Updating the BQSR Gatherer to the new file format

This is important for quick turnaround in the analysis cycle of the new covariates. Also added a dummy unit test that doesn't really test anything (disabled), but helps in debugging.

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java

@@ -0,0 +1,124 @@
+/*
+ * Copyright (c) 2011 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.bqsr;
+
+import org.broadinstitute.sting.commandline.Gatherer;
+import org.broadinstitute.sting.gatk.walkers.recalibration.RecalDatumOptimized;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.text.XReadLines;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.PrintStream;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+/**
+ * User: carneiro
+ * Date: 3/29/11
+ */
+
+
+public class BQSRGatherer extends Gatherer  {
+
+    /////////////////////////////
+    // Private Member Variables
+    /////////////////////////////
+    private static final String EOF_MARKER = "EOF";
+
+    private HashMap<String, RecalDatumOptimized> dataMap = new HashMap<String, RecalDatumOptimized>();
+
+
+    private void addCSVData (String line) {
+        String[] covariates = line.split(",");
+        String key = "";
+        RecalDatumOptimized values;
+
+        for (int i = 0; i < covariates.length-3; i++)
+            key += covariates[i] + ",";
+
+        if (covariates.length < 3)
+            throw new ReviewedStingException("Line only has 1 covariate : " + line);
+
+        values = new RecalDatumOptimized(Long.parseLong(covariates[covariates.length - 3]), Long.parseLong(covariates[covariates.length - 2]));
+
+        RecalDatumOptimized currentValues = dataMap.get(key);
+        if (currentValues == null)
+            dataMap.put(key, values);
+        else
+            currentValues.increment(values);
+
+    }
+
+    @Override
+    public void gather(List<File> inputs, File output) {
+        PrintStream o;
+        try {
+            o = new PrintStream(output);
+        } catch ( FileNotFoundException e) {
+            throw new UserException("File to be output by CountCovariates Gather function was not found");
+        }
+
+        boolean sawEOF = false;
+        boolean printedHeader = false;
+
+        // Read input files
+        for ( File RECAL_FILE : inputs) {
+            try {
+                for ( String line : new XReadLines(RECAL_FILE) ) {
+                    if ( EOF_MARKER.equals(line) ) {
+                        sawEOF = true;                      // sanity check
+                        break;
+                    }
+
+                    else if(line.startsWith("#"))  {
+                        if (!printedHeader)
+                            o.println(line);
+                    }
+
+                    else                                    // Found a line of data
+                        addCSVData(line);                   // Parse the line and add the data to the HashMap
+                }
+
+            } catch ( FileNotFoundException e ) {
+                throw new UserException.CouldNotReadInputFile(RECAL_FILE, "Can not find input file", e);
+            }
+
+            if ( !sawEOF ) {
+                final String errorMessage = "No EOF marker was present in the recal covariates table; this could mean that the file is corrupted!";
+                throw new UserException.MalformedFile(RECAL_FILE, errorMessage);
+            }
+            printedHeader = true;
+        }
+
+        // Write output file from dataMap
+        for(Map.Entry<String, RecalDatumOptimized> entry : dataMap.entrySet())
+            o.println(entry.getKey() + entry.getValue().outputToCSV());
+        o.println("EOF");
+    }
+}

public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationArgumentCollection.java

@@ -27,7 +27,6 @@ package org.broadinstitute.sting.gatk.walkers.bqsr;
 
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.walkers.recalibration.CountCovariatesGatherer;
 
 import java.io.PrintStream;
 import java.util.Collections;
@@ -59,7 +58,7 @@ public class RecalibrationArgumentCollection {
      * three items are the data- that is, number of observations for this combination of covariates, number of reference mismatches,
      * and the raw empirical quality score calculated by phred-scaling the mismatch rate.
      */
-    @Gather(CountCovariatesGatherer.class)
+    @Gather(BQSRGatherer.class)
     @Output
     protected PrintStream RECAL_FILE;
 

public/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java

@@ -0,0 +1,29 @@
+package org.broadinstitute.sting.gatk.walkers.bqsr;
+
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.util.LinkedList;
+import java.util.List;
+
+/**
+ * @author Mauricio Carneiro
+ * @since 3/7/12
+ */
+public class BQSRGathererUnitTest {
+    RecalibrationArgumentCollection RAC;
+
+    private static File recal1 = new File("public/testdata/exampleCSV.csv");
+    private static File recal2 = new File("public/testdata/exampleCSV.2.csv");
+
+    @Test(enabled = false)
+    public void testCombineTwoFiles() {
+        BQSRGatherer gatherer = new BQSRGatherer();
+        List<File> recalFiles = new LinkedList<File> ();
+        File output = new File("foo.csv");
+        
+        recalFiles.add(recal1);
+        recalFiles.add(recal2);
+        gatherer.gather(recalFiles, output);
+    }
+}