From bee7f655b7f8f01bf4885b69a089ff28d2e3cfba Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Sat, 7 Mar 2015 21:53:32 -0500
Subject: [PATCH] Log a warning if using incompatible arguments in
 DepthOfCoverage

Add reference gene list file
---
 .../walkers/coverage/DepthOfCoverage.java     | 18 +++++++++-
 .../DepthOfCoverageIntegrationTest.java       | 33 +++++++++++++++++++
 2 files changed, 50 insertions(+), 1 deletion(-)

diff --git a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java
index 20c480901..92395a4f9 100644
--- a/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java
+++ b/public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverage.java
@@ -26,6 +26,7 @@
 package org.broadinstitute.gatk.tools.walkers.coverage;
 
 import htsjdk.samtools.SAMReadGroupRecord;
+import org.apache.log4j.Logger;
 import org.broadinstitute.gatk.engine.walkers.*;
 import org.broadinstitute.gatk.utils.commandline.*;
 import org.broadinstitute.gatk.engine.CommandLineGATK;
@@ -108,7 +109,6 @@ import java.util.*;
  *   [-ct 4 -ct 6 -ct 10] \
  *   [-L my_capture_genes.interval_list]
  * </pre>
- *
  */
 // todo -- cache the map from sample names to means in the print functions, rather than regenerating each time
 // todo -- support for granular histograms for total depth; maybe n*[start,stop], bins*sqrt(n)
@@ -120,6 +120,13 @@ import java.util.*;
 @PartitionBy(PartitionType.NONE)
 @Downsample(by= DownsampleType.NONE, toCoverage=Integer.MAX_VALUE)
 public class DepthOfCoverage extends LocusWalker<Map<DoCOutputType.Partition,Map<String,int[]>>, CoveragePartitioner> implements TreeReducible<CoveragePartitioner> {
+    private final static Logger logger = Logger.getLogger(DepthOfCoverage.class);
+
+    /**
+     * Warning message for when the incompatible arguments --calculateCoverageOverGenes and --omitIntervalStatistics are used together.
+     */
+    private static final String incompatibleArgsMsg = "The arguments --calculateCoverageOverGenes and --omitIntervalStatistics are incompatible. Using them together will result in an empty gene summary output file.";
+
     @Output
     @Multiplex(value=DoCOutputMultiplexer.class,arguments={"partitionTypes","refSeqGeneList","omitDepthOutput","omitIntervals","omitSampleSummary","omitLocusTable"})
     Map<DoCOutputType,PrintStream> out;
@@ -172,6 +179,9 @@ public class DepthOfCoverage extends LocusWalker<Map<DoCOutputType.Partition,Map
 
     /**
      * Specify a RefSeq file for use in aggregating coverage statistics over genes.
+     *
+     * A warning will be logged and no output file will be produced if --calculateCoverageOverGenes and --omitIntervalStatistics are enabled.
+     *
      */
     @Argument(fullName = "calculateCoverageOverGenes", shortName = "geneList", doc = "Calculate coverage statistics over this list of genes", required = false)
     File refSeqGeneList = null;
@@ -259,8 +269,14 @@ public class DepthOfCoverage extends LocusWalker<Map<DoCOutputType.Partition,Map
 
     public boolean includeReadsWithDeletionAtLoci() { return includeDeletions && ! ignoreDeletionSites; }
 
+    public static String incompatibleArgsMsg() { return incompatibleArgsMsg; }
+
     public void initialize() {
 
+        if ( omitIntervals && refSeqGeneList != null ){
+            logger.warn(incompatibleArgsMsg);
+        }
+
         if ( printBinEndpointsAndExit ) {
             int[] endpoints = DepthOfCoverageStats.calculateBinEndpoints(start,stop,nBins);
             System.out.print("[ ");
diff --git a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java
index 61785e8d6..f000513d2 100644
--- a/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java
+++ b/public/gatk-tools-public/src/test/java/org/broadinstitute/gatk/tools/walkers/coverage/DepthOfCoverageIntegrationTest.java
@@ -27,8 +27,12 @@ package org.broadinstitute.gatk.tools.walkers.coverage;
 
 import org.broadinstitute.gatk.engine.walkers.WalkerTest;
 import org.testng.annotations.Test;
+import org.testng.Assert;
+
+import org.apache.commons.io.FileUtils;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
@@ -178,4 +182,33 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
 
     @Test public void testRefNWithNs() { testRefNHandling(true, "24cd2da2e4323ce6fd76217ba6dc2834"); }
     @Test public void testRefNWithoutNs() { testRefNHandling(false, "4fc0f1a2e968f777d693abcefd4fb7af"); }
+
+
+    @Test
+    public void testIncompatibleArgs() throws IOException {
+        final String[] intervals = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/fhs_jhs_30_targts.interval_list"};
+        final String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/FHS_indexed_subset.bam"};
+        final String refSeqGeneListFile = privateTestDir + "geneTrackHg18Chr1Interval.refSeq";
+
+        final String logFileName = new String("testIncompatibleArgs.log");
+        final String cmd = buildRootCmd(hg18Reference,new ArrayList<>(Arrays.asList(bams)),new ArrayList<>(Arrays.asList(intervals))) + " --omitIntervalStatistics --calculateCoverageOverGenes " + refSeqGeneListFile + " -log " + logFileName;
+        final WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
+
+        // output file
+        final File outputFile = createTempFile("DepthOfCoverageIncompatibleArgs",".tmp");
+        spec.setOutputFileLocation(outputFile);
+
+        execute("testIncompatibleArgs",spec);
+
+        // check that only the sample gene summary output file is empty
+        Assert.assertEquals( createTempFileFromBase(outputFile.getAbsolutePath()+".sample_gene_summary").length(), 0 );
+        Assert.assertNotEquals( createTempFileFromBase(outputFile.getAbsolutePath()+".sample_cumulative_coverage_counts").length(), 0 );
+        Assert.assertNotEquals( createTempFileFromBase(outputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions").length(), 0 );
+        Assert.assertNotEquals( createTempFileFromBase(outputFile.getAbsolutePath()+".sample_statistics").length(), 0 );
+        Assert.assertNotEquals( createTempFileFromBase(outputFile.getAbsolutePath()+".sample_summary").length(), 0 );
+
+        // check the log for the warning message
+        File file = new File(logFileName);
+        Assert.assertTrue(FileUtils.readFileToString(file).contains(DepthOfCoverage.incompatibleArgsMsg()));
+    }
 }