From 711cbd3b5a70709d4b6d7e1d6d1bcfedce642ea9 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Tue, 26 Feb 2013 13:49:00 -0500
Subject: [PATCH] Archiving CoverageBySample

This walker was not updated since 2009, and users were getting wrong answers when running it with ReduceReads. I don't want to deal with this because DiagnoseTargets does everything this walker does.
---
 .../sting/gatk/examples/CoverageBySample.java | 108 ------------------
 1 file changed, 108 deletions(-)
 delete mode 100644 public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java

diff --git a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java b/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
deleted file mode 100644
index c96fe564c..000000000
--- a/public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java
+++ /dev/null
@@ -1,108 +0,0 @@
-/*
-* Copyright (c) 2012 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.examples;
-
-import net.sf.samtools.SAMReadGroupRecord;
-import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.help.HelpConstants;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-
-import java.io.PrintStream;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-
-/**
- * Computes the coverage per sample for every position (use with -L argument!).
- */
-@DocumentedGATKFeature( groupName = HelpConstants.DOCS_CAT_QC, extraDocs = {CommandLineGATK.class} )
-public class CoverageBySample extends LocusWalker<Integer, Integer> {
-    @Output
-    protected PrintStream out;    
-
-    private HashSet<String> sampleNames = new HashSet<String>();
-
-    public boolean requiresReads() { return true; }
-
-    public void initialize() {
-
-        List<SAMReadGroupRecord> read_groups = this.getToolkit().getSAMFileHeader().getReadGroups();
-
-        for ( SAMReadGroupRecord record : read_groups ) {
-            String sample = record.getSample();
-            if ( sample != null )
-                sampleNames.add(sample);
-        } 
-    }
-
-    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
-
-        HashMap<String, Integer> depthBySample = new HashMap<String, Integer>();
-        for ( String sample : sampleNames )
-            depthBySample.put(sample, 0);
-
-        ReadBackedPileup pileup = context.getPileup();
-        for ( PileupElement p : pileup ) {
-
-            SAMReadGroupRecord readGroup = p.getRead().getReadGroup();
-            if ( readGroup == null )
-                continue;
-
-            String sample = readGroup.getSample();
-            if ( sample != null ) {
-                int oldDepth = depthBySample.get(sample);
-                depthBySample.put(sample, oldDepth + 1);
-            }
-        }
-
-        for ( Map.Entry<String, Integer> sample : depthBySample.entrySet() ) {
-            out.printf("  %s %8d%n", sample.getKey(), sample.getValue());
-        }
-
-        return 1;
-    }
-
-
-    public void onTraversalDone(Integer result) {
-        out.println("Processed " + result + " loci.");
-    }
-
-    public Integer reduceInit() {
-		return 0;
-    }
-
-    public Integer reduce(Integer value, Integer sum) {
-        return sum + value;
-    }
-}