implementation of the Gatherer class for CountCovariates, which makes it now scatter/gatherable. Kudos to the @Gather annotation Khalid just introduced!

QuickCCTest is my test script for the gatherer.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5547 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesGatherer.java

@@ -30,27 +30,24 @@ public class CountCovariatesGatherer extends Gatherer {
     private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
     private static final String EOF_MARKER = "EOF";
 
-    private HashMap<String, int[]> dataMap;
+    private HashMap<String, RecalDatumOptimized> dataMap;
 
 
     private void addCSVData (String line) {
         String[] covariates = line.split(",");
         String key = "";
-        int [] values = new int[3];
+        RecalDatumOptimized values;
 
         for (int i = 0; i < covariates.length-3; i++) {
             key += covariates[i] + ",";
         }
 
-        for (int i = covariates.length-3; i < covariates.length; i++) {
+        values = new RecalDatumOptimized(Integer.parseInt(covariates[covariates.length-3]),
-            values[i] = Integer.parseInt(covariates[i].trim());
+                                         Integer.parseInt(covariates[covariates.length-2]));
-        }
 
         if (dataMap.get(key) != null) {
-            int [] currentValues = dataMap.get(key);
+            RecalDatumOptimized currentValues = dataMap.get(key);
-            for (int i = 0; i < 2; i++) {
+            values.increment(currentValues);
-                values[i] += currentValues[i];// todo -- update the third value using the CountCovariatesWalker function
-            }
         }
 
         dataMap.put(key, values);
@@ -58,7 +55,7 @@ public class CountCovariatesGatherer extends Gatherer {
 
     @Override
     public void gather(List<File> inputs, File output) {
-        dataMap = new HashMap<String, int[]>();
+        dataMap = new HashMap<String, RecalDatumOptimized>();
         PrintStream o;
         try {
             o = new PrintStream(output);
@@ -67,7 +64,7 @@ public class CountCovariatesGatherer extends Gatherer {
         }
 
         boolean sawEOF = false;
-        boolean headerPrinted = false;
+        boolean printedHeader = false;
 
         // Read input files
         for ( File RECAL_FILE : inputs) {
@@ -76,11 +73,12 @@ public class CountCovariatesGatherer extends Gatherer {
                     if ( EOF_MARKER.equals(line) ) {
                         sawEOF = true;    // sanity check
                     }
-                    else if( COMMENT_PATTERN.matcher(line).matches() || COVARIATE_PATTERN.matcher(line).matches() ) {
+                    else if(COMMENT_PATTERN.matcher(line).matches()) {
-                        if (!headerPrinted) {
+                        ;                 // It doesn't make any sense to print intermediate comments, unless we merge them somehow (would require strict definition for the header)
-                            headerPrinted = true;
+                    }
+                    else if (COVARIATE_PATTERN.matcher(line).matches()) {
+                        if (!printedHeader)
                             o.println(line);
-                        }                 // Skip over the header (could check if headers are the same, but probably not necessary)
                     }
                     else {                // Found a line of data
                         addCSVData(line); // Parse the line and add the data to the HashMap
@@ -95,14 +93,15 @@ public class CountCovariatesGatherer extends Gatherer {
                 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(String key : dataMap.keySet()) {
-            int [] values = dataMap.get(key);
+            RecalDatumOptimized values = dataMap.get(key);
-            String v = "," + values[0] + "," + values[1] + "," + values[2];
+            String v = values.getNumObservations() + "," + values.getNumMismatches() + "," + values.empiricalQualByte();
             o.println(key + v);
         }
-
+        o.println("EOF");
     }
 }

java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CountCovariatesWalker.java

@@ -92,13 +92,13 @@ public class CountCovariatesWalker extends LocusWalker<CountCovariatesWalker.Cou
     @ArgumentCollection private RecalibrationArgumentCollection RAC = new RecalibrationArgumentCollection();
 
     @Output
-    @Gather(CountCovariatesGatherer.class)
     PrintStream out;
 
     /////////////////////////////
     // Command Line Arguments
     /////////////////////////////
     @Output(fullName="recal_file", shortName="recalFile", required=true, doc="Filename for the outputted covariates table recalibration file")
+    @Gather(CountCovariatesGatherer.class)
     public PrintStream RECAL_FILE;
 
     @Argument(fullName="list", shortName="ls", doc="List the available covariates and exit", required=false)

scala/qscript/oneoffs/carneiro/QuickCCTest.scala

@@ -33,6 +33,8 @@ class QuickCCTest extends QScript {
 
   def script = {
 
+    val recal = new File("recal.csv")
+
     val cc = new CountCovariates()
     cc.reference_sequence = reference
     cc.input_file :+= input
@@ -40,7 +42,8 @@ class QuickCCTest extends QScript {
     cc.intervalsString = intervals
     cc.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
     cc.scatterCount = 4
-    cc.recal_file = new File("recal.csv")
+    cc.recal_file = recal
+    cc.memoryLimit = 4
 
     add(cc);
   }