Added some fixes and new iterator tests

--This lin e, and those below, will be ignored--

A    gatk/iterators
AM   gatk/iterators/BoundedReadIteratorTest.java
M    gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@420 348d0f76-0448-11de-a6fe-93d51630548a

java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java

@@ -75,7 +75,7 @@ public class SAMBAMDataSourceTest extends BaseTest {
 
 
     /** Test out that we can shard the file and iterate over every read */
-    //@Test
+    @Test
     public void testLinearBreakIterateAll() {
         logger.warn("Executing testLinearBreakIterateAll");
         // the sharding strat.
@@ -103,6 +103,11 @@ public class SAMBAMDataSourceTest extends BaseTest {
                     readCount++;
                 }
                 datum.close();
+
+                // if we're over 100 shards, break out
+                if (count > 100) {
+                    break;
+                }
             }
         }
         catch (SimpleDataSourceLoadException e) {

java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorTest.java

@@ -0,0 +1,131 @@
+package org.broadinstitute.sting.gatk.iterators;
+
+import static junit.framework.Assert.fail;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.gatk.dataSources.shards.Shard;
+import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategy;
+import org.broadinstitute.sting.gatk.dataSources.shards.ShardStrategyFactory;
+import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SAMBAMDataSource;
+import org.broadinstitute.sting.gatk.dataSources.simpleDataSources.SimpleDataSourceLoadException;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ *
+ * User: aaron
+ * Date: Apr 14, 2009
+ * Time: 5:48:48 PM
+ *
+ * The Broad Institute
+ * SOFTWARE COPYRIGHT NOTICE AGREEMENT 
+ * This software and its documentation are copyright 2009 by the
+ * Broad Institute/Massachusetts Institute of Technology. All rights are reserved.
+ *
+ * This software is supplied without any warranty or guaranteed support whatsoever. Neither
+ * the Broad Institute nor MIT can be responsible for its use, misuse, or functionality.
+ *
+ */
+
+
+/**
+ * @author aaron
+ * @version 1.0
+ * @date Apr 14, 2009
+ * <p/>
+ * Class BoundedReadIteratorTest
+ * <p/>
+ * A descriptions should go here. Blame aaron if it's missing.
+ */
+public class BoundedReadIteratorTest extends BaseTest {
+
+    /** the file list and the fasta sequence */
+    private List<String> fl;
+    private FastaSequenceFile2 seq;
+
+    /**
+     * This function does the setup of our parser, before each method call.
+     * <p/>
+     * Called before every test case method.
+     */
+    @Before
+    public void doForEachTest() {
+        fl = new ArrayList<String>();
+
+        // sequence
+        seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+        GenomeLoc.setupRefContigOrdering(seq.getSequenceDictionary());
+    }
+
+
+    /** Test out that we can shard the file and iterate over every read */
+    @Test
+    public void testBounding() {
+        logger.warn("Executing testBounding");
+        // the sharding strat.
+        ShardStrategy strat = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, seq.getSequenceDictionary(), 100000);
+        int count = 0;
+
+
+        // setup the test files
+        fl.add(seqLocation + "/dirseq/analysis/cancer_exome/twoflowcell_sams/TCGA-06-0188.aligned.duplicates_marked.bam");
+
+        // our target read
+        final long boundedReadCount = 100;
+        long shardReadCount = 0;
+
+        try {
+            SAMBAMDataSource data = new SAMBAMDataSource(fl);
+
+            // make sure we have a shard
+            if (!strat.hasNext()) {
+                fail("Our shatter didn't give us a single piece, this is bad");
+            }
+            Shard sd = strat.next();
+
+
+            MergingSamRecordIterator2 datum = data.seek(sd.getGenomeLoc());
+            MergingSamRecordIterator2 datum2 = data.seek(sd.getGenomeLoc());
+
+            // check the reads in the shard
+            for (SAMRecord r : datum) {
+                shardReadCount++;
+
+            }
+
+            // create the bounded iterator
+            BoundedReadIterator iter = new BoundedReadIterator(datum2, boundedReadCount);
+
+            // now see how many reads are in the bounded iterator
+            int readCount = 0;
+            for (SAMRecord r : iter) {
+                readCount++;
+
+            }
+
+            // close the iterators
+            datum.close();
+            datum2.close();
+
+            // check to see that the sizes are the same
+            assertEquals(boundedReadCount,readCount);
+            assertTrue(readCount < shardReadCount);
+
+
+        }
+        catch (SimpleDataSourceLoadException e) {
+            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+            fail("testLinearBreakIterateAll: We Should get a SimpleDataSourceLoadException");
+        }
+
+
+    }
+}