From 244a217ee7d219269e658bc246d3d623cc158287 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Tue, 8 Mar 2016 12:45:09 -0500
Subject: [PATCH] Fix sample_gene_summary reports header order

---
 .../walkers/coverage/DepthOfCoverage.java     | 45 ++++++++++---------
 .../DepthOfCoverageIntegrationTest.java       | 24 ++++++++++
 2 files changed, 48 insertions(+), 21 deletions(-)

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 1907cbe8f..82e1723c0 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
@@ -433,7 +433,7 @@ public class DepthOfCoverage extends LocusWalker<Map<DoCOutputType.Partition,Map
             printGeneStats(statsByInterval);
         }
 
-        if ( statsByInterval.size() > 0 ) {
+        if ( !statsByInterval.isEmpty() ) {
             for(DoCOutputType.Partition partition: partitionTypes) {
                 if ( checkType(statsByInterval.get(0).getSecond().getCoverageByAggregationType(partition) ,partition) ) {
                     printIntervalStats(statsByInterval,
@@ -544,27 +544,30 @@ public class DepthOfCoverage extends LocusWalker<Map<DoCOutputType.Partition,Map
         summaryHeader.append(separator);
         summaryHeader.append("average_coverage");
 
-        for ( String s : statsByTarget.get(0).second.getCoverageByAggregationType(DoCOutputType.Partition.sample).getAllSamples() ) {
-            summaryHeader.append(separator);
-            summaryHeader.append(s);
-            summaryHeader.append("_total_cvg");
-            summaryHeader.append(separator);
-            summaryHeader.append(s);
-            summaryHeader.append("_mean_cvg");
-            summaryHeader.append(separator);
-            summaryHeader.append(s);
-            summaryHeader.append("_granular_Q1");
-            summaryHeader.append(separator);
-            summaryHeader.append(s);
-            summaryHeader.append("_granular_median");
-            summaryHeader.append(separator);
-            summaryHeader.append(s);
-            summaryHeader.append("_granular_Q3");
-            for ( int thresh : coverageThresholds ) {
+        if ( !statsByGene.isEmpty() ) {
+            // Only need to get the first item in statsByGene since all have the same samples
+            for (String s : statsByGene.get(0).second.getAllSamples()) {
                 summaryHeader.append(separator);
                 summaryHeader.append(s);
-                summaryHeader.append("_%_above_");
-                summaryHeader.append(thresh);
+                summaryHeader.append("_total_cvg");
+                summaryHeader.append(separator);
+                summaryHeader.append(s);
+                summaryHeader.append("_mean_cvg");
+                summaryHeader.append(separator);
+                summaryHeader.append(s);
+                summaryHeader.append("_granular_Q1");
+                summaryHeader.append(separator);
+                summaryHeader.append(s);
+                summaryHeader.append("_granular_median");
+                summaryHeader.append(separator);
+                summaryHeader.append(s);
+                summaryHeader.append("_granular_Q3");
+                for (int thresh : coverageThresholds) {
+                    summaryHeader.append(separator);
+                    summaryHeader.append(s);
+                    summaryHeader.append("_%_above_");
+                    summaryHeader.append(thresh);
+                }
             }
         }
 
@@ -982,7 +985,7 @@ public class DepthOfCoverage extends LocusWalker<Map<DoCOutputType.Partition,Map
     }
 
     public boolean checkType(DepthOfCoverageStats stats, DoCOutputType.Partition type ) {
-        if ( stats.getHistograms().size() < 1 ) {
+        if ( stats.getHistograms().isEmpty() ) {
             logger.warn("The histogram per partition type "+type.toString()+" was empty\n"+
                     "Do your read groups have this type? (Check your .bam header).");
             return false;
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 9c421fb0a..65b469600 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
@@ -211,4 +211,28 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
         File file = new File(logFileName);
         Assert.assertTrue(FileUtils.readFileToString(file).contains(DepthOfCoverage.incompatibleArgsMsg()));
     }
+
+    @Test
+    public void testSampleGeneSummaryHeaderFix(){
+        final String[] intervals = {privateTestDir+"intervals.list"};
+        final String[] bams = {privateTestDir+"U145055CM2013D16882_snippet.bam", privateTestDir+"U145055PF2013D20189_snippet.bam", privateTestDir+"ControleMan1_snippet.bam"};
+        String cmd = buildRootCmd(b37KGReference, new ArrayList<String>(Arrays.asList(bams)), new ArrayList<String>(Arrays.asList(intervals))) +
+                " -geneList "+privateTestDir+"ENSG00000186092.rod";
+
+        WalkerTestSpec spec = new WalkerTestSpec(cmd, 0, new ArrayList<String>());
+
+        File baseOutputFile = WalkerTest.createTempFile("depthOfCoverageSampleGeneSummaryHeaderFix", ".tmp");
+        spec.setOutputFileLocation(baseOutputFile);
+
+        spec.addAuxFile("0b698e9d6c28479c378bf64182100e11", baseOutputFile);
+        spec.addAuxFile("97a782ce07fc487d0945b60f66721048", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_counts"));
+        spec.addAuxFile("02cd919ef71d8bcfb1c1622b7a683033", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_cumulative_coverage_proportions"));
+        spec.addAuxFile("799d8ff6a12d3109f985953ce91ab17c", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_gene_summary"));
+        spec.addAuxFile("c9624eaa0a800da0b457daa752f7ed92", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_statistics"));
+        spec.addAuxFile("34ac6759bff2d34890a30a44f8887336", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_interval_summary"));
+        spec.addAuxFile("166b97db63a95c3ceb44d790d98a6fc1", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_statistics"));
+        spec.addAuxFile("77e03df80132408c6c773cdb1f835e83", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".sample_summary"));
+
+        execute("testSampleGeneSummaryHeaderFix", spec);
+    }
 }