some very old tests relied on cancer data that got moved. Reset one to use data in the validation directory, the other to the artificial sam utils (the best approach).

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2767 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -129,7 +129,7 @@ public class SAMBAMDataSourceTest extends BaseTest {
         logger.warn("Executing testMergingTwoBAMFiles");
 
         // setup the test files
-        fl.add(new File(seqLocation + "/dirseq/analysis/cancer_exome/twoflowcell_sams/TCGA-06-0188.aligned.duplicates_marked.bam"));
+        fl.add(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"));
         Reads reads = new Reads(fl);                   
 
         // the sharding strat.
@@ -170,8 +170,8 @@ public class SAMBAMDataSourceTest extends BaseTest {
 
         // setup the data and the counter before our second run
         fl.clear();
-        fl.add(new File(seqLocation + "/dirseq/analysis/cancer_exome/twoflowcell_sams/TCGA-06-0188-01A-01W.aligned.duplicates_marked.bam"));
-        fl.add(new File(seqLocation + "/dirseq/analysis/cancer_exome/twoflowcell_sams/TCGA-06-0188-10B-01W.aligned.duplicates_marked.bam"));
+        fl.add(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"));
+        fl.add(new File(validationDataLocation + "/NA12878.chrom6.SLX.SRP000032.2009_06.selected.bam"));
         reads = new Reads(fl);
 
         count = 0;

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

@@ -1,6 +1,8 @@
 package org.broadinstitute.sting.gatk.iterators;
 
 import static junit.framework.Assert.fail;
+
+import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMRecord;
 import net.sf.picard.reference.ReferenceSequenceFile;
 import org.broadinstitute.sting.BaseTest;
@@ -15,12 +17,16 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
+
+import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
 
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
 
 
@@ -84,62 +90,51 @@ public class BoundedReadIteratorTest extends BaseTest {
     @Test
     public void testBounding() {
         logger.warn("Executing testBounding");
+        // total reads expected
+        final int expected = 20;
+        // bound by ten reads
+        BoundedReadIterator iter = new BoundedReadIterator(new testIterator(), expected);
 
-        // setup the test files
-        fl.add(new File(seqLocation + "/dirseq/analysis/cancer_exome/twoflowcell_sams/TCGA-06-0188.aligned.duplicates_marked.bam"));
-        Reads reads = new Reads(fl);
-
-        SAMDataSource data = new IndexDrivenSAMDataSource(reads);
-        // the sharding strat.
-        ShardStrategy strat = ShardStrategyFactory.shatter(data,ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, seq.getSequenceDictionary(), 100000);
         int count = 0;
-
-        // our target read
-        final long boundedReadCount = 100;
-        long shardReadCount = 0;
-
-        try {
-            // 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();
-
-
-            StingSAMIterator datum = data.seek(sd);
-            StingSAMIterator datum2 = data.seek(sd);
-
-            // check the reads in the shard
-            for (SAMRecord r : datum) {
-                shardReadCount++;
-
-            }
-
-            // create the bounded iterator
-            BoundedReadIterator iter = new BoundedReadIterator(StingSAMIteratorAdapter.adapt(reads,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");
+        for (SAMRecord rec: iter) {
+            count++;
         }
 
-
+        Assert.assertEquals(expected,count);
     }
 }
+
+class testIterator implements StingSAMIterator {
+    SAMFileHeader header;
+    testIterator() {
+        header = ArtificialSAMUtils.createArtificialSamHeader(1,1,2000);
+    }
+    /**
+     * Gets source information for the reads.  Contains information about the original reads
+     * files, plus information about downsampling, etc.
+     *
+     * @return
+     */
+    public Reads getSourceInfo() {
+        return null;
+    }
+
+    public void close() {
+
+    }
+
+    public boolean hasNext() {
+        return true;
+    }
+
+    public SAMRecord next() {
+        return ArtificialSAMUtils.createArtificialRead(header,"blah",0,1,100);
+    }
+
+    public void remove() {
+    }
+
+    public Iterator<SAMRecord> iterator() {
+        return this;
+    }
+}