Some minor fixes to the last check-in

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@387 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactory.java

@@ -1,6 +1,10 @@
 package org.broadinstitute.sting.gatk.dataSources.shards;
 
 import net.sf.samtools.SAMSequenceDictionary;
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.utils.GenomeLoc;
+
+import java.util.List;
 
 /**
  *
@@ -34,6 +38,12 @@ public class ShardStrategyFactory {
         LINEAR, EXPONENTIAL, READS
     }
 
+    /** our log, which we want to capture anything from this class */
+        private static Logger logger = Logger.getLogger(ShardStrategyFactory.class);
+
+
+
+
     /**
      * get a new shatter strategy
      *
@@ -73,6 +83,27 @@ public class ShardStrategyFactory {
         }
     }
 
+
+    /**
+     * get a new shatter strategy
+     *
+     * @param strat        what's our strategy - SHATTER_STRATEGY type
+     * @param dic          the seq dictionary
+     * @param startingSize the starting size
+     * @return
+     */
+    static public ShardStrategy shatter(SHATTER_STRATEGY strat, SAMSequenceDictionary dic, long startingSize, List<GenomeLoc> lst) {
+        switch (strat) {
+            case LINEAR:
+                return new LinearLocusShardStrategy(dic, startingSize); // , lst);
+            case EXPONENTIAL:
+                return new ExpGrowthLocusShardStrategy(dic, startingSize); // , lst);
+            default:
+                throw new RuntimeException("Strategy: " + strat + " isn't implemented");
+        }
+
+    }
+
     /**
      * convert between types
      *

java/test/org/broadinstitute/sting/gatk/dataSources/shards/ShardStrategyFactoryTest.java

@@ -40,7 +40,7 @@ import java.util.ArrayList;
  */
 public class ShardStrategyFactoryTest {
 
-    FastaSequenceFile2 seq = null;
+    private static FastaSequenceFile2 seq;
 
     /**
      * This function (because of the @BeforeClass tag) gets called only once ever,
@@ -48,7 +48,7 @@ public class ShardStrategyFactoryTest {
      */
     @BeforeClass
     public static void doBeforeAnyTests() {
-
+        seq = new FastaSequenceFile2(new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
     }
 
     /**
@@ -68,7 +68,7 @@ public class ShardStrategyFactoryTest {
      */
     @Before
     public void doForEachTest() {
-        seq = new FastaSequenceFile2(new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+
     }
 
     /**
@@ -111,12 +111,7 @@ public class ShardStrategyFactoryTest {
         SAMSequenceRecord s = dic.getSequence(1);
         // Character stream writing
 
-        System.err.println("Trying to sleep");
-        try {
-            Thread.sleep(5000);
-        } catch (InterruptedException e) {
-            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
-        }
+       
         int stop = s.getSequenceLength();
         int size = 10000;
         int location = 1;