From 8e2f5471a1e6909a8f00bc3a2e60047d8f492cee Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 9 Apr 2009 14:58:05 +0000
Subject: [PATCH] Some cleanup to the data source, and another JUnit test case.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@344 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../simpleDataSources/SAMBAMDataSource.java   |   3 -
 .../SAMBAMDataSourceTest.java                 | 106 ++++++++++++++++++
 2 files changed, 106 insertions(+), 3 deletions(-)
 create mode 100755 java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java

diff --git a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSource.java
index 8e698c568..2c2a913bd 100644
--- a/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSource.java
@@ -34,9 +34,6 @@ public class SAMBAMDataSource implements SimpleDataSource {
     // our sam file readers
     private final ArrayList<SAMFileReader> readers = new ArrayList<SAMFileReader>();
 
-    // do we care that the SAM files respect the sort order.
-    private boolean matchedSortOrders = true;
-
     // are we set to locus mode or read mode for dividing
     private boolean locusMode = true;
 
diff --git a/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
new file mode 100755
index 000000000..281cebd32
--- /dev/null
+++ b/java/test/org/broadinstitute/sting/gatk/dataSources/simpleDataSources/SAMBAMDataSourceTest.java
@@ -0,0 +1,106 @@
+package org.broadinstitute.sting.gatk.dataSources.simpleDataSources;
+
+import static junit.framework.Assert.fail;
+import net.sf.samtools.SAMRecord;
+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.iterators.MergingSamRecordIterator2;
+import org.broadinstitute.sting.utils.FastaSequenceFile2;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ *
+ * User: aaron
+ * Date: Apr 8, 2009
+ * Time: 8:14:23 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 8, 2009
+ * <p/>
+ * Class SAMBAMDataSourceTest
+ * <p/>
+ * A descriptions should go here. Blame aaron if it's missing.
+ */
+public class SAMBAMDataSourceTest {
+
+    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>();
+        fl.add("/humgen/gsa-scr1/aaron/stink/NA12892.bam");
+
+        // sequence
+        seq = new FastaSequenceFile2(new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
+    }
+
+    /**
+     * Tears down the test fixture after each call.
+     * <p/>
+     * Called after every test case method.
+     */
+    @After
+    public void undoForEachTest() {
+
+    }
+
+
+    /** Test out that we can shard the file and iterate over every read */
+    @Test
+    public void testLinearBreakIterateAll() {
+        // the sharding strat.
+        ShardStrategy strat = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR, seq.getSequenceDictionary(), 100000);
+        int count = 0;
+
+        try {
+            SAMBAMDataSource data = new SAMBAMDataSource(fl);
+            for (Shard sh : strat) {
+                int readCount = 0;
+                count++;
+
+                System.out.println("Start : " + sh.getGenomeLoc().getStart() + " stop : " + sh.getGenomeLoc().getStop() + " contig " + sh.getGenomeLoc().getContig());
+                System.out.println("count = " + count);
+                MergingSamRecordIterator2 datum = data.seek(sh.getGenomeLoc());
+
+                // for the first couple of shards make sure we can see the reads
+                if (count < 5) {
+                    for (SAMRecord r : datum) {
+                    }
+                    readCount++;
+                }
+                datum.close();
+            }
+        }
+        catch (SimpleDataSourceLoadException e) {
+            e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
+            fail("testLinearBreakIterateAll: We Should get a SimpleDataSourceLoadException");
+        }
+    }
+
+}