Merge pull request #160 from broadinstitute/rp_bqsr_gatherer_works_with_empty_tables

Updating BQSR RecalibrationEngine to work correctly with empty BQSR tabl...

protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGatherer.java

@@ -65,7 +65,7 @@ import java.util.List;
 
 public class BQSRGatherer extends Gatherer  {
     
-    private static final String EMPTY_INPUT_LIST = "list of inputs files is empty";
+    private static final String EMPTY_INPUT_LIST = "list of inputs files is empty or there is no usable data in any input file";
     private static final String MISSING_OUTPUT_FILE = "missing output file name";
 
     @Override
@@ -80,6 +80,8 @@ public class BQSRGatherer extends Gatherer  {
         RecalibrationReport generalReport = null;
         for (File input : inputs) {
             final RecalibrationReport inputReport = new RecalibrationReport(input);
+            if( inputReport.isEmpty() ) { continue; }
+
             if (generalReport == null)
                 generalReport = inputReport;
             else

protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/RecalibrationEngine.java

@@ -178,7 +178,7 @@ public class RecalibrationEngine {
         final NestedIntegerArray<RecalDatum> byQualTable = finalRecalibrationTables.getQualityScoreTable();
 
         // iterate over all values in the qual table
-        for ( NestedIntegerArray.Leaf<RecalDatum> leaf : byQualTable.getAllLeaves() ) {
+        for ( final NestedIntegerArray.Leaf<RecalDatum> leaf : byQualTable.getAllLeaves() ) {
             final int rgKey = leaf.keys[0];
             final int eventIndex = leaf.keys[2];
             final RecalDatum rgDatum = byReadGroupTable.get(rgKey, eventIndex);
@@ -206,7 +206,9 @@ public class RecalibrationEngine {
      */
     @Requires("! finalized")
     private RecalibrationTables mergeThreadLocalRecalibrationTables() {
-        if ( recalibrationTablesList.isEmpty() ) throw new IllegalStateException("recalibration tables list is empty");
+        if ( recalibrationTablesList.isEmpty() ) {
+            recalibrationTablesList.add( new RecalibrationTables(covariates, numReadGroups, maybeLogStream) );
+        }
 
         RecalibrationTables merged = null;
         for ( final RecalibrationTables table : recalibrationTablesList ) {

protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationReport.java

@@ -372,4 +372,11 @@ public class RecalibrationReport {
     public Covariate[] getCovariates() {
         return requestedCovariates;
     }
+
+    /**
+     * @return true if the report has no data
+     */
+    public boolean isEmpty() {
+        return recalibrationTables.isEmpty();
+    }
 }

protected/java/src/org/broadinstitute/sting/utils/recalibration/RecalibrationTables.java

@@ -124,6 +124,16 @@ public final class RecalibrationTables {
         return tables.size();
     }
 
+    /**
+     * @return true if all the tables contain no RecalDatums
+     */
+    public boolean isEmpty() {
+        for( final NestedIntegerArray<RecalDatum> table : tables ) {
+            if( !table.getAllValues().isEmpty() ) { return false; }
+        }
+        return true;
+    }
+
     /**
      * Allocate a new quality score table, based on requested parameters
      * in this set of tables, without any data in it.  The return result

protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRGathererUnitTest.java

@@ -69,6 +69,7 @@ public class BQSRGathererUnitTest extends BaseTest {
     private static File recal3 = new File(privateTestDir + "HiSeq.1mb.1RG.sg3.table");
     private static File recal4 = new File(privateTestDir + "HiSeq.1mb.1RG.sg4.table");
     private static File recal5 = new File(privateTestDir + "HiSeq.1mb.1RG.sg5.table");
+    private static File recalEmpty = new File(privateTestDir + "HiSeq.1mb.1RG.empty.table");
 
     private static File recal_original = new File(privateTestDir + "HiSeq.1mb.1RG.noSG.table");
 
@@ -110,6 +111,26 @@ public class BQSRGathererUnitTest extends BaseTest {
         testReports(originalReport, calculatedReport);
     }
 
+    @Test(enabled = true)
+    public void testGatherBQSRWithEmptyFile() {
+        BQSRGatherer gatherer = new BQSRGatherer();
+        List<File> recalFiles = new LinkedList<File> ();
+        final File output = BaseTest.createTempFile("BQSRgathererTest", ".table");
+
+        recalFiles.add(recal1);
+        recalFiles.add(recal2);
+        recalFiles.add(recal3);
+        recalFiles.add(recal4);
+        recalFiles.add(recal5);
+        recalFiles.add(recalEmpty);
+        gatherer.gather(recalFiles, output);
+
+        GATKReport originalReport = new GATKReport(recal_original);
+        GATKReport calculatedReport = new GATKReport(output);
+
+        testReports(originalReport, calculatedReport);
+    }
+
     private void testReports(final GATKReport originalReport, final GATKReport calculatedReport) {
 
         // test the Arguments table