From 18b0114e25eb30399403eb6d5eaea4cb1ea8b15f Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Mon, 19 Jul 2010 17:27:23 +0000
Subject: [PATCH] remove FixBAMSortOrder walker.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3830 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/FixBAMSortOrderTag.java      | 87 -------------------
 1 file changed, 87 deletions(-)
 delete mode 100644 java/src/org/broadinstitute/sting/gatk/walkers/FixBAMSortOrderTag.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/FixBAMSortOrderTag.java b/java/src/org/broadinstitute/sting/gatk/walkers/FixBAMSortOrderTag.java
deleted file mode 100644
index bdcf20dd0..000000000
--- a/java/src/org/broadinstitute/sting/gatk/walkers/FixBAMSortOrderTag.java
+++ /dev/null
@@ -1,87 +0,0 @@
-/*
- * Copyright (c) 2010 The Broad Institute
- *
- * 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.gatk.walkers;
-
-/*  Motivation: BAM files created by samtools which are sorted often don't
- *   have the sort order set to 'coordinate' in the BAM header (instead it's
- *   marked as 'unsorted'.  Because BAMs are binary files, there's no way to
- *   easily change the tag.
- *
- *  This walker rewrites a BAM file so that the output is identical to the input
- *   except that the sort order tag is set to 'coordinate'.
- *
- *  Important note: to run properly in the GATK, the '-U' flag must be used so that
- *   the input BAM file not be rejected by the system.
- */
-
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
-import org.broadinstitute.sting.commandline.Argument;
-import net.sf.samtools.SAMFileWriter;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMFileWriterFactory;
-
-import java.io.File;
-
-/**
- * Fixes slightly corrupted BAM files by rewriting the input BAM file, altering
- * the header by changing the sort order tag (SO) to coordinate sort order.  Will NOT
- * verify the contents of the file to ensure that the data is actually in coordinate sorted
- * order. 
- */
-public class FixBAMSortOrderTag extends ReadWalker<SAMRecord, SAMFileWriter> {
-
-    @Argument(required=true, shortName="out_bam", doc="The samfile to output to")
-    public File SAM_FILE_OUTPUT_LOCATION;
-
-    @Argument(required=false, shortName="sortorder", doc="the sort order to emit in")
-    public SAMFileHeader.SortOrder SORT_ORDER=SAMFileHeader.SortOrder.coordinate;
-
-    @Override
-    public SAMRecord map(ReferenceContext ref, SAMRecord read, ReadMetaDataTracker metaDataTracker) {
-        return read;
-    }
-
-    @Override
-    public SAMFileWriter reduceInit() {
-        SAMFileHeader header = GenomeAnalysisEngine.instance.getSAMFileHeader();
-        header.setSortOrder(SORT_ORDER);
-        SAMFileWriterFactory factory = new SAMFileWriterFactory();
-        return factory.makeBAMWriter(header,false,SAM_FILE_OUTPUT_LOCATION);
-    }
-
-    @Override
-    public SAMFileWriter reduce(SAMRecord value, SAMFileWriter sum) {
-        sum.addAlignment(value);
-        return sum;
-    }
-
-    public void onTraversalDone(SAMFileWriter result) {
-        result.close();
-    }
-}