Ensure position data type is in set of data types in ctors rather than in...

Ensure position data type is in set of data types in ctors rather than in makeDataProvider(), in order to avoid ConcurrentModificationException.

src/java/net/sf/picard/illumina/parser/IlluminaDataProviderFactory.java

@@ -95,6 +95,7 @@ public class IlluminaDataProviderFactory {
         this.barcodeCycle = null;
         this.barcodeLength = null;
         this.dataTypes = new HashSet<IlluminaDataType>(Arrays.asList(dataTypes));
+        addPositionDataType();
 
         if(readStructure == null) {
             this.readStructure = computeReadStructure();
@@ -129,6 +130,7 @@ public class IlluminaDataProviderFactory {
         this.barcodeCycle = barcodeCycle;
         this.barcodeLength = barcodeLength;
         this.dataTypes = new HashSet<IlluminaDataType>(Arrays.asList(dataTypes));
+        addPositionDataType();
         this.readStructure = computeReadStructure();
     }
 
@@ -171,6 +173,28 @@ public class IlluminaDataProviderFactory {
         }
 
         final int totalCycles = readStructure.totalCycles;
+
+        final Map<IlluminaParser, Set<IlluminaDataType>> parsersToDataType = new HashMap<IlluminaParser, Set<IlluminaDataType>>();
+        final SortedSet<IlluminaDataType> toSupport = new TreeSet<IlluminaDataType>(dataTypes);
+        while(!toSupport.isEmpty()) {
+            final IlluminaParser parser = getPreferredParser(toSupport.first(), tiles, totalCycles, outputLengths);
+            final Set<IlluminaDataType> providedTypes = new HashSet<IlluminaDataType>(parser.supportedTypes());
+            providedTypes.retainAll(toSupport); //provide only those we want
+            toSupport.removeAll(providedTypes); //remove the ones we want from the set still needing support
+            parsersToDataType.put(parser, providedTypes);
+        }
+
+        for(final IlluminaParser parser : parsersToDataType.keySet()) {
+            parser.verifyData(readStructure, tiles);
+        }
+
+        return new IlluminaDataProvider(readStructure, parsersToDataType, basecallDirectory, lane);
+    }
+
+    /**
+     * Ensure that position data type is present even if not specified, if one of the files containing position is being read.
+     */
+    private void addPositionDataType() {
         if(!dataTypes.contains(IlluminaDataType.Position)) {
             boolean addPosition = false;
             for(final IlluminaDataType dt : dataTypes) {
@@ -188,22 +212,6 @@ public class IlluminaDataProviderFactory {
                 dataTypes.add(IlluminaDataType.Position);
             }
         }
-
-        final Map<IlluminaParser, Set<IlluminaDataType>> parsersToDataType = new HashMap<IlluminaParser, Set<IlluminaDataType>>();
-        final SortedSet<IlluminaDataType> toSupport = new TreeSet<IlluminaDataType>(dataTypes);
-        while(!toSupport.isEmpty()) {
-            final IlluminaParser parser = getPreferredParser(toSupport.first(), tiles, totalCycles, outputLengths);
-            final Set<IlluminaDataType> providedTypes = new HashSet<IlluminaDataType>(parser.supportedTypes());
-            providedTypes.retainAll(toSupport); //provide only those we want
-            toSupport.removeAll(providedTypes); //remove the ones we want from the set still needing support
-            parsersToDataType.put(parser, providedTypes);
-        }
-
-        for(final IlluminaParser parser : parsersToDataType.keySet()) {
-            parser.verifyData(readStructure, tiles);
-        }
-
-        return new IlluminaDataProvider(readStructure, parsersToDataType, basecallDirectory, lane);
     }
 
     /**