From 2909d61916c40e9d0ae5562ed911bdd4c4f7b5f0 Mon Sep 17 00:00:00 2001
From: Yossi Farjoun <farjoun@gmail.com>
Date: Tue, 13 Dec 2016 15:09:18 -0500
Subject: [PATCH] - remove reference to @Deprecated VariantContextWriterFactory
 in htsdjk prior to removal from that codebase.

---
 src/main/java/picard/vcf/GatherVcfs.java | 36 +++++++++++++++++++-------------
 1 file changed, 21 insertions(+), 15 deletions(-)

diff --git a/src/main/java/picard/vcf/GatherVcfs.java b/src/main/java/picard/vcf/GatherVcfs.java
index c69907bc4..729fb616d 100644
--- a/src/main/java/picard/vcf/GatherVcfs.java
+++ b/src/main/java/picard/vcf/GatherVcfs.java
@@ -1,29 +1,27 @@
 package picard.vcf;
 
-import htsjdk.samtools.util.BlockCompressedInputStream;import htsjdk.samtools.util.BlockCompressedOutputStream;import htsjdk.samtools.util.BlockCompressedStreamConstants;import htsjdk.samtools.util.CloseableIterator;import htsjdk.samtools.util.CloserUtil;import htsjdk.samtools.util.CollectionUtil;import htsjdk.samtools.util.RuntimeIOException;import picard.PicardException;
-import picard.cmdline.CommandLineProgram;
-import picard.cmdline.CommandLineProgramProperties;
-import picard.cmdline.Option;
-import picard.cmdline.StandardOptionDefinitions;
-import htsjdk.samtools.util.IOUtil;
-import htsjdk.samtools.util.Log;
-import htsjdk.samtools.util.PeekableIterator;
-import htsjdk.samtools.util.ProgressLogger;
 import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.samtools.util.*;
+import htsjdk.tribble.AbstractFeatureReader;
 import htsjdk.variant.variantcontext.VariantContext;
 import htsjdk.variant.variantcontext.VariantContextComparator;
 import htsjdk.variant.variantcontext.writer.Options;
 import htsjdk.variant.variantcontext.writer.VariantContextWriter;
-import htsjdk.variant.variantcontext.writer.VariantContextWriterFactory;
+import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
+import picard.PicardException;
+import picard.cmdline.CommandLineProgram;
+import picard.cmdline.CommandLineProgramProperties;
+import picard.cmdline.Option;
+import picard.cmdline.StandardOptionDefinitions;
 import picard.cmdline.programgroups.VcfOrBcf;
 
 import java.io.File;
 import java.io.FileInputStream;
 import java.io.FileOutputStream;
 import java.io.IOException;
-import java.lang.IllegalArgumentException;import java.lang.IllegalStateException;import java.lang.Override;import java.lang.String;import java.util.EnumSet;
+import java.util.EnumSet;
 import java.util.List;
 import java.util.SortedSet;
 import java.util.TreeSet;
@@ -90,7 +88,7 @@ protected int doWork() {
     /** Checks (via filename checking) that all files appear to be block compressed files. */
     private boolean areAllBlockCompressed(final List<File> input) {
         for (final File f : input) {
-            if (VariantContextWriterFactory.isBCFOutput(f) || !VariantContextWriterFactory.isCompressedVcf(f)) return false;
+            if (VCFFileReader.isBCF(f) || !AbstractFeatureReader.hasBlockCompressedExtension(f)) return false;
         }
 
         return true;
@@ -142,9 +140,17 @@ private static void gatherConventionally(final SAMSequenceDictionary sequenceDic
                                       final boolean createIndex,
                                       final List<File> inputFiles,
                                       final File outputFile) {
-        final EnumSet<Options> options = EnumSet.copyOf(VariantContextWriterFactory.DEFAULT_OPTIONS);
-        if (createIndex) options.add(Options.INDEX_ON_THE_FLY); else options.remove(Options.INDEX_ON_THE_FLY);
-        final VariantContextWriter out = VariantContextWriterFactory.create(outputFile, sequenceDictionary, options);
+        final EnumSet<Options> options = EnumSet.copyOf(VariantContextWriterBuilder.DEFAULT_OPTIONS);
+        if (createIndex){
+            options.add(Options.INDEX_ON_THE_FLY);
+        } else {
+            options.remove(Options.INDEX_ON_THE_FLY);
+        }
+        final VariantContextWriter out = new VariantContextWriterBuilder()
+                .setOptions(options)
+                .setOutputFile(outputFile)
+                .setReferenceDictionary(sequenceDictionary)
+                .build();
 
         final ProgressLogger progress = new ProgressLogger(log, 10000);
         VariantContext lastContext = null;