lib: Add "getCount" to ProgressLogger. #TASK-6217

Author: j-coll

commons-lib/src/main/java/org/opencb/commons/ProgressLogger.java

@@ -205,7 +205,7 @@ protected synchronized void log(long count, String extraMessage, long currentTim
             // Remove old points that are outside the progress rate window
             times.removeFirst();
         }
-        long totalCount = getTotalCount();
+        long totalCount = this.totalCount;
 
         StringBuilder sb = new StringBuilder(message).append(count);
         if (totalCount > 0) {
@@ -284,10 +284,6 @@ private void updateFutureTotalCount() {
         }
     }
 
-    private long getTotalCount() {
-        return this.totalCount;
-    }
-
     private void updateBatchSize() {
         batchSize = Math.max((double) totalCount / numLinesLog, MIN_BATCH_SIZE);
     }
@@ -299,6 +295,10 @@ private static Future<Long> getFuture(Callable<Long> totalCountCallable) {
         return future;
     }
 
+    public long getCount() {
+        return count.get();
+    }
+
     public <T> Task<T, T> asTask() {
         return asTask(null);
     }

commons-lib/src/main/java/org/opencb/commons/io/DataReader.java

@@ -18,10 +18,8 @@
 
 import org.opencb.commons.run.Task;
 
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-import java.util.NoSuchElementException;
+import java.util.*;
+import java.util.function.Consumer;
 import java.util.stream.Stream;
 import java.util.stream.StreamSupport;
 
@@ -163,4 +161,16 @@ public T next() {
         };
     }
 
+    @Override
+    default void forEach(Consumer<? super T> action) {
+        forEach(action, 1);
+    }
+
+    default void forEach(Consumer<? super T> action, int batchSize) {
+        Objects.requireNonNull(action);
+        for (Iterator<T> iterator = this.iterator(batchSize); iterator.hasNext();) {
+            T t = iterator.next();
+            action.accept(t);
+        }
+    }
 }