Small change for Matt -- output partition types in lexicographic order.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4365 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java

@@ -148,15 +148,18 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
             PrintStream out = getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary);
             out.printf("%s\t%s","Locus","Total_Depth");
             for (DoCOutputType.Partition type : partitionTypes ) {
-                // mhanna 22 Aug 2010 - Deliberately force this header replacement to make sure integration tests pass.
+                out.printf("\t%s_%s","Average_Depth",type.toString());
-                // TODO: Update integration tests and get rid of this.
-                String typeName = (type == DoCOutputType.Partition.readgroup ? "read_group" : type.toString());
-                out.printf("\t%s_%s","Average_Depth",typeName);
             }
+            
             // get all the samples
             HashSet<String> allSamples = getSamplesFromToolKit(partitionTypes);
+            ArrayList<String> allSampleList = new ArrayList<String>(allSamples.size());
+            for ( String s : allSamples ) {
+                allSampleList.add(s);
+            }
+            Collections.sort(allSampleList);
 
-            for ( String s : allSamples) {
+            for ( String s : allSampleList) {
                 out.printf("\t%s_%s","Depth_for",s);
                 if ( printBaseCounts ) {
                     out.printf("\t%s_%s",s,"base_counts");
@@ -258,6 +261,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
 
     public CoveragePartitioner reduce(Map<DoCOutputType.Partition,Map<String,int[]>> thisMap, CoveragePartitioner prevReduce) {
         if ( ! omitDepthOutput ) {
+            //checkOrder(prevReduce); // tests prevReduce.getIdentifiersByType().get(t) against the initialized header order
             printDepths(getCorrectStream(null, DoCOutputType.Aggregation.locus, DoCOutputType.FileType.summary),thisMap,prevReduce.getIdentifiersByType());
             // this is an additional iteration through thisMap, plus dealing with IO, so should be much slower without
             // turning on omit
@@ -757,6 +761,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
     }
 
     private void checkOrder(CoveragePartitioner ag) {
+        // make sure the ordering stored at initialize() is propagated along reduce
         for (DoCOutputType.Partition t : partitionTypes ) {
             List<String> order = orderCheck.get(t);
             List<String> namesInAg = ag.getIdentifiersByType().get(t);

java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java

@@ -77,6 +77,9 @@ public class PackageUtils {
         for( Class<? extends T> type: allTypes ) {
             if( JVMUtils.isConcrete(type) )
                 concreteTypes.add(type);
+            else {
+                System.out.printf("%s %s %s%n","Class",type.getSimpleName()," is not concrete. Skipping.");
+            }
         }
 
         return concreteTypes;

java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageB36IntegrationTest.java

@@ -72,4 +72,19 @@ public class DepthOfCoverageB36IntegrationTest extends WalkerTest {
         execute("testMapQ0Only",spec);
     }
 
+    @Test
+    public void testLotsOfSamples() {
+        File baseOutputFile = this.createTempFile("testManySamples",".tmp");
+        this.setOutputFileLocation(baseOutputFile);
+        String[] intervals = {"1:1105290-1105295"};
+        String[] bams = {"/humgen/gsa-hpprojects/GATK/data/Validation_Data/pilot3.CEU+TSI.5loci.bam"};
+        String cmd = buildRootCmd(b36KGReference, new ArrayList<String>(Arrays.asList(bams)), new ArrayList<String>(Arrays.asList(intervals)));
+
+        WalkerTestSpec spec = new WalkerTestSpec(cmd,0,new ArrayList<String>());
+
+        spec.addAuxFile("c9561b52344536d2b06ab97b0bb1a234",baseOutputFile);
+
+        execute("testLotsOfSamples",spec);
+    }
+
 }

java/test/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageIntegrationTest.java

@@ -55,7 +55,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
 
         // now add the expected files that get generated
-        spec.addAuxFile("494c174ea0773bda98297a0cbdc188eb", baseOutputFile);
+        spec.addAuxFile("423571e4c05e7934322172654ac6dbb7", baseOutputFile);
         spec.addAuxFile("9df5e7e07efeb34926c94a724714c219", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_counts"));
         spec.addAuxFile("b9a7748e5aec4dc06daed893c901c00d", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_cumulative_coverage_proportions"));
         spec.addAuxFile("9cd395f47b329b9dd00ad024fcac9929", createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_statistics"));
@@ -89,7 +89,7 @@ public class DepthOfCoverageIntegrationTest extends WalkerTest {
         String cmd = buildRootCmd(hg18Reference,new ArrayList<String>(Arrays.asList(bams)),new ArrayList<String>(Arrays.asList(intervals))) + " -mmq 0 -mbq 5 --maxBaseQuality 4 -dels -baseCounts -pt readgroup -pt sample -pt library --outputFormat csv";
         WalkerTestSpec spec = new WalkerTestSpec(cmd,0, new ArrayList<String>());
 
-        spec.addAuxFile("d570c27d82a80ebd2852e9d34aff4e87",baseOutputFile);
+        spec.addAuxFile("6ccd7d8970ba98cb95fe41636a070c1c",baseOutputFile);
         spec.addAuxFile("0ee40f3e5091536c14e077b77557083a",createTempFileFromBase(baseOutputFile.getAbsolutePath()+".library_interval_summary"));
 
         execute("testNoCoverageDueToFiltering",spec);