Added integration Tests for DiagnoseTargets

Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java

@@ -126,7 +126,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
     @Argument(fullName = "print_debug_log", shortName = "dl", doc = "Used only for debugging the walker. Prints extra info to screen", required = false)
     private boolean debug = false;
 
-    private HashMap<GenomeLoc, IntervalStatistics> intervalMap = null;                                                  // interval => statistics
+    private HashMap<GenomeLoc, IntervalStatistics> intervalMap = null;                                                  // maps each interval => statistics
     private PeekableIterator<GenomeLoc> intervalListIterator;                                                           // an iterator to go over all the intervals provided as we traverse the genome
     private Set<String> samples = null;                                                                                 // all the samples being processed
     private final Allele SYMBOLIC_ALLELE = Allele.create("<DT>", false);                                                // avoid creating the symbolic allele multiple times
@@ -137,7 +137,7 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
         super.initialize();
 
         if (getToolkit().getIntervals() == null)
-            throw new UserException("This tool currently only works if you provide one or more interval");
+            throw new UserException("This tool only works if you provide one or more intervals. ( Use the -L argument )");
 
         thresholds = new ThresHolder(minimumBaseQuality, minimumMappingQuality, minimumCoverage, maximumCoverage, minMedianDepth, maxInsertSize, votePercentage, lowMedianDepthPercentage, badMateStatusThreshold, coverageStatusThreshold, excessiveCoverageThreshold, qualityStatusThreshold);
 
@@ -201,6 +201,20 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
         return loc;
     }
 
+    private GenomeLoc getFinishedIntervalSpan(GenomeLoc pos) {
+        GenomeLoc loc = null;
+        for (GenomeLoc interval : intervalMap.keySet()) {
+            if (interval.isBefore(pos)) {
+                if (loc == null)
+                    loc = interval;
+                else
+                    loc = interval.union(loc);
+            }
+        }
+
+        return loc;
+    }
+
     /**
      * Removes all intervals that are behind the current reference locus from the intervalMap
      *
@@ -208,19 +222,17 @@ public class DiagnoseTargets extends LocusWalker<Long, Long> {
      * @param refBase  the reference allele
      */
     private void removePastIntervals(GenomeLoc refLocus, byte refBase) {
-        // if all intervals are safe
+        // if there are statistics to output/ check to see that we can output them in order
-        if (getIntervalMapSpan() != null && getIntervalMapSpan().isBefore(refLocus)) {
+        if (getFinishedIntervalSpan(refLocus) != null &&
-            for (GenomeLoc interval : intervalMap.keySet()) {
+                getIntervalMapSpan().getStart() == getFinishedIntervalSpan(refLocus).getStart()) {
-                outputStatsToVCF(intervalMap.get(interval), Allele.create(refBase, true));
+
-                intervalMap.remove(interval);
+            for (GenomeLoc interval : intervalMap.keySet()) {
-            }
+                if (interval.isBefore(refLocus)) {
-        }
+                    outputStatsToVCF(intervalMap.get(interval), Allele.create(refBase, true));
+                    intervalMap.remove(interval);
+                }
+            }
 
-        GenomeLoc interval = intervalListIterator.peek();                                                               // clean up all intervals that we might have skipped because there was no data
-        while (interval != null && interval.isBefore(refLocus)) {
-            interval = intervalListIterator.next();
-            outputStatsToVCF(createIntervalStatistic(interval), Allele.create(refBase, true));
-            interval = intervalListIterator.peek();
         }
     }
 

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/SampleStatistics.java

@@ -280,7 +280,7 @@ class SampleStatistics {
                 read.getAlignmentStart() < read.getMateAlignmentStart())
             return false;
 
-        // TODO note: IGV uses a different alorithm for insert size, there should be a common util class that does this for you
+        // TODO note: IGV uses a different algorithm for insert size, there should be a common util class that does this for you
         // mates are too far apart
         if (Math.abs(read.getAlignmentStart() - read.getMateAlignmentStart()) > thresholds.getMaximumInsertSize())
             return false;

public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargetsIntegrationTest.java

@@ -0,0 +1,53 @@
+/*
+ * Copyright (c) 2012, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+public class DiagnoseTargetsIntegrationTest extends WalkerTest {
+    final static String REF = b37KGReference;
+    final String singleSample = validationDataLocation + "NA12878.HiSeq.b37.chr20.10_11mb.bam";
+    final String multiSample = validationDataLocation + "CEUTrio.HiSeq.b37.chr20.10_11mb.bam";
+    final String L = validationDataLocation + "DT-itest.interval_list";
+
+    private void DTTest(String testName, String args, String md5) {
+        String base = String.format("-T DiagnoseTargets -R %s -L %s", REF, L) + " -o %s ";
+        WalkerTestSpec spec = new WalkerTestSpec(base + args, Arrays.asList(md5));
+        executeTest(testName, spec);
+    }
+
+    @Test(enabled = true)
+    public void testSingleSample() {
+        DTTest("testSingleSample ", "-I " + singleSample + " -max 75", "2df47009571fe83ead779c94be97fe96");
+    }
+
+    @Test(enabled = true)
+    public void testMultiSample() {
+        DTTest("testMultiSample ", "-I " + multiSample, "6f0c070b9671e1d007ce6374c3183014");
+    }
+}