added option to override memory requirements, added redistribute core for map phase

Author: ddecap

halvade/src/be/ugent/intec/halvade/tools/AlignerInstance.java

@@ -69,6 +69,7 @@ public abstract class AlignerInstance {
     protected AlignerInstance(Mapper.Context context, String bin) throws IOException, URISyntaxException {
         AlignerInstance.context = context;
         header = null;
+        containers = HalvadeConf.getMapContainerCount(context.getConfiguration());
         containerMinusTasksLeft = HalvadeConf.lessTasksLeftThanContainers(context.getConfiguration());
         redistribute = HalvadeConf.getRedistribute(context.getConfiguration());
         writableRecord = new SAMRecordWritable();

halvade/src/be/ugent/intec/halvade/utils/HalvadeConf.java

@@ -269,6 +269,9 @@ public static boolean addTaskRunning(Configuration conf, String val) throws IOEx
     public static void setMapContainerCount(Configuration conf, int val) {
         conf.setInt(totalContainers, val);
     }
+    public static int getMapContainerCount(Configuration conf) {
+        return conf.getInt(totalContainers, 1);
+    }
     public static int lessTasksLeftThanContainers(Configuration conf) throws IOException, URISyntaxException {
         int containers = conf.getInt(totalContainers, 1);        
         int tasks = 0;