From 0720d248cede75c4afc4e5d3099742980b2682a2 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 23 Apr 2009 18:01:22 +0000
Subject: [PATCH] Adding the test case for by reads sharding of BAM data
 sources

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@509 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../simpleDataSources/SAMByReadsTest.java     | 123 ++++++++++++++++++
 1 file changed, 123 insertions(+)
 create mode 100755 java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java

diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java
new file mode 100755
index 000000000..f1f9ede0a
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMByReadsTest.java
@@ -0,0 +1,123 @@
+package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
+
+import static junit.framework.Assert.fail;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.gatk.iterators.BoundedReadIterator;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
+import static org.junit.Assert.assertEquals;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+
+/**
+ *
+ * User: aaron
+ * Date: Apr 15, 2009
+ * Time: 7:12:59 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 15, 2009
+ * <p/>
+ * Class SAMByReadsTest
+ * <p/>
+ * Test sam traversal by reads FIX ME
+ */
+public class SAMByReadsTest extends BaseTest {
+
+    private FastaSequenceFile2 seq;
+    private List<String> fl;
+
+    /**
+     * 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 testTotalReadCount() {
+        logger.warn("Executing testTotalReadCount");
+        // the sharding strat.
+        //ShardStrategy strat = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, seq.getSequenceDictionary(), 100000);
+
+        try {
+            Thread.sleep(5000);
+        } catch (InterruptedException e) {
+            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+        }
+
+        // setup the test files
+        fl.add("/humgen/gsa-scr1/GATK_Data/Validation_Data/10035.5.clean.bam");
+
+        // make sure we don't see dupes
+        HashSet<String> names = new HashSet<String>();
+
+        
+        try {
+            SAMDataSource data = new SAMDataSource(fl);
+            final int targetReadCount = 500000;
+
+            // check the total read count
+            final int totalReads = 1782980;
+
+            int readsSeen = 0;
+            BoundedReadIterator iter;
+
+
+            while ((iter = data.seek(targetReadCount)) != null) {
+                int readcnt = 0;
+              
+                for (SAMRecord r : iter) {
+                    String readName = r.getReadName();
+                    if (names.contains(readName)) {
+                        fail("We saw read " + readName + " twice");
+                    }
+                    names.add(readName);
+                    readcnt++;
+                }
+
+                
+                readsSeen += readcnt;
+                logger.warn("Seen " + readsSeen + " reads.");
+
+            }
+            // make sure we've seen all the reads
+            assertEquals(totalReads,readsSeen);
+        }
+        
+        catch (SimpleDataSourceLoadException e) {
+            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+            fail("testLinearBreakIterateAll: We Should not get a SimpleDataSourceLoadException");
+        }
+
+
+    }
+}