From e2311294c0d42e02cc8bd0201042d88a841f799d Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Mon, 14 May 2012 09:46:06 -0400
Subject: [PATCH] Removed unused ManualSortingVCFWriter

---
 .../vcf/writer/ManualSortingVCFWriter.java    | 52 -------------------
 1 file changed, 52 deletions(-)
 delete mode 100755 public/java/src/org/broadinstitute/sting/utils/codecs/vcf/writer/ManualSortingVCFWriter.java

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/writer/ManualSortingVCFWriter.java b/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/writer/ManualSortingVCFWriter.java
deleted file mode 100755
index ff349e032..000000000
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/writer/ManualSortingVCFWriter.java
+++ /dev/null
@@ -1,52 +0,0 @@
-/*
- * Copyright (c) 2010.
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.codecs.vcf.writer;
-
-/**
- * this class writes VCF files, allowing records to be passed in unsorted.
- */
-public class ManualSortingVCFWriter extends SortingVCFWriterBase {
-
-    /**
-     * create a local-sorting VCF writer, given an inner VCF writer to write to
-     *
-     * @param innerWriter        the VCFWriter to write to
-     * @param takeOwnershipOfInner Should this Writer close innerWriter when it's done with it
-     */
-    public ManualSortingVCFWriter(VCFWriter innerWriter, boolean takeOwnershipOfInner) {
-        super(innerWriter, takeOwnershipOfInner);
-    }
-
-    public ManualSortingVCFWriter(VCFWriter innerWriter) {
-        super(innerWriter);
-    }
-
-    // Note that if mostUpstreamWritableLoc = null, then ALL records will be emitted (since not currently waiting for anything)
-    public void setmostUpstreamWritableLocus(Integer mostUpstreamWritableLoc) {
-        this.mostUpstreamWritableLoc = mostUpstreamWritableLoc;
-        emitSafeRecords();
-    }
-}
\ No newline at end of file