From ac1b289d550c680042bab5696ecfb9dd6ba52f2f Mon Sep 17 00:00:00 2001
From: alecw <alecw@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 25 Nov 2009 21:41:42 +0000
Subject: [PATCH] Add tile to ReadHashDatum, and implement TileCovariate

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2166 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../recalibration/CovariateCounterWalker.java |  8 ++--
 .../walkers/recalibration/ReadHashDatum.java  |  6 ++-
 .../TableRecalibrationWalker.java             |  6 ++-
 .../walkers/recalibration/TileCovariate.java  | 46 +++++++++++++++++++
 4 files changed, 61 insertions(+), 5 deletions(-)
 create mode 100644 java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
index 903b588f8..6aa325a25 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CovariateCounterWalker.java
@@ -18,6 +18,7 @@ import java.util.*;
 
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMReadGroupRecord;
+import edu.mit.broad.picard.illumina.parser.IlluminaUtil;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -237,7 +238,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
         logger.info( "The covariates being used here: " );
         logger.info( requestedCovariates );
 
-        if(estimatedCapacity > 300 * 40 * 200 * 16) { estimatedCapacity = 300 * 40 * 200 * 16; }  // Don't want to crash with out of heap space exception
+        if(estimatedCapacity > 300 * 40 * 200 * 16 || estimatedCapacity < 0) // could be negative if overflowed
+        { estimatedCapacity = 300 * 40 * 200 * 16; }  // Don't want to crash with out of heap space exception
         dataManager = new RecalDataManager( estimatedCapacity );
         readDatumHashMap = new IdentityHashMap<SAMRecord, ReadHashDatum>();
     }
@@ -347,8 +349,8 @@ public class CovariateCounterWalker extends LocusWalker<Integer, PrintStream> {
                     if( FORCE_PLATFORM != null ) {
                         platform = FORCE_PLATFORM;
                     }
-
-                    readDatum = new ReadHashDatum( readGroupId, platform, quals, bases, isNegStrand, mappingQuality, length );
+                    Integer tile = IlluminaUtil.getTileFromReadName(read.getReadName());
+                    readDatum = new ReadHashDatum( readGroupId, platform, quals, bases, isNegStrand, mappingQuality, length, tile );
                     readDatumHashMap.put( read, readDatum );
                     sizeOfReadDatumHashMap++;
                 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadHashDatum.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadHashDatum.java
index 0cd8d4c1c..79af1ae7e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadHashDatum.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/ReadHashDatum.java
@@ -13,8 +13,10 @@ public class ReadHashDatum {
     public boolean isNegStrand;
     public int mappingQuality;
     public int length;
+    public Integer tile;
 
-    public ReadHashDatum(String _readGroup, String _platform, byte[] _quals, byte[] _bases, boolean _isNegStrand, int _mappingQuality, int _length) {
+    public ReadHashDatum(String _readGroup, String _platform, byte[] _quals, byte[] _bases, boolean _isNegStrand,
+                         int _mappingQuality, int _length, Integer _tile) {
         readGroup = _readGroup;
         platform = _platform;
         quals = _quals;
@@ -22,6 +24,7 @@ public class ReadHashDatum {
         isNegStrand = _isNegStrand;
         mappingQuality = _mappingQuality;
         length = _length;
+        tile = _tile;
     }
 
     public ReadHashDatum(ReadHashDatum that) {
@@ -32,5 +35,6 @@ public class ReadHashDatum {
         this.isNegStrand = that.isNegStrand;
         this.mappingQuality = that.mappingQuality;
         this.length = that.length;
+        this.tile = that.tile;
     }
 }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
index 2ac1ed925..6c8b39068 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
@@ -15,6 +15,8 @@ import java.util.regex.Pattern;
 import java.io.File;
 import java.io.FileNotFoundException;
 
+import edu.mit.broad.picard.illumina.parser.IlluminaUtil;
+
 /*
  * Copyright (c) 2009 The Broad Institute
  *
@@ -332,7 +334,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
             platform = FORCE_PLATFORM;
         }
 
-        ReadHashDatum readDatum = new ReadHashDatum( readGroupId, platform, originalQuals, bases, isNegStrand, read.getMappingQuality(), bases.length );
+        Integer tile = IlluminaUtil.getTileFromReadName(read.getReadName());
+        ReadHashDatum readDatum = new ReadHashDatum( readGroupId, platform, originalQuals, bases, isNegStrand,
+                read.getMappingQuality(), bases.length, tile );
 
         // For each base in the read
         for( int iii = startPos; iii < stopPos; iii++ ) { // Skip first or last base because there is no dinuc depending on the direction of the read
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java
new file mode 100644
index 000000000..cfa78bb67
--- /dev/null
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TileCovariate.java
@@ -0,0 +1,46 @@
+/*
+ * 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 org.broadinstitute.sting.utils.StingException;
+
+/**
+ * @author alecw@broadinstitute.org
+ */
+public class TileCovariate implements Covariate {
+    public Comparable getValue(final ReadHashDatum readDatum, final int offset) {
+        if (readDatum.tile == null) {
+            throw new StingException("Tile number not defined for read");
+        }
+        return readDatum.tile;
+    }
+
+    public Comparable getValue(final String str) {
+        return Integer.parseInt( str );
+    }
+
+    public int estimatedNumberOfBins() {
+        return 120;
+    }
+}