From d00d4fd4d651a72bbd4fb5078d0f7d28783af15b Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 14 Jun 2011 14:11:47 +0000
Subject: [PATCH] Obsolete covariate class

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5993 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../walkers/recalibration/TileCovariate.java  | 69 -------------------
 1 file changed, 69 deletions(-)
 delete mode 100644 java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java
deleted file mode 100644
index c1b4a58a9..000000000
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java
+++ /dev/null
@@ -1,69 +0,0 @@
-/*
- * The MIT License
- *
- * Copyright (c) 2009 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.recalibration;
-
-import net.sf.samtools.SAMRecord;
-import net.sf.picard.util.IlluminaUtil;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-
-/**
- * @author alecw@broadinstitute.org
- */
-
-public class TileCovariate implements ExperimentalCovariate {
-
-    private boolean exceptionWhenNoTile = false;
-
-    // Initialize any member variables using the command-line arguments passed to the walkers
-    public void initialize( final RecalibrationArgumentCollection RAC ) {
-        exceptionWhenNoTile = RAC.EXCEPTION_IF_NO_TILE;
-    }
-
-
-    // Used to pick out the covariate's value from attributes of the read
-    public Comparable getValue(final SAMRecord read, final int offset) {
-        Integer tile = IlluminaUtil.getTileFromReadName(read.getReadName());
-        if (tile == null) {
-            if( exceptionWhenNoTile ) {
-                throw new UserException.MalformedBAM(read, "Tile covariate specified but tile number not defined for read: " + read.getReadName() );
-            } else {
-                return -1;
-            }
-        }
-        return tile;
-    }
-
-    // Used to get the covariate's value from input csv file in TableRecalibrationWalker
-    public Comparable getValue(final String str) {
-        return Integer.parseInt( str );
-    }
-
-    public void getValues(SAMRecord read, Comparable[] comparable) {
-        final Comparable tileCovariateValue = getValue(read, 0);
-        for(int i = 0; i < read.getReadLength(); i++) {
-            comparable[i] = tileCovariateValue;
-        }
-    }
-}