/hadoop_bam/util/SAMOutputPreparer.java b/src/main/java/org/seqdoop/hadoop_bam/util/SAMOutputPreparer.java
@@ -22,6 +22,7 @@
 
 package org.seqdoop.hadoop_bam.util;
 
+import java.io.File;
 import java.io.FilterOutputStream;
 import java.io.IOException;
 import java.io.OutputStream;
@@ -101,7 +102,7 @@ private OutputStream prepareSAMOrBAMStream(
 		final String text = sw.toString();
 
 		if (format == SAMFormat.BAM) {
-			out = new BlockCompressedOutputStream(out, null);
+                    out = new BlockCompressedOutputStream(out, (File) null);
 			out.write(BAM_MAGIC);
 			writeInt32(out, text.length());
 		}

diff --git a/src/main/java/org/seqdoop/hadoop_bam/util/VCFFileMerger.java b/src/main/java/org/seqdoop/hadoop_bam/util/VCFFileMerger.java
@@ -8,6 +8,7 @@
 import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
 import htsjdk.variant.vcf.VCFHeader;
 import java.io.BufferedInputStream;
+import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.io.OutputStream;
@@ -95,7 +96,7 @@ private static boolean writeHeader(OutputStream out, Path outputPath, List<Path>
     boolean gzipCompressed = isGzipCompressed(parts);
     OutputStream headerOut;
     if (blockCompressed) {
-      headerOut = new BlockCompressedOutputStream(out, null);
+      headerOut = new BlockCompressedOutputStream(out, (File) null);
     } else if (gzipCompressed) {
       headerOut = new GZIPOutputStream(out);
     } else {